DatabaseID	StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
CTDB0001	Research	24440784	Paolo Fontana, Rita Genesio, Alberto Casertano, Gerarda Cappuccio, Angela Mormile, Lucio Nitsch, Achille Iolascon, Generoso Andria, Daniela Melis	Loeys-Dietz syndrome type 4, caused by chromothripsis, involving the TGFB2 gene	Gene	2014 Jan	1,9,21	Loeys-Dietz syndrome	Array CGH	Homo sapiens	24440784_1	NimbleGen CGX-6 PKI Array	chr1:212338589-217573448:-1;chr1:236581779-237907878:-1;chr21:34848660-35675464:-1;chr9:485809-644518:-1		CENPF;CHRM3;CLIC6;ESRRG;KANK1;KCNK2;KCTD3;PTPN14;RCAN1;RRP15;RUNX1;SMYD2;SPATA17;TGFB2;USH2A	Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy	The TGF-beta signaling pathway controls cellular proliferation, growth and differentiation and regulates several functions of the connective tissue. Disruption of genes coding for components of the TGF-beta signaling pathway or its interactors, such as fibrillin-1, has been shown to cause several human pathologies. Large deletions and non-sense mutations in TGFB2 gene have been recently described in patients with aortic aneurysm, scoliosis, arachnodactyly, chest deformities, joint hyper-flexibility, and mild intellectual disability; this condition has been called Loeys-Dietz syndrome, type 4. In this paper we describe an 18-year-old girl with borderline mental impairment, seizures, retinal degeneration, short stature, congenital hip dysplasia, severe and worsening joint hypermobility, scoliosis, progressive deformation of the long bones, aortic dilatation and platelet disorder. Molecular study of DNA by Array CGH demonstrated four de novo microdeletions: TGFB2 is among the genes deleted and we consider it the obvious candidate for the clinical phenotype. The multiple chromosomal rearrangements detected in the current patient can be ascribed to an event of constitutional chromothripsis.	NCBI 36/hg18				No	NA
CTDB0020	Research	23915422	Rita Genesio, Valentina Ronga, Pia Castelluccio, Gennaro Fioretti, Angela Mormile, Graziella Leone, Anna Conti, Maria Luigia Cavaliere, Lucio Nitsch	Pure 16q21q22.1 deletion in a complex rearrangement possibly caused by a chromothripsis event	Mol Cytogenet	2013 Aug	12,16	Congenital heart defects	Array CGH	Homo sapiens	23915422_1	4x44 CytoChip array			HSD11B2		Background: Partial monosomies of chromosome 16q are rare and overlapping effects from complex chromosomal rearrangements often hamper genotype-phenotype correlations for such imbalances. Here, we report the clinical features of an isolated partial monosomy 16q21q22.1 in a boy with a complex de novo rearrangement possibly resulting from a chromothripsis event. Results: The patient presented with low birth weight, microcephaly, developmental delay, facial dysmorphisms, short stature, dysmorphic ears and cardiopathy. Standard and molecular cytogenetics showed a complex rearrangement characterised by a pericentromeric inversion in one of chromosomes 12 and an inverted insertional translocation of the 12q14q21.1 region, from the rearranged chromosome 12, into the q21q22.1 tract of a chromosome 16. Array CGH analysis unravelled a partial 16q21q22.1 monosomy, localised in the rearranged chromosome 16. Conclusions: The comparison of the present case to other 16q21q22 monosomies contributed to narrow down the critical region for cardiac anomalies in the 16q22 deletion syndrome. However, more cases, well characterised both for phenotypic signs and genomic details, are needed to further restrict candidate regions for phenotypic signs in 16q deletions. The present case also provided evidence that a very complex rearrangement, possibly caused by a chromothripsis event, might be hidden behind a classical phenotype that is specific for a syndrome.	GRCh37/hg19				No	NA
CTDB0044	Research	24143197	Heng Gu, Jian-hui Jiang, Jian-ying Li, Ya-nan Zhang, Xing-sheng Dong, Yang-yu Huang, Xinming Son, Xinyan Lu, Zheng Chen	A Familial Cri-du-Chat/5p Deletion Syndrome Resulted from Rare Maternal Complex Chromosomal Rearrangements (CCRs) and/or Possible Chromosome 5p Chromothripsis	PLoS One	2013 Oct	5	Cri-du-chat syndrome	Array CGH	Homo sapiens	mother	Agilent 4x180K array			LOC340094;ADAMTS16;KIAA0947;FLJ33360;MED10;UBE2QL1;LOC255167;NSUN2;SRD5A1;PAPD7;MIR4278	Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China	Cri-du-Chat syndrome (MIM 123450) is a chromosomal syndrome characterized by the characteristic features, including cat-like cry and chromosome 5p deletions. We report a family with five individuals showing chromosomal rearrangements involving 5p, resulting from rare maternal complex chromosomal rearrangements (CCRs), diagnosed post- and pre-natally by comprehensive molecular and cytogenetic analyses. Two probands, including a four-and-half-year-old brother and his two-and-half-year-old sister, showed no diagnostic cat cry during infancy, but presented with developmental delay, dysmorphic and autistic features. Both patients had an interstitial deletion del(5)(p13.3p15.33) spanning about 26.22 Mb. The phenotypically normal mother had de novo CCRs involving 11 breakpoints and three chromosomes: ins(11;5) (q23;p14.1p15.31),ins(21;5)(q21;p13.3p14.1),ins(21;5)(q21;p15.31p15.33),inv(7)(p22q32)dn. In addition to these two children, she had three first-trimester miscarriages, two terminations due to the identification of the 5p deletion and one delivery of a phenotypically normal daughter. The unaffected daughter had the maternal ins(11;5) identified prenatally and an identical maternal allele haplotype of 5p. Array CGH did not detect any copy number changes in the mother, and revealed three interstitial deletions within 5p15.33-p13.3, in the unaffected daughter, likely products of the maternal insertions ins(21;5). Chromothripsis has been recently reported as a mechanism drives germline CCRs in pediatric patients with congenital defects. We postulate that the unique CCRs in the phenotypically normal mother could resulted from chromosome 5p chromothripsis, that further resulted in the interstitial 5p deletions in the unaffected daughter. Further high resolution sequencing based analysis is needed to determine whether chromothripsis is also present as a germline structural variation in phenotypically normal individuals in this family.	GRCh37/hg19				No	NA
CTDB0045	Research	24143197	Heng Gu, Jian-hui Jiang, Jian-ying Li, Ya-nan Zhang, Xing-sheng Dong, Yang-yu Huang, Xinming Son, Xinyan Lu, Zheng Chen	A Familial Cri-du-Chat/5p Deletion Syndrome Resulted from Rare Maternal Complex Chromosomal Rearrangements (CCRs) and/or Possible Chromosome 5p Chromothripsis	PLoS One	2013 Oct	5	Cri-du-chat syndrome	Array CGH	Homo sapiens	daughter	Agilent 4x180K array			LOC340094;ADAMTS16;KIAA0947;FLJ33360;MED10;UBE2QL1;LOC255167;NSUN2;SRD5A1;PAPD7;MIR4278	Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China	Cri-du-Chat syndrome (MIM 123450) is a chromosomal syndrome characterized by the characteristic features, including cat-like cry and chromosome 5p deletions. We report a family with five individuals showing chromosomal rearrangements involving 5p, resulting from rare maternal complex chromosomal rearrangements (CCRs), diagnosed post- and pre-natally by comprehensive molecular and cytogenetic analyses. Two probands, including a four-and-half-year-old brother and his two-and-half-year-old sister, showed no diagnostic cat cry during infancy, but presented with developmental delay, dysmorphic and autistic features. Both patients had an interstitial deletion del(5)(p13.3p15.33) spanning about 26.22 Mb. The phenotypically normal mother had de novo CCRs involving 11 breakpoints and three chromosomes: ins(11;5) (q23;p14.1p15.31),ins(21;5)(q21;p13.3p14.1),ins(21;5)(q21;p15.31p15.33),inv(7)(p22q32)dn. In addition to these two children, she had three first-trimester miscarriages, two terminations due to the identification of the 5p deletion and one delivery of a phenotypically normal daughter. The unaffected daughter had the maternal ins(11;5) identified prenatally and an identical maternal allele haplotype of 5p. Array CGH did not detect any copy number changes in the mother, and revealed three interstitial deletions within 5p15.33-p13.3, in the unaffected daughter, likely products of the maternal insertions ins(21;5). Chromothripsis has been recently reported as a mechanism drives germline CCRs in pediatric patients with congenital defects. We postulate that the unique CCRs in the phenotypically normal mother could resulted from chromosome 5p chromothripsis, that further resulted in the interstitial 5p deletions in the unaffected daughter. Further high resolution sequencing based analysis is needed to determine whether chromothripsis is also present as a germline structural variation in phenotypically normal individuals in this family.	GRCh37/hg19				No	NA
CTDB0047	Research	24304937	MA Jacoby, RE De Jesus Pizarro, J Shao, DC Koboldt, RS Fulton, G Zhou, RK Wilson, MJ Walter	The DNA double-strand break response is abnormal in myeloblasts from patients with therapy-related acute myeloid leukemia	Leukemia	2013 Dec	3,7	Acute myeloid leukemia	Array CGH	Homo sapiens	189941	NimbleGen custom 2x720K array	chr12:11708326-22796431:-1;chr17:7517325-7518692:-1;chr3:103782198-106696566:-1;chr3:11079219-12582443:-1;chr3:113846696-114463826:-1;chr3:123948788-124132968:-1;chr3:169461120-170271699:-1;chr3:170375166-171616698:-1;chr3:171702102-173816191:-1;chr4:12024504-13146333:-1;chr5:105204558-180814163:-1;chr5:94263666-103717142:-1;chr7:18448564-19027294:-1;chr7:26521475-56468938:-1;chr7:62090285-70977718:-1;chr7:78426592-81535151:-1;chr7:81940100-87814558:-1;chr7:89133633-158816035:-1		TP53	Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO, USA	The complex chromosomal aberrations found in therapy-related acute myeloid leukemia (t-AML) suggest that the DNA double-strand break (DSB) response may be altered. In this study we examined the DNA DSB response of primary bone marrow cells from t-AML patients and performed next-generation sequencing of 37 canonical homologous recombination (HR) and non-homologous end-joining (NHEJ) DNA repair genes, and a subset of DNA damage response genes using tumor and paired normal DNA obtained from t-AML patients. Our results suggest that the majority of t-AML patients (11 of 15) have tumor-cell intrinsic, functional dysregulation of their DSB response. Distinct patterns of abnormal DNA damage response in myeloblasts correlated with acquired genetic alterations in TP53 and the presence of inferred chromothripsis. Furthermore, the presence of trisomy 8 in tumor cells was associated with persistently elevated levels of DSBs. Although tumor-acquired point mutations or small indels in canonical HR and NHEJ genes do not appear to be a dominant means by which t-AML leukemogenesis occurs, our functional studies suggest that an abnormal response to DNA damage is a common finding in t-AML.		GSE53250		PRJEB8343	Yes	NA
CTDB0048	Research	24304937	MA Jacoby, RE De Jesus Pizarro, J Shao, DC Koboldt, RS Fulton, G Zhou, RK Wilson, MJ Walter	The DNA double-strand break response is abnormal in myeloblasts from patients with therapy-related acute myeloid leukemia	Leukemia	2013 Dec	3	Acute myeloid leukemia	Array CGH	Homo sapiens	530447	NimbleGen custom 2x720K array	chr21:31315314-46915712:1;chr22:14735065-49565939:1;chr3:142706131-150187585:-1;chr3:156299137-199381715:-1;chr3:20043408-31915861:-1;chr3:35197820-38538003:-1;chr3:41756417-48479360:-1;chr3:62156517-69781020:-1;chr3:69795134-75771557:-1;chr3:79933983-99089183:-1;chr5:55790692-67822695:-1;chr5:70841242-180593129:-1;chr7:22509353-57453201:-1;chr7:77985837-158816035:-1;chr9:28278165-29708951:-1		TP53	Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO, USA	The complex chromosomal aberrations found in therapy-related acute myeloid leukemia (t-AML) suggest that the DNA double-strand break (DSB) response may be altered. In this study we examined the DNA DSB response of primary bone marrow cells from t-AML patients and performed next-generation sequencing of 37 canonical homologous recombination (HR) and non-homologous end-joining (NHEJ) DNA repair genes, and a subset of DNA damage response genes using tumor and paired normal DNA obtained from t-AML patients. Our results suggest that the majority of t-AML patients (11 of 15) have tumor-cell intrinsic, functional dysregulation of their DSB response. Distinct patterns of abnormal DNA damage response in myeloblasts correlated with acquired genetic alterations in TP53 and the presence of inferred chromothripsis. Furthermore, the presence of trisomy 8 in tumor cells was associated with persistently elevated levels of DSBs. Although tumor-acquired point mutations or small indels in canonical HR and NHEJ genes do not appear to be a dominant means by which t-AML leukemogenesis occurs, our functional studies suggest that an abnormal response to DNA damage is a common finding in t-AML.		GSE53250		PRJEB8343	Yes	NA
CTDB0049	Research	24304937	MA Jacoby, RE De Jesus Pizarro, J Shao, DC Koboldt, RS Fulton, G Zhou, RK Wilson, MJ Walter	The DNA double-strand break response is abnormal in myeloblasts from patients with therapy-related acute myeloid leukemia	Leukemia	2013 Dec	8	Acute myeloid leukemia	Array CGH	Homo sapiens	377512	NimbleGen custom 2x720K array	chr11:128800686-130257349:1;chr11:94227338-94952730:1;chr15:18422770-22846333:-1;chr2:236856627-241034230:-1;chr5:55540994-56620186:-1;chr5:93926699-158579837:-1;chr7:100907744-158816035:-1;chr8:110969199-116510809:1;chr8:116520326-120009329:-1;chr8:120983709-128749745:1;chr8:128750703-129002866:-1;chr8:129007972-129285458:1;chr8:129221549-130450443:-1;chr8:130456187-133444071:1;chr8:133476865-142859461:-1;chr8:16975-32351253:1;chr8:80504328-80762667:-1;chr8:80768366-84206585:1;chr8:86369737-87949326:1;chr8:90475849-108195805:1		TP53	Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO, USA	The complex chromosomal aberrations found in therapy-related acute myeloid leukemia (t-AML) suggest that the DNA double-strand break (DSB) response may be altered. In this study we examined the DNA DSB response of primary bone marrow cells from t-AML patients and performed next-generation sequencing of 37 canonical homologous recombination (HR) and non-homologous end-joining (NHEJ) DNA repair genes, and a subset of DNA damage response genes using tumor and paired normal DNA obtained from t-AML patients. Our results suggest that the majority of t-AML patients (11 of 15) have tumor-cell intrinsic, functional dysregulation of their DSB response. Distinct patterns of abnormal DNA damage response in myeloblasts correlated with acquired genetic alterations in TP53 and the presence of inferred chromothripsis. Furthermore, the presence of trisomy 8 in tumor cells was associated with persistently elevated levels of DSBs. Although tumor-acquired point mutations or small indels in canonical HR and NHEJ genes do not appear to be a dominant means by which t-AML leukemogenesis occurs, our functional studies suggest that an abnormal response to DNA damage is a common finding in t-AML.		GSE53250		PRJEB8343	Yes	NA
CTDB0072	Research	25756553	van Engen-van Grunsven AC, Baar MP, Pfundt R, Rijntjes J, Kusters-Vandevelde HV, Delbecq AL, Keunen JE, Klevering JB, Wesseling P, Blokx WA, Groenen PJ.	Whole-genome copy-number analysis identifies new leads for chromosomal aberrations involved in the oncogenesis and metastastic behavior of uveal melanomas.	Melanoma Res	2015 Jun	13	Uveal melanoma	Array CGH	Homo sapiens	UM11	Affymetrix OncoScan Array				Departments of aPathology bHuman Genetics cOphthalmology, Radboud University Medical Center dDepartment of Pathology, Canisius Wilhelmina Hospital, Nijmegen eDepartment of Pathology, VU University Medical Center, Amsterdam, The Netherlands	To further elucidate the genetic underpinnings of uveal melanoma (UM) and identify new markers that correlate with disease outcome, archival formalin-fixed, paraffin-embedded enucleation specimens from 25 patients with UM and a mean follow-up of 14 years were analyzed for whole-genome copy-number alterations using OncoScan analysis. Copy-number alterations of chromosomes 1, 3, 6, and 8 were also analyzed in these tumors using multiplex ligation-dependent probe-amplification, and mutations in GNAQ, GNA11, and BAP1 were searched for by Sanger sequencing. Our study confirms the previously reported GNAQ and GNA11 mutation frequencies in UMs as well as the presence of monosomy 3 as a factor strongly indicating poor prognosis. Two cases with metastatic disease, but without monosomy of chromosome 3, showed loss of a small region in the distal part of chromosome 2p. Also, UMs leading to metastatic disease had more chromosomal aberrations than those without metastases. Three UMs lacking a GNAQ or a GNA11 mutation showed a gain of chromosome 8q; one of these cases showed extensive chromothripsis. Another case (with suspect lung metastasis) showed focal chromothripsis. Our whole-genome copy-number analysis shows that focal loss of chromosome 2p may be involved in the metastatic spread of UMs without monosomy 3; metastatic UMs carry more chromosomal aberrations than those without metastases; and chromothripsis may play a role in the oncogenesis of UMs, but does not necessarily indicate a poor prognosis. The clinical and particularly diagnostic utility of these findings needs to be corroborated in a larger set of patients with UM.	GRCh37/hg19				Yes	NA
CTDB0073	Research	25756553	van Engen-van Grunsven AC, Baar MP, Pfundt R, Rijntjes J, Kusters-Vandevelde HV, Delbecq AL, Keunen JE, Klevering JB, Wesseling P, Blokx WA, Groenen PJ.	Whole-genome copy-number analysis identifies new leads for chromosomal aberrations involved in the oncogenesis and metastastic behavior of uveal melanomas.	Melanoma Res	2015 Jun	1,3,6	Uveal melanoma	Array CGH	Homo sapiens	UM25	Affymetrix OncoScan Array				Departments of aPathology bHuman Genetics cOphthalmology, Radboud University Medical Center dDepartment of Pathology, Canisius Wilhelmina Hospital, Nijmegen eDepartment of Pathology, VU University Medical Center, Amsterdam, The Netherlands	To further elucidate the genetic underpinnings of uveal melanoma (UM) and identify new markers that correlate with disease outcome, archival formalin-fixed, paraffin-embedded enucleation specimens from 25 patients with UM and a mean follow-up of 14 years were analyzed for whole-genome copy-number alterations using OncoScan analysis. Copy-number alterations of chromosomes 1, 3, 6, and 8 were also analyzed in these tumors using multiplex ligation-dependent probe-amplification, and mutations in GNAQ, GNA11, and BAP1 were searched for by Sanger sequencing. Our study confirms the previously reported GNAQ and GNA11 mutation frequencies in UMs as well as the presence of monosomy 3 as a factor strongly indicating poor prognosis. Two cases with metastatic disease, but without monosomy of chromosome 3, showed loss of a small region in the distal part of chromosome 2p. Also, UMs leading to metastatic disease had more chromosomal aberrations than those without metastases. Three UMs lacking a GNAQ or a GNA11 mutation showed a gain of chromosome 8q; one of these cases showed extensive chromothripsis. Another case (with suspect lung metastasis) showed focal chromothripsis. Our whole-genome copy-number analysis shows that focal loss of chromosome 2p may be involved in the metastatic spread of UMs without monosomy 3; metastatic UMs carry more chromosomal aberrations than those without metastases; and chromothripsis may play a role in the oncogenesis of UMs, but does not necessarily indicate a poor prognosis. The clinical and particularly diagnostic utility of these findings needs to be corroborated in a larger set of patients with UM.	GRCh37/hg19				Yes	NA
CTDB0075	Research	25979483	Kim TM, Jung SH, An CH, Lee SH, Baek IP, Kim M, Park SW, Rhee JK, Lee SH, Chung YJ	Subclonal genomic architectures of primary and metastatic colorectal cancer based on intratumoral genetic heterogeneity.	Clin Cancer Res	2015 May	2	Colorectal cancer	Array CGH	Homo sapiens	CRC3	Agilent SurePrint G3 Human CGH Microarray 180K				Center for Cancer Evolution, Medical Research Center, The Catholic University of Korea	PURPOSE: The intratumoral heterogeneity (ITH) and the evolution of genomic architectures associated with the development of distant metastases are not well understood in colorectal cancers (CRCs). EXPERIMENTAL DESIGN: We performed multiregion biopsies of primary and liver metastatic regions from five CRCs with whole-exome sequencing and copy number profiling. RESULTS: In addition to a substantial level of genetic ITH, multiregion genetic profiling identifies the subclonal mutational architecture leading to the region-based or spatial categorization of somatic mutations and the inference of intratumoral evolutionary history of cancers. The universal mutations (those observed in all the regional biopsies) are enriched in known cancer genes such as APC and TP53 with distinct mutational spectra compared to biopsy- or region-specific mutations suggesting that major operative mutational mechanisms and their selective pressures are not constant across the metastatic progression. The phylogenies inferred from genomic data show branching evolutionary patterns where some primary biopsies are often segregated with metastastic lesions. Our analyses also revealed that copy number changes such as the chromosomal gains of c-MYC and chromothripsis can be region-specific and the potential source of genetic ITH. CONCLUSIONS: Our data shows that the genetic ITH is prevalent in CRC serving as a potential driving force to generate metastasis-initiating clones and also as a means to infer the intratumoral evolutionary history of cancers. The paucity of recurrent metastasis-clonal events suggests that CRC distant metastases may not follow a uniform course of genomic evolution, which should be considered in the genetic diagnosis and the selection of therapeutic targets for the advanced CRC.	GRCh37/hg19	GSE58512			Yes	NA
CTDB0076	Research	25979483	Kim TM, Jung SH, An CH, Lee SH, Baek IP, Kim M, Park SW, Rhee JK, Lee SH, Chung YJ	Subclonal genomic architectures of primary and metastatic colorectal cancer based on intratumoral genetic heterogeneity.	Clin Cancer Res	2015 May	16	Colorectal cancer	Array CGH	Homo sapiens	CRC5	Agilent SurePrint G3 Human CGH Microarray 180K				Center for Cancer Evolution, Medical Research Center, The Catholic University of Korea	PURPOSE: The intratumoral heterogeneity (ITH) and the evolution of genomic architectures associated with the development of distant metastases are not well understood in colorectal cancers (CRCs). EXPERIMENTAL DESIGN: We performed multiregion biopsies of primary and liver metastatic regions from five CRCs with whole-exome sequencing and copy number profiling. RESULTS: In addition to a substantial level of genetic ITH, multiregion genetic profiling identifies the subclonal mutational architecture leading to the region-based or spatial categorization of somatic mutations and the inference of intratumoral evolutionary history of cancers. The universal mutations (those observed in all the regional biopsies) are enriched in known cancer genes such as APC and TP53 with distinct mutational spectra compared to biopsy- or region-specific mutations suggesting that major operative mutational mechanisms and their selective pressures are not constant across the metastatic progression. The phylogenies inferred from genomic data show branching evolutionary patterns where some primary biopsies are often segregated with metastastic lesions. Our analyses also revealed that copy number changes such as the chromosomal gains of c-MYC and chromothripsis can be region-specific and the potential source of genetic ITH. CONCLUSIONS: Our data shows that the genetic ITH is prevalent in CRC serving as a potential driving force to generate metastasis-initiating clones and also as a means to infer the intratumoral evolutionary history of cancers. The paucity of recurrent metastasis-clonal events suggests that CRC distant metastases may not follow a uniform course of genomic evolution, which should be considered in the genetic diagnosis and the selection of therapeutic targets for the advanced CRC.	GRCh37/hg19	GSE58512			Yes	NA
CTDB0078	Research	25811670	Hermsen R, Toonen P, Kuijk E, Youssef SA, Kuiper R, van Heesch S, de Bruin A, Cuppen E, Simonis M	Lack of major genome instability in tumors of p53 null rats.	PLoS One	2015 Mar	6	Xenograft tumor	Array CGH	Mus musculus	103	NimbleGen Hubrecht Rat 2.1M HX1				Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands	Tumorigenesis is often associated with loss of tumor suppressor genes (such as TP53), genomic instability and telomere lengthening. Previously, we generated and characterized a rat p53 knockout model in which the homozygous rats predominantly develop hemangiosarcomas whereas the heterozygous rats mainly develop osteosarcomas. Using genome-wide analyses, we find that the tumors that arise in the heterozygous and homozygous Tp53C273X mutant animals are also different in their genomic instability profiles. While p53 was fully inactivated in both heterozygous and homozygous knockout rats, tumors from homozygous animals show very limited aneuploidy and low degrees of somatic copy number variation as compared to the tumors from heterozygous animals. In addition, complex structural rearrangements such as chromothripsis and breakage-fusion-bridge cycles were never found in tumors from homozygous animals, while these were readily detectable in tumors from heterozygous animals. Finally, we measured telomere length and telomere lengthening pathway activity and found that tumors of homozygous animals have longer telomeres but do not show clear telomerase or alternative lengthening of telomeres (ALT) activity differences as compared to the tumors from heterozygous animals. Taken together, our results demonstrate that host p53 status in this rat p53 knockout model has a large effect on both tumor type and genomic instability characteristics, where full loss of functional p53 is not the main driver of large-scale structural variations. Our results also suggest that chromothripsis primarily occurs under p53 heterozygous rather than p53 null conditions.	RGSC3.4	GSE55895			Yes	NA
CTDB0079	Research	25811670	Hermsen R, Toonen P, Kuijk E, Youssef SA, Kuiper R, van Heesch S, de Bruin A, Cuppen E, Simonis M	Lack of major genome instability in tumors of p53 null rats.	PLoS One	2015 Mar	1	Xenograft tumor	Array CGH	Mus musculus	170	NimbleGen Hubrecht Rat 2.1M HX1			Myc	Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands	Tumorigenesis is often associated with loss of tumor suppressor genes (such as TP53), genomic instability and telomere lengthening. Previously, we generated and characterized a rat p53 knockout model in which the homozygous rats predominantly develop hemangiosarcomas whereas the heterozygous rats mainly develop osteosarcomas. Using genome-wide analyses, we find that the tumors that arise in the heterozygous and homozygous Tp53C273X mutant animals are also different in their genomic instability profiles. While p53 was fully inactivated in both heterozygous and homozygous knockout rats, tumors from homozygous animals show very limited aneuploidy and low degrees of somatic copy number variation as compared to the tumors from heterozygous animals. In addition, complex structural rearrangements such as chromothripsis and breakage-fusion-bridge cycles were never found in tumors from homozygous animals, while these were readily detectable in tumors from heterozygous animals. Finally, we measured telomere length and telomere lengthening pathway activity and found that tumors of homozygous animals have longer telomeres but do not show clear telomerase or alternative lengthening of telomeres (ALT) activity differences as compared to the tumors from heterozygous animals. Taken together, our results demonstrate that host p53 status in this rat p53 knockout model has a large effect on both tumor type and genomic instability characteristics, where full loss of functional p53 is not the main driver of large-scale structural variations. Our results also suggest that chromothripsis primarily occurs under p53 heterozygous rather than p53 null conditions.	RGSC3.4	GSE55895			Yes	NA
CTDB0080	Research	25811670	Hermsen R, Toonen P, Kuijk E, Youssef SA, Kuiper R, van Heesch S, de Bruin A, Cuppen E, Simonis M	Lack of major genome instability in tumors of p53 null rats.	PLoS One	2015 Mar	10,13	Xenograft tumor	Array CGH	Mus musculus	153	NimbleGen Hubrecht Rat 2.1M HX1			Vegfa	Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands	Tumorigenesis is often associated with loss of tumor suppressor genes (such as TP53), genomic instability and telomere lengthening. Previously, we generated and characterized a rat p53 knockout model in which the homozygous rats predominantly develop hemangiosarcomas whereas the heterozygous rats mainly develop osteosarcomas. Using genome-wide analyses, we find that the tumors that arise in the heterozygous and homozygous Tp53C273X mutant animals are also different in their genomic instability profiles. While p53 was fully inactivated in both heterozygous and homozygous knockout rats, tumors from homozygous animals show very limited aneuploidy and low degrees of somatic copy number variation as compared to the tumors from heterozygous animals. In addition, complex structural rearrangements such as chromothripsis and breakage-fusion-bridge cycles were never found in tumors from homozygous animals, while these were readily detectable in tumors from heterozygous animals. Finally, we measured telomere length and telomere lengthening pathway activity and found that tumors of homozygous animals have longer telomeres but do not show clear telomerase or alternative lengthening of telomeres (ALT) activity differences as compared to the tumors from heterozygous animals. Taken together, our results demonstrate that host p53 status in this rat p53 knockout model has a large effect on both tumor type and genomic instability characteristics, where full loss of functional p53 is not the main driver of large-scale structural variations. Our results also suggest that chromothripsis primarily occurs under p53 heterozygous rather than p53 null conditions.	RGSC3.4	GSE55895			Yes	NA
CTDB0081	Research	25811670	Hermsen R, Toonen P, Kuijk E, Youssef SA, Kuiper R, van Heesch S, de Bruin A, Cuppen E, Simonis M	Lack of major genome instability in tumors of p53 null rats.	PLoS One	2015 Mar	7	Xenograft tumor	Array CGH	Mus musculus	82	NimbleGen Hubrecht Rat 2.1M HX1				Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands	Tumorigenesis is often associated with loss of tumor suppressor genes (such as TP53), genomic instability and telomere lengthening. Previously, we generated and characterized a rat p53 knockout model in which the homozygous rats predominantly develop hemangiosarcomas whereas the heterozygous rats mainly develop osteosarcomas. Using genome-wide analyses, we find that the tumors that arise in the heterozygous and homozygous Tp53C273X mutant animals are also different in their genomic instability profiles. While p53 was fully inactivated in both heterozygous and homozygous knockout rats, tumors from homozygous animals show very limited aneuploidy and low degrees of somatic copy number variation as compared to the tumors from heterozygous animals. In addition, complex structural rearrangements such as chromothripsis and breakage-fusion-bridge cycles were never found in tumors from homozygous animals, while these were readily detectable in tumors from heterozygous animals. Finally, we measured telomere length and telomere lengthening pathway activity and found that tumors of homozygous animals have longer telomeres but do not show clear telomerase or alternative lengthening of telomeres (ALT) activity differences as compared to the tumors from heterozygous animals. Taken together, our results demonstrate that host p53 status in this rat p53 knockout model has a large effect on both tumor type and genomic instability characteristics, where full loss of functional p53 is not the main driver of large-scale structural variations. Our results also suggest that chromothripsis primarily occurs under p53 heterozygous rather than p53 null conditions.	RGSC3.4	GSE55895			Yes	NA
CTDB0082	Research	25811670	Hermsen R, Toonen P, Kuijk E, Youssef SA, Kuiper R, van Heesch S, de Bruin A, Cuppen E, Simonis M	Lack of major genome instability in tumors of p53 null rats.	PLoS One	2015 Mar	3,8,10	Xenograft tumor	Array CGH	Mus musculus	97	NimbleGen Hubrecht Rat 2.1M HX1				Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands	Tumorigenesis is often associated with loss of tumor suppressor genes (such as TP53), genomic instability and telomere lengthening. Previously, we generated and characterized a rat p53 knockout model in which the homozygous rats predominantly develop hemangiosarcomas whereas the heterozygous rats mainly develop osteosarcomas. Using genome-wide analyses, we find that the tumors that arise in the heterozygous and homozygous Tp53C273X mutant animals are also different in their genomic instability profiles. While p53 was fully inactivated in both heterozygous and homozygous knockout rats, tumors from homozygous animals show very limited aneuploidy and low degrees of somatic copy number variation as compared to the tumors from heterozygous animals. In addition, complex structural rearrangements such as chromothripsis and breakage-fusion-bridge cycles were never found in tumors from homozygous animals, while these were readily detectable in tumors from heterozygous animals. Finally, we measured telomere length and telomere lengthening pathway activity and found that tumors of homozygous animals have longer telomeres but do not show clear telomerase or alternative lengthening of telomeres (ALT) activity differences as compared to the tumors from heterozygous animals. Taken together, our results demonstrate that host p53 status in this rat p53 knockout model has a large effect on both tumor type and genomic instability characteristics, where full loss of functional p53 is not the main driver of large-scale structural variations. Our results also suggest that chromothripsis primarily occurs under p53 heterozygous rather than p53 null conditions.	RGSC3.4	GSE55895			Yes	NA
CTDB0083	Research	25811670	Hermsen R, Toonen P, Kuijk E, Youssef SA, Kuiper R, van Heesch S, de Bruin A, Cuppen E, Simonis M	Lack of major genome instability in tumors of p53 null rats.	PLoS One	2015 Mar	3,10	Xenograft tumor	Array CGH	Mus musculus	112	NimbleGen Hubrecht Rat 2.1M HX1			Mycn;Alk	Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands	Tumorigenesis is often associated with loss of tumor suppressor genes (such as TP53), genomic instability and telomere lengthening. Previously, we generated and characterized a rat p53 knockout model in which the homozygous rats predominantly develop hemangiosarcomas whereas the heterozygous rats mainly develop osteosarcomas. Using genome-wide analyses, we find that the tumors that arise in the heterozygous and homozygous Tp53C273X mutant animals are also different in their genomic instability profiles. While p53 was fully inactivated in both heterozygous and homozygous knockout rats, tumors from homozygous animals show very limited aneuploidy and low degrees of somatic copy number variation as compared to the tumors from heterozygous animals. In addition, complex structural rearrangements such as chromothripsis and breakage-fusion-bridge cycles were never found in tumors from homozygous animals, while these were readily detectable in tumors from heterozygous animals. Finally, we measured telomere length and telomere lengthening pathway activity and found that tumors of homozygous animals have longer telomeres but do not show clear telomerase or alternative lengthening of telomeres (ALT) activity differences as compared to the tumors from heterozygous animals. Taken together, our results demonstrate that host p53 status in this rat p53 knockout model has a large effect on both tumor type and genomic instability characteristics, where full loss of functional p53 is not the main driver of large-scale structural variations. Our results also suggest that chromothripsis primarily occurs under p53 heterozygous rather than p53 null conditions.	RGSC3.4	GSE55895			Yes	NA
CTDB0084	Research	25811670	Hermsen R, Toonen P, Kuijk E, Youssef SA, Kuiper R, van Heesch S, de Bruin A, Cuppen E, Simonis M	Lack of major genome instability in tumors of p53 null rats.	PLoS One	2015 Mar	5	Xenograft tumor	Array CGH	Mus musculus	142	NimbleGen Hubrecht Rat 2.1M HX1			Vegfa	Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands	Tumorigenesis is often associated with loss of tumor suppressor genes (such as TP53), genomic instability and telomere lengthening. Previously, we generated and characterized a rat p53 knockout model in which the homozygous rats predominantly develop hemangiosarcomas whereas the heterozygous rats mainly develop osteosarcomas. Using genome-wide analyses, we find that the tumors that arise in the heterozygous and homozygous Tp53C273X mutant animals are also different in their genomic instability profiles. While p53 was fully inactivated in both heterozygous and homozygous knockout rats, tumors from homozygous animals show very limited aneuploidy and low degrees of somatic copy number variation as compared to the tumors from heterozygous animals. In addition, complex structural rearrangements such as chromothripsis and breakage-fusion-bridge cycles were never found in tumors from homozygous animals, while these were readily detectable in tumors from heterozygous animals. Finally, we measured telomere length and telomere lengthening pathway activity and found that tumors of homozygous animals have longer telomeres but do not show clear telomerase or alternative lengthening of telomeres (ALT) activity differences as compared to the tumors from heterozygous animals. Taken together, our results demonstrate that host p53 status in this rat p53 knockout model has a large effect on both tumor type and genomic instability characteristics, where full loss of functional p53 is not the main driver of large-scale structural variations. Our results also suggest that chromothripsis primarily occurs under p53 heterozygous rather than p53 null conditions.	RGSC3.4	GSE55895			Yes	NA
CTDB0085	Research	25811670	Hermsen R, Toonen P, Kuijk E, Youssef SA, Kuiper R, van Heesch S, de Bruin A, Cuppen E, Simonis M	Lack of major genome instability in tumors of p53 null rats.	PLoS One	2015 Mar	10,17	Xenograft tumor	Array CGH	Mus musculus	202	NimbleGen Hubrecht Rat 2.1M HX1				Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands	Tumorigenesis is often associated with loss of tumor suppressor genes (such as TP53), genomic instability and telomere lengthening. Previously, we generated and characterized a rat p53 knockout model in which the homozygous rats predominantly develop hemangiosarcomas whereas the heterozygous rats mainly develop osteosarcomas. Using genome-wide analyses, we find that the tumors that arise in the heterozygous and homozygous Tp53C273X mutant animals are also different in their genomic instability profiles. While p53 was fully inactivated in both heterozygous and homozygous knockout rats, tumors from homozygous animals show very limited aneuploidy and low degrees of somatic copy number variation as compared to the tumors from heterozygous animals. In addition, complex structural rearrangements such as chromothripsis and breakage-fusion-bridge cycles were never found in tumors from homozygous animals, while these were readily detectable in tumors from heterozygous animals. Finally, we measured telomere length and telomere lengthening pathway activity and found that tumors of homozygous animals have longer telomeres but do not show clear telomerase or alternative lengthening of telomeres (ALT) activity differences as compared to the tumors from heterozygous animals. Taken together, our results demonstrate that host p53 status in this rat p53 knockout model has a large effect on both tumor type and genomic instability characteristics, where full loss of functional p53 is not the main driver of large-scale structural variations. Our results also suggest that chromothripsis primarily occurs under p53 heterozygous rather than p53 null conditions.	RGSC3.4	GSE55895			Yes	NA
CTDB0086	Research	25811670	Hermsen R, Toonen P, Kuijk E, Youssef SA, Kuiper R, van Heesch S, de Bruin A, Cuppen E, Simonis M	Lack of major genome instability in tumors of p53 null rats.	PLoS One	2015 Mar	6	Xenograft tumor	Array CGH	Mus musculus	9	NimbleGen Hubrecht Rat 2.1M HX1				Hubrecht Institute, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands	Tumorigenesis is often associated with loss of tumor suppressor genes (such as TP53), genomic instability and telomere lengthening. Previously, we generated and characterized a rat p53 knockout model in which the homozygous rats predominantly develop hemangiosarcomas whereas the heterozygous rats mainly develop osteosarcomas. Using genome-wide analyses, we find that the tumors that arise in the heterozygous and homozygous Tp53C273X mutant animals are also different in their genomic instability profiles. While p53 was fully inactivated in both heterozygous and homozygous knockout rats, tumors from homozygous animals show very limited aneuploidy and low degrees of somatic copy number variation as compared to the tumors from heterozygous animals. In addition, complex structural rearrangements such as chromothripsis and breakage-fusion-bridge cycles were never found in tumors from homozygous animals, while these were readily detectable in tumors from heterozygous animals. Finally, we measured telomere length and telomere lengthening pathway activity and found that tumors of homozygous animals have longer telomeres but do not show clear telomerase or alternative lengthening of telomeres (ALT) activity differences as compared to the tumors from heterozygous animals. Taken together, our results demonstrate that host p53 status in this rat p53 knockout model has a large effect on both tumor type and genomic instability characteristics, where full loss of functional p53 is not the main driver of large-scale structural variations. Our results also suggest that chromothripsis primarily occurs under p53 heterozygous rather than p53 null conditions.	RGSC3.4	GSE55895			Yes	NA
CTDB0087	Research	25537021	Zhao X, Zhao YJ, Lin Q, Yu L, Liu Z, Lindsay H, Kogiso M, Rao P, Li XN, Lu X	Cytogenetic landscape of paired neurospheres and traditional monolayer cultures in pediatric malignant brain tumors.	Neuro Oncol	2015 Jul	2,3,8,10	Xenograft tumor	Array CGH	Mus musculus	IC-1227AA					Laboratory of Molecular Neuro-Oncology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas	BACKGROUND: New therapeutic targets are needed to eliminate cancer stem cells (CSCs). We hypothesize that direct comparison of paired CSCs and nonstem tumor cells (NSTCs) will facilitate identification of primary driver chromosomal aberrations that can serve as diagnostic markers and/or therapeutic targets. METHODS: We applied spectral karyotyping and G-banding to matched pairs of neurospheres (CSC-enriched cultures) and fetal bovine serum-based monolayer cultures (enriched with NSTCs) from 16 patient-derived orthotopic xenograft mouse models, including 9 medulloblastomas (MBs) and 7 high-grade gliomas (HGGs), followed by direct comparison of their numerical and structural abnormalities. RESULTS: Chromosomal aberrations were detected in neurospheres of all 16 models, and 82.0% numerical and 82.4% structural abnormalities were maintained in their matching monolayer cultures. Among the shared abnormalities, recurrent clonal changes were identified including gain of chromosomes 18 and 7 and loss of chromosome 10/10q (5/16 models), isochromosome 17q in 2 MBs, and a new breakpoint of 13q14 in 3 HGGs. Chromothripsis-like evidence was also observed in 3 HGG pairs. Additionally, we noted 20 numerical and 15 structural aberrations that were lost from the neurospheres and found 26 numerical and 23 structural aberrations that were only present in the NSTCs. Compared with MBs, the neurosphere karyotypes of HGG were more complex, with fewer chromosomal aberrations preserved in their matching NSTCs. CONCLUSION: Self-renewing CSCs in MBs and pediatric HGGs harbor recurrent numerical and structural aberrations that were maintained in the matching monolayer cultures. These primary chromosomal changes may represent new markers for anti-CSC therapies.					Yes	NA
CTDB0088	Research	25537021	Zhao X, Zhao YJ, Lin Q, Yu L, Liu Z, Lindsay H, Kogiso M, Rao P, Li XN, Lu X	Cytogenetic landscape of paired neurospheres and traditional monolayer cultures in pediatric malignant brain tumors.	Neuro Oncol	2015 Jul	12	Xenograft tumor	Array CGH	Mus musculus	IC-1502GBM					Laboratory of Molecular Neuro-Oncology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas	BACKGROUND: New therapeutic targets are needed to eliminate cancer stem cells (CSCs). We hypothesize that direct comparison of paired CSCs and nonstem tumor cells (NSTCs) will facilitate identification of primary driver chromosomal aberrations that can serve as diagnostic markers and/or therapeutic targets. METHODS: We applied spectral karyotyping and G-banding to matched pairs of neurospheres (CSC-enriched cultures) and fetal bovine serum-based monolayer cultures (enriched with NSTCs) from 16 patient-derived orthotopic xenograft mouse models, including 9 medulloblastomas (MBs) and 7 high-grade gliomas (HGGs), followed by direct comparison of their numerical and structural abnormalities. RESULTS: Chromosomal aberrations were detected in neurospheres of all 16 models, and 82.0% numerical and 82.4% structural abnormalities were maintained in their matching monolayer cultures. Among the shared abnormalities, recurrent clonal changes were identified including gain of chromosomes 18 and 7 and loss of chromosome 10/10q (5/16 models), isochromosome 17q in 2 MBs, and a new breakpoint of 13q14 in 3 HGGs. Chromothripsis-like evidence was also observed in 3 HGG pairs. Additionally, we noted 20 numerical and 15 structural aberrations that were lost from the neurospheres and found 26 numerical and 23 structural aberrations that were only present in the NSTCs. Compared with MBs, the neurosphere karyotypes of HGG were more complex, with fewer chromosomal aberrations preserved in their matching NSTCs. CONCLUSION: Self-renewing CSCs in MBs and pediatric HGGs harbor recurrent numerical and structural aberrations that were maintained in the matching monolayer cultures. These primary chromosomal changes may represent new markers for anti-CSC therapies.					Yes	NA
CTDB0089	Research	25537021	Zhao X, Zhao YJ, Lin Q, Yu L, Liu Z, Lindsay H, Kogiso M, Rao P, Li XN, Lu X	Cytogenetic landscape of paired neurospheres and traditional monolayer cultures in pediatric malignant brain tumors.	Neuro Oncol	2015 Jul	5,X	Xenograft tumor	Array CGH	Mus musculus	IC-3752GBM					Laboratory of Molecular Neuro-Oncology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas	BACKGROUND: New therapeutic targets are needed to eliminate cancer stem cells (CSCs). We hypothesize that direct comparison of paired CSCs and nonstem tumor cells (NSTCs) will facilitate identification of primary driver chromosomal aberrations that can serve as diagnostic markers and/or therapeutic targets. METHODS: We applied spectral karyotyping and G-banding to matched pairs of neurospheres (CSC-enriched cultures) and fetal bovine serum-based monolayer cultures (enriched with NSTCs) from 16 patient-derived orthotopic xenograft mouse models, including 9 medulloblastomas (MBs) and 7 high-grade gliomas (HGGs), followed by direct comparison of their numerical and structural abnormalities. RESULTS: Chromosomal aberrations were detected in neurospheres of all 16 models, and 82.0% numerical and 82.4% structural abnormalities were maintained in their matching monolayer cultures. Among the shared abnormalities, recurrent clonal changes were identified including gain of chromosomes 18 and 7 and loss of chromosome 10/10q (5/16 models), isochromosome 17q in 2 MBs, and a new breakpoint of 13q14 in 3 HGGs. Chromothripsis-like evidence was also observed in 3 HGG pairs. Additionally, we noted 20 numerical and 15 structural aberrations that were lost from the neurospheres and found 26 numerical and 23 structural aberrations that were only present in the NSTCs. Compared with MBs, the neurosphere karyotypes of HGG were more complex, with fewer chromosomal aberrations preserved in their matching NSTCs. CONCLUSION: Self-renewing CSCs in MBs and pediatric HGGs harbor recurrent numerical and structural aberrations that were maintained in the matching monolayer cultures. These primary chromosomal changes may represent new markers for anti-CSC therapies.					Yes	NA
CTDB0094	Research	25736334	Wang JC, Fisker T, Sahoo T	Constitutional chromothripsis involving chromosome 19 in a child with subtle dysmorphic features.	Am J Med Genet A	2015 Apr	19	Dysmorphia	Array CGH	Homo sapiens	25736334_1	4x180 k oligonucleotide array				Cytogenetics Laboratory, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Ontario, Canada	Chromothripsis is defined as a single event wherein tens to hundreds of chromosomal rearrangements occur in a limited number of genomic regions, although the minimum threshold for the number of breaks and regions involved in chromothripsis has not been defined.	GRCh37/hg19				No	NA
CTDB0110	Research	21925314	Liu P, Erez A, Nagamani SC, Dhar SU, Kolodziejska KE, Dharmadhikari AV, Cooper ML, Wiszniewska J, Zhang F, Withers MA, Bacino CA, Campos-Acevedo LD, Delgado MR, Freedenberg D, Garnica A, Grebe TA, Hernandez-Almaguer D, Immken L, Lalani SR, McLean SD, Nort	Chromosome Catastrophes Involve Replication Mechanisms Generating Complex Genomic Rearrangements	Cell	2011 Sep	9	Dysmorphia	Array CGH	Homo sapiens	BAB3103	Nimblegen 4.2M Array				Department of Molecular and Human Genetics	Complex genomic rearrangements (CGRs) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, achromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here, we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated, we observed localization and multiple copy number changes including deletions, duplications, and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism's life cycle.	GRCh37/hg19				No	NA
CTDB0111	Research	21925314	Liu P, Erez A, Nagamani SC, Dhar SU, Kolodziejska KE, Dharmadhikari AV, Cooper ML, Wiszniewska J, Zhang F, Withers MA, Bacino CA, Campos-Acevedo LD, Delgado MR, Freedenberg D, Garnica A, Grebe TA, Hernandez-Almaguer D, Immken L, Lalani SR, McLean SD, Nort	Chromosome Catastrophes Involve Replication Mechanisms Generating Complex Genomic Rearrangements	Cell	2011 Sep	22	Dysmorphia	Array CGH	Homo sapiens	BAB3104	Nimblegen 4.2M Array				Department of Molecular and Human Genetics	Complex genomic rearrangements (CGRs) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, achromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here, we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated, we observed localization and multiple copy number changes including deletions, duplications, and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism's life cycle.	GRCh37/hg19				No	NA
CTDB0112	Research	21925314	Liu P, Erez A, Nagamani SC, Dhar SU, Kolodziejska KE, Dharmadhikari AV, Cooper ML, Wiszniewska J, Zhang F, Withers MA, Bacino CA, Campos-Acevedo LD, Delgado MR, Freedenberg D, Garnica A, Grebe TA, Hernandez-Almaguer D, Immken L, Lalani SR, McLean SD, Nort	Chromosome Catastrophes Involve Replication Mechanisms Generating Complex Genomic Rearrangements	Cell	2011 Sep	9	Dysmorphia	Array CGH	Homo sapiens	BAB3105	Nimblegen 4.2M Array				Department of Molecular and Human Genetics	Complex genomic rearrangements (CGRs) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, achromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here, we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated, we observed localization and multiple copy number changes including deletions, duplications, and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism's life cycle.	GRCh37/hg19				No	NA
CTDB0136	Research	23271725	Hirsch D, Kemmerling R, Davis S, Camps J, Meltzer PS, Ried T, Gaiser T	Chromothripsis and Focal Copy Number Alterations Determine Poor Outcome in Malignant Melanoma	Cancer Res	2013 Mar	5,15	Melanoma	Array CGH	Homo sapiens	case20	Agilent CGH Microarrays 4x180 K				Genetics Branch, Center for Cancer Research, National Cancer Institute/NIH, Bethesda, Maryland 20892, USA	Genetic changes during tumorigenesis are usually acquired sequentially. However, a recent study showed that in 2% to 3% of all cancers a single catastrophic event, termed chromothripsis, can lead to massive genomic rearrangements confined to one or a few chromosomes. To explore whether the degree of genomic instability and chromothripsis influences prognosis in cancer, we retrospectively applied array-comparative genomic hybridization (aCGH) to 20 malignant melanomas that showed, despite comparable conventional clinical and pathologic parameters, a profoundly different clinical course. We compared 10 patients who died of malignant melanoma 3.7 years (median, range 0.9-7.6 years) after diagnosis with 10 patients who survived malignant melanoma and had a median disease-free survival of 14.8 years (range 12.5-16.7 years; P = 0.00001). We observed a striking association between the degree of chromosomal instability, both numerical and structural, and outcome. Malignant melanomas associated with good prognosis showed only few chromosomal imbalances (mean 1.6 alterations per case), predominantly whole chromosome or chromosome arm gains and losses, whereas malignant melanomas with poor prognosis harbored significantly more chromosomal aberrations (13.9 per case; P = 0.008). Array-based CGH showed that these aberrations were mostly focal events, culminating in two cases in a pattern consistent with the phenomenon of chromothripsis, which was confirmed by paired-end sequencing. This is the first description of chromothripsis in primary malignant melanomas. Our study therefore links focal copy number alterations and chromothripsis with poor outcome in patients with malignant melanomas (P = 0.0002) and provides a genetic approach to predict outcome in malignant melanomas.	GRCh37/hg19				Yes	NA
CTDB0143	Research	25074542	Xiang DB, Wei B, Abraham SC, Huo L, Albarracin CT, Zhang H, Babiera G, Caudle AS, Akay CL, Rao P, Zhao YJ, Lu X, Wu Y	Molecular cytogenetic characterization of mammary neuroendocrine carcinoma.	Hum Pathol	2014 Sep	1,6,8,15	Neuroendocrine carcinoma	Array CGH	Homo sapiens	Case2	Chroma Technology				Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030	Primary mammary neuroendocrine carcinoma (NEC) is an uncommon entity that accounts for 2% to 5% of breast carcinomas. Recent reports have shown that NEC of the breast is an aggressive subtype of mammary carcinoma that is distinct from invasive ductal carcinoma, not otherwise specified, and have suggested that these tumors have a poorer prognosis than invasive ductal carcinoma, not otherwise specified. In this study, we provide the first cytogenetic characterization of mammary NEC using both conventional G-banding and spectral karyotype on a group of 7 tumors. We identified clonal chromosomal aberrations in 5 (71.4%) cases, with 4 of them showing complex karyotypes. Of these, recurrent numerical aberrations included gain of chromosome 7 (n = 2) and loss of chromosome 15 (n = 2). Recurrent clonal structural chromosomal aberrations involved chromosomes 1 (n = 3), 3 (n = 2), 6q (n = 3), and 17q (n = 3). Of the 4 (57.1%) cases with complex karyotypes, 2 showed evidence of chromothripsis, a phenomenon in which tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. One of these had evidence of chromothripsis involving chromosomes 1, 6, 8, and 15. The other also had evidence of chromosome 8 chromothripsis, making this a recurrent finding shared by both cases. We also found that mammary NEC shared some cytogenetic abnormalities--such as trisomy 7 and 12--with other neuroendocrine tumors in the lung and gastrointestinal tract, suggesting trisomy 7 and 12 as potential common molecular aberrations in neuroendocrine tumors. To our knowledge, this is the first report on molecular cytogenetic characterization of mammary NEC.					Yes	NA
CTDB0144	Research	25074542	Xiang DB, Wei B, Abraham SC, Huo L, Albarracin CT, Zhang H, Babiera G, Caudle AS, Akay CL, Rao P, Zhao YJ, Lu X, Wu Y	Molecular cytogenetic characterization of mammary neuroendocrine carcinoma.	Hum Pathol	2014 Sep	8	Neuroendocrine carcinoma	Array CGH	Homo sapiens	Case5	Chroma Technology				Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030	Primary mammary neuroendocrine carcinoma (NEC) is an uncommon entity that accounts for 2% to 5% of breast carcinomas. Recent reports have shown that NEC of the breast is an aggressive subtype of mammary carcinoma that is distinct from invasive ductal carcinoma, not otherwise specified, and have suggested that these tumors have a poorer prognosis than invasive ductal carcinoma, not otherwise specified. In this study, we provide the first cytogenetic characterization of mammary NEC using both conventional G-banding and spectral karyotype on a group of 7 tumors. We identified clonal chromosomal aberrations in 5 (71.4%) cases, with 4 of them showing complex karyotypes. Of these, recurrent numerical aberrations included gain of chromosome 7 (n = 2) and loss of chromosome 15 (n = 2). Recurrent clonal structural chromosomal aberrations involved chromosomes 1 (n = 3), 3 (n = 2), 6q (n = 3), and 17q (n = 3). Of the 4 (57.1%) cases with complex karyotypes, 2 showed evidence of chromothripsis, a phenomenon in which tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. One of these had evidence of chromothripsis involving chromosomes 1, 6, 8, and 15. The other also had evidence of chromosome 8 chromothripsis, making this a recurrent finding shared by both cases. We also found that mammary NEC shared some cytogenetic abnormalities--such as trisomy 7 and 12--with other neuroendocrine tumors in the lung and gastrointestinal tract, suggesting trisomy 7 and 12 as potential common molecular aberrations in neuroendocrine tumors. To our knowledge, this is the first report on molecular cytogenetic characterization of mammary NEC.					Yes	NA
CTDB0148	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	7,11	Breast cancer	Array CGH	Homo sapiens	T61	Agilent 244K CGH array			CCND1	Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	NA
CTDB0149	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	6	Breast cancer	Array CGH	Homo sapiens	T23	Agilent 244K CGH array				Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	NA
CTDB0150	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	8,19	Breast cancer	Array CGH	Homo sapiens	T46	Agilent 244K CGH array				Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	NA
CTDB0151	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	11	Breast cancer	Array CGH	Homo sapiens	T147	Agilent 244K CGH array			CCND1	Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	NA
CTDB0152	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	9	Breast cancer	Array CGH	Homo sapiens	T190	Agilent 244K CGH array				Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	NA
CTDB0153	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	8	Breast cancer	Array CGH	Homo sapiens	T199	Agilent 244K CGH array			MYC;PVT1	Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	MYC,PVT1
CTDB0154	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	7	Breast cancer	Array CGH	Homo sapiens	T79	Agilent 244K CGH array				Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	NA
CTDB0155	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	6,8,17	Breast cancer	Array CGH	Homo sapiens	T333	Agilent 244K CGH array			ERBB2	Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	NA
CTDB0156	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	8,17	Breast cancer	Array CGH	Homo sapiens	T111	Agilent 244K CGH array			BCAS3;ERBB2	Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	NA
CTDB0157	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	17	Breast cancer	Array CGH	Homo sapiens	T207	Agilent 244K CGH array			ERBB2	Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	NA
CTDB0158	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	8,17,21	Breast cancer	Array CGH	Homo sapiens	T74	Agilent 244K CGH array			MYC	Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	NA
CTDB0159	Research	25011954	Przybytkowski E, Lenkiewicz E, Barrett MT, Klein K, Nabavi S, Greenwood CM, Basik M	Chromosome-breakage genomic instability and chromothripsis in breast cancer.	BMC Genomics	2014 Jul	17,21	Breast cancer	Array CGH	Homo sapiens	T64	Agilent 244K CGH array				Department of Oncology, Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, Quebec H3T-1E2, Canada	BACKGROUND: Chromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome. RESULTS: We performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers. CONCLUSIONS: Our results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.	GRCh37/hg19				Yes	NA
CTDB0164	Research	25144242	Kodama T, Motoi N, Ninomiya H, Sakamoto H, Kitada K, Tsukaguchi T, Satoh Y, Nomura K, Nagano H, Ishii N, Terui Y, Hatake K, Ishikawa Y	A novel mechanism of EML4-ALK rearrangement mediated by chromothripsis in a patient-derived cell line.	J Thorac Oncol	2014 Nov	2	Non Small-cell lung cancer	Array CGH	Homo sapiens	JFCR-LC649	Agilent SurePrint G3 1M CGH array			EML4;ALK	Department of Pathology, The Cancer Institute Hospital, Tokyo, Japan	INTRODUCTION: EML4-ALK is a driver oncogene in non-small-cell lung cancer (NSCLC) and has been developed into a promising molecular target for antitumor agents. Although EML4-ALK is reported to be formed by inversion of chromosome 2, other mechanisms of this gene fusion remain unknown. This study aimed to examine the mechanism of EML4-ALK rearrangement using a novel cell line with the EML4-ALK fusion gene. METHODS: An EML4-ALK-positive cell line, termed JFCR-LC649, was established from pleomorphic carcinoma, a rare subtype of NSCLC. We investigated the chromosomal aberrations using fluorescence in situ hybridization and comparative genomic hybridization (CGH). Alectinib/CH5424802, a selective ALK inhibitor, was evaluated in the antitumor activity against JFCR-LC649 in vitro and in vivo xenograft model. RESULTS: We established an EML4-ALK-positive cell line, termed JFCR-LC649, derived from a patient with NSCLC and revealed that the JFCR-LC649 cells harbor variant 3 of the EML4-ALK fusion with twofold copy number gain. Interestingly, comparative genomic hybridization and metaphase-fluorescence in situ hybridization analysis showed that in addition to two normal chromosome 2, JFCR-LC649 cells contained two aberrant chromosome 2 that were fragmented and scattered. These observations provided the first evidence that EML4-ALK fusion in JFCR-LC649 cells was formed in chromosome 2 by a distinct mechanism of genomic rearrangement, termed chromothripsis. Furthermore, a selective ALK inhibitor alectinib/CH5424802 suppressed tumor growth of the JFCR-LC649 cells through inhibition of phospho-ALK in vitro and in vivo in a xenograft model. CONCLUSION: Our results suggested that chromothripsis may be a mechanism of oncogenic rearrangement of EML4-ALK. In addition, alectinib was effective against EML4-ALK-positive tumors with ALK copy number gain mediated by chromothripsis.					Yes	EML4,ALK
CTDB0167	Research	26040972	Gamba BF, Richieri-Costa A, Costa S, Rosenberg C, Ribeiro-Bicudo LA	Chromothripsis with at least 12 breaks at 1p36.33-p35.3 in a boy with multiple congenital anomalies.	Mol Genet Genomics	2015 Jun	1	Congenital abnormality	Array CGH	Homo sapiens	26040972_1	Oxford Gene Technology CytosureTM 4X180K array	chr1:1023846-2761528:-1;chr1:3696933-5200401:-1;chr1:6882352-7718050:-1;chr1:14012378-14992103:-1;chr1:17213968-20934341:-1;chr1:24146844-30208750:1			Department of Genetics, Institute of Biosciences, University of Sao Paulo State, Botucatu, SP, Brazil	Terminal deletion in the short arm of chromosome 1 results in a disorder described as 1p36 deletion syndrome. The resulting phenotype varies among patients including mental retardation, developmental delay, sensorineural hearing loss, seizures, heart defects, and distinct facies. In the present case, we performed array-comparative genomic hybridization in a boy with multiple congenital malformations presenting some features overlapping the 1p36 deletion phenotype for whom chromosomal analysis did not reveal a terminal deletion in 1p. Results showed complex chromosome rearrangements involving the 1p36.33-p35.3 region. While the mechanism of origin of these rearrangements is still unclear, chromothripsis-a single catastrophic event leading to shattering chromosomes or chromosome regions and rejoining of the segments-has been described to occur in a fraction of cancers. The presence of at least 12 clustered breaks at 1p and apparent lack of mosaicism in the present case suggests that a single event like chromothripsis occurred. This finding suggests that chromothripsis is responsible for some constitutive complex chromosome rearrangements.	GRCh37/hg19				No	NA
CTDB0286	Research	22123490	Kitada K, Aida S, Aikawa S	Coamplification of multiple regions of chromosome 2, including MYCN, in a single patchwork amplicon in cancer cell lines	Cytogenetic and Genome Research	2011 Nov 	2	Neuroblastoma	Array CGH	Homo sapiens	IMR-32	Agilent SurePrint G3 human CGH arrays	chr10:0-135374737:0;chr11:0-134452384:0;chr12:0-132349534:0;chr13:0-114142980:0;chr14:0-106368585:0;chr15:0-100338915:0;chr16:0-88827254:0;chr17:0-78774742:0;chr18:0-76117153:0;chr19:0-63811651:0;chr1:0-247249719:0;chr20:0-62435964:0;chr21:0-46944323:0;chr22:0-49691432:0;chr2:0-14657088:0;chr2:14657089-16041259:1;chr2:16041260-17219745:0;chr2:17219746-17233242:1;chr2:17233243-29549878:0;chr2:29549879-29777721:1;chr2:29777722-53254629:0;chr2:53254630-53454473:1;chr2:53454474-66346579:0;chr2:66346580-66576580:1;chr2:66576581-68025605:0;chr2:68025606-69255606:1;chr2:69255607-242951149:0;chr3:0-199501827:0;chr4:0-191273063:0;chr5:0-180857866:0;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0	hs2:69255606-69255606,hs2:17233242-17233242;hs2:17219746-17219746,hs2:14657089-14657089;hs2:16041259-16041259,hs2:53454473-53454473;hs2:53254630-53254630,hs2:29777721-29777721;hs2:29549879-29549879,hs2:66346580-66346580	MYCN;ANTXR1;NNG1;MEIS1	Kamakura Research Laboratories, Chugai Pharmaceutical Co. Ltd., Kamakura, Japan	Coamplification of multiple segments of chromosome 2, including an MYCN-bearing segment, was examined in 2 cancer cell lines, NCI-H69 (lung cancer) and IMR-32 (neuroblastoma). High-resolution array-CGH analysis revealed 13 and 6 highly amplified segments located at different sites in chromosome 2 in NCI-H69 and IMR-32, respectively. FISH analysis demonstrated that these segments were co-localized in double minutes in NCI-H69 and in homogeneously staining regions in IMR-32. Connectivity of the segments was determined by a PCR assay using designed primer sets. It was found that all the segments were connected to each other irrespective of their order and orientation against the genome sequence, and a single chain-like cluster was configured in both cell lines. Such patchwork structures of the amplicons suggest the possibility that massive genomic rearrangements, explained by the single catastrophic event model, are involved in the formation of the amplicons, enabling the coamplification of different chromosomal regions including the MYCN locus. The model comprises massive fragmentation of chromosomes and random rejoining of the fragments.	NCBI 36/hg18				Yes	ANTXR1,NNG1
CTDB0287	Research	22123490	Kitada K, Aida S, Aikawa S	Coamplification of multiple regions of chromosome 2, including MYCN, in a single patchwork amplicon in cancer cell lines	Cytogenetic and Genome Research	2011 Nov 	2	Small cell lung cancer	Array CGH	Homo sapiens	NCI-H69	Agilent SurePrint G3 human CGH arrays	chr10:0-135374737:0;chr11:0-134452384:0;chr12:0-132349534:0;chr13:0-114142980:0;chr14:0-106368585:0;chr15:0-100338915:0;chr16:0-88827254:0;chr17:0-78774742:0;chr18:0-76117153:0;chr19:0-63811651:0;chr1:0-247249719:0;chr20:0-62435964:0;chr21:0-46944323:0;chr22:0-49691432:0;chr2:0-15968981:0;chr2:134993920-135131902:1;chr2:135131903-137295959:0;chr2:137295960-137307960:1;chr2:137307961-140224587:0;chr2:140224588-140612621:1;chr2:140612622-145554322:0;chr2:145554323-145604323:1;chr2:145604324-242951149:0;chr2:15968982-16082369:1;chr2:16082370-16091320:0;chr2:16091321-16106321:1;chr2:16106322-53013053:0;chr2:53013054-53044885:1;chr2:53044886-53058402:0;chr2:53058403-53115124:1;chr2:53115125-53132779:0;chr2:53132780-53387222:1;chr2:53387223-53401052:0;chr2:53401053-53770309:1;chr2:53682561-53768531:1;chr2:53770310-53784166:0;chr2:53784167-53813298:1;chr2:53813299-77065691:0;chr2:77065692-77074080:1;chr2:77074081-86584943:0;chr2:86584944-86587727:1;chr2:86587728-134993919:0;chr3:0-199501827:0;chr4:0-191273063:0;chr5:0-180857866:0;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0	hs2:16106321-16106321,hs2:145554323-145554323;hs2:145604323-145604323,hs2:77065692-77065692;hs2:77074080-77074080,hs2:86584944-86584944;hs2:86587727-86587727,hs2:53813298-53813298;hs2:53784167-53784167,hs2:15968982-15968982;hs2:16082369-16082369,hs2:53682561-53682561;hs2:53768531-53768531,hs2:53770309-53770309;hs2:53401053-53401053,hs2:53387222-53387222;hs2:53132780-53132780,hs2:53115124-53115124;hs2:53058403-53058403,hs2:140224588-140224588;hs2:140612621-140612621,hs2:134993920-134993920;hs2:135131902-135131902,hs2:53013054-53013054;hs2:53044885-53044885,hs2:137295960-137295960	MYCN	Kamakura Research Laboratories, Chugai Pharmaceutical Co. Ltd., Kamakura, Japan	Coamplification of multiple segments of chromosome 2, including an MYCN-bearing segment, was examined in 2 cancer cell lines, NCI-H69 (lung cancer) and IMR-32 (neuroblastoma). High-resolution array-CGH analysis revealed 13 and 6 highly amplified segments located at different sites in chromosome 2 in NCI-H69 and IMR-32, respectively. FISH analysis demonstrated that these segments were co-localized in double minutes in NCI-H69 and in homogeneously staining regions in IMR-32. Connectivity of the segments was determined by a PCR assay using designed primer sets. It was found that all the segments were connected to each other irrespective of their order and orientation against the genome sequence, and a single chain-like cluster was configured in both cell lines. Such patchwork structures of the amplicons suggest the possibility that massive genomic rearrangements, explained by the single catastrophic event model, are involved in the formation of the amplicons, enabling the coamplification of different chromosomal regions including the MYCN locus. The model comprises massive fragmentation of chromosomes and random rejoining of the fragments.	NCBI 36/hg18				Yes	NA
CTDB0320	Research	25178926	Conconi D, Panzeri E, Redaelli S, Bovo G, Vigano P, Strada G, Dalpra L, Bentivegna A	Chromosomal imbalances in human bladder urothelial carcinoma: similarities and differences between biopsy samples and cancer stem-like cells	BMC Cancer	2014 Sep 	6	Bladder cancer	Array CGH	Homo sapiens	36	Agilent SurePrint G3 Human CGH Microarray 8X60K	chr10:0-135374737:0;chr11:0-134452384:0;chr12:0-132349534:0;chr13:0-114142980:0;chr14:0-106368585:0;chr15:0-100338915:0;chr16:0-88827254:0;chr17:0-78774742:0;chr18:0-76117153:0;chr19:0-63811651:0;chr1:0-247249719:0;chr20:0-62435964:0;chr21:0-46944323:0;chr22:0-49691432:0;chr2:0-242951149:0;chr3:0-199501827:0;chr4:0-191273063:0;chr5:0-180857866:0;chr6:0-1135232:0;chr6:107207520-108013375:1;chr6:108013376-112208261:0;chr6:112208262-112512304:1;chr6:112512305-120033768:0;chr6:1135233-1135233:-1;chr6:1135234-3051601:0;chr6:11627813-14525354:1;chr6:120033769-122974823:1;chr6:122974824-123422158:0;chr6:123422159-124568813:1;chr6:124568814-125346033:0;chr6:125346034-132823273:1;chr6:132823274-146392494:0;chr6:14525355-16403510:0;chr6:146392495-170732174:-1;chr6:16403511-22397156:1;chr6:170732175-170899992:0;chr6:21107860-22397156:1;chr6:22397157-25428028:0;chr6:25428029-26797455:1;chr6:26797456-27107707:0;chr6:27107708-27263190:-1;chr6:27263191-27579787:0;chr6:27579788-30302271:-1;chr6:30302272-36788265:0;chr6:3051602-3600958:1;chr6:3600959-11627812:0;chr6:36788266-37917098:1;chr6:37917099-37957570:0;chr6:37957571-41426791:-1;chr6:41426792-41474744:0;chr6:41474745-48648336:1;chr6:41716419-43012857:1;chr6:45987212-47657919:1;chr6:48648337-49627984:0;chr6:49627985-52912395:-1;chr6:52912396-53384802:0;chr6:53384803-57298946:1;chr6:57298947-82896725:0;chr6:82896726-83392667:1;chr6:83392668-84856797:0;chr6:84856798-86137353:1;chr6:86137354-107207519:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Surgery and Translational Medicine, University of Milan-Bicocca, via Cadore 48, 20052 Monza, Italy	BACKGROUND: The existence of two distinct groups of tumors with different clinical characteristic is a remarkable feature of transitional cell carcinomas (TCCs) of the bladder. More than 70% are low-grade (LG) non-infiltrating (NI) cancers at diagnosis, but 60-80% of them recur at least one time and 10-20% progress in stage and grade. On the other hand, about 20% of tumors show muscle invasion (IN) and have a poor prognosis with <50% survival after 5 years. This study focuses on the complexity of the bladder cancer genome, and for the first time to our knowledge, on the possibility to compare genomic alterations of in vitro selected cancer stem-like cells (CSCs), and their original biopsy in order to identify different genomic signature already present in the early stages of tumorigenesis of LG and HG tumors. METHODS: We initially used conventional chromosome analysis on TCC biopsies with different histotypes (LG vs HG) in order to detect rough differences between them. Then, we performed array comparative genomic hybridization (aCGH) on 10 HG and 10 LG tumors providing an overview of copy number alterations (CNAs). Finally, we made a comparison of the overall CNAs in 16 biopsies and their respective CSCs isolated from them. RESULTS: Our findings indicate that LG and HG bladder cancer differ with regard to their genomic profile even in the early stage of tumorigenesis; moreover, we identified a subgroup of LG samples with a higher tendency to lose genomic regions which could represent a more aggressive phenotype. CONCLUSIONS: The outcomes not only provide valuable information to deeper studying TCC carcinogenesis, but also could help in the clinic for diagnosis and prognosis of patients who will benefit from a more aggressive therapy. 	NCBI 36/hg18				Yes	NA
CTDB0321	Research	25178926	Conconi D, Panzeri E, Redaelli S, Bovo G, Vigano P, Strada G, Dalpra L, Bentivegna A	Chromosomal imbalances in human bladder urothelial carcinoma: similarities and differences between biopsy samples and cancer stem-like cells	BMC Cancer	2014 Sep 	6	Bladder cancer	Array CGH	Homo sapiens	37	Agilent SurePrint G3 Human CGH Microarray 8X60K	chr10:0-135374737:0;chr11:0-134452384:0;chr12:0-132349534:0;chr13:0-114142980:0;chr14:0-106368585:0;chr15:0-100338915:0;chr16:0-88827254:0;chr17:0-78774742:0;chr18:0-76117153:0;chr19:0-63811651:0;chr1:0-247249719:0;chr20:0-62435964:0;chr21:0-46944323:0;chr22:0-49691432:0;chr2:0-242951149:0;chr3:0-199501827:0;chr4:0-191273063:0;chr5:0-180857866:0;chr6:0-295011:0;chr6:11110371-17397320:1;chr6:170734369-170899992:0;chr6:17397321-18704208:0;chr6:18704209-30343121:1;chr6:295012-9584745:-1;chr6:30343122-39615526:0;chr6:39615527-41420057:1;chr6:41420058-42438437:0;chr6:42438438-46607938:1;chr6:46607939-48489132:0;chr6:48489133-55026820:-1;chr6:55026821-55152486:0;chr6:55152487-57298946:1;chr6:57298947-62815576:0;chr6:62815577-170734368:-1;chr6:9584746-11110370:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Surgery and Translational Medicine, University of Milan-Bicocca, via Cadore 48, 20052 Monza, Italy	BACKGROUND: The existence of two distinct groups of tumors with different clinical characteristic is a remarkable feature of transitional cell carcinomas (TCCs) of the bladder. More than 70% are low-grade (LG) non-infiltrating (NI) cancers at diagnosis, but 60-80% of them recur at least one time and 10-20% progress in stage and grade. On the other hand, about 20% of tumors show muscle invasion (IN) and have a poor prognosis with <50% survival after 5 years. This study focuses on the complexity of the bladder cancer genome, and for the first time to our knowledge, on the possibility to compare genomic alterations of in vitro selected cancer stem-like cells (CSCs), and their original biopsy in order to identify different genomic signature already present in the early stages of tumorigenesis of LG and HG tumors. METHODS: We initially used conventional chromosome analysis on TCC biopsies with different histotypes (LG vs HG) in order to detect rough differences between them. Then, we performed array comparative genomic hybridization (aCGH) on 10 HG and 10 LG tumors providing an overview of copy number alterations (CNAs). Finally, we made a comparison of the overall CNAs in 16 biopsies and their respective CSCs isolated from them. RESULTS: Our findings indicate that LG and HG bladder cancer differ with regard to their genomic profile even in the early stage of tumorigenesis; moreover, we identified a subgroup of LG samples with a higher tendency to lose genomic regions which could represent a more aggressive phenotype. CONCLUSIONS: The outcomes not only provide valuable information to deeper studying TCC carcinogenesis, but also could help in the clinic for diagnosis and prognosis of patients who will benefit from a more aggressive therapy. 	NCBI 36/hg18				Yes	NA
CTDB0344	Research	23010713	Zehentner BK, Hartmann L, Johnson KR, Stephenson CF, Chapman DB, de Baca ME, Wells DA, Loken MR, Tirtorahardjo B, Gunn SR, Lim L	Array-based karyotyping in plasma cell neoplasia after plasma cell enrichment increases detection of genomic aberrations	American Journal of Clinical Pathology	2012 Oct	17	Plasma cell neoplasm	Array CGH	Homo sapiens	MA-MMHL-48					Hematologics Inc, 3161 Elliott Ave, Ste 200, Seattle, WA 98121, USA	The discovery of genomic abnormalities present in monoclonal plasma cells has diagnostic, prognostic, and disease-monitoring implications in plasma cell neoplasms (PCNs). However, technical and disease-related limitations hamper the detection of these abnormalities using cytogenetic analysis or fluorescence in situ hybridization (FISH). In this study, 28 bone marrow specimens with known PCNs were examined for the presence of genomic abnormalities using microarray analysis after plasma cell enrichment. Cytogenetic analysis was performed on 15 of 28 samples, revealing disease-related genomic aberrations in only 3 (20%) of 15 cases. FISH analysis was performed on enriched plasma cells and detected aberrations in 84.6% of specimens while array comparative genomic hybridization (aCGH) detected abnormalities in 89.3% of cases. Furthermore, aCGH revealed additional abnormalities in 24 cases compared with FISH alone. We conclude that aCGH after plasma cell enrichment, in combination with FISH, is a valuable approach for routine clinical use in achieving a more complete genetic characterization of patients with PCN.	GRCh37/hg19				Yes	NA
CTDB0423	Research	26305789	Salaverria I, Martin-Garcia D, Lopez C, Clot G, Garcia-Aragones M, Navarro A, Delgado J, Baumann T, Pinyol M, Martin-Guerrero I, Carrio A, Costa D, Queiros AC, Jayne S, Aymerich M, Villamor N, Colomer D, Gonzalez M, Lopez-Guillermo A, Campo E, Dyer MJ, Siebert R, Armengol L, Bea S	Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia	Genes Chromosomes Cancer	2015 Nov	10	Chronic lymphocytic leukemia	Array CGH	Homo sapiens	36	qChip Hemo array	chr10:19322471-20590077:-1;chr10:23733538-25127913:-1;chr10:31647733-36030348:-1;chr10:42418957-46617713:-1;chr10:68811448-75236059:-1;chr10:86477031-86941847:-1;chr10:92351887-94425619:-1;chr10:98597009-112387473:-1;chr10:112829155-114159955:-1;chr10:116716050-118484839:-1;chr10:119239140-124047569:-1		GBF1;NFKB2;PSD;FBXL5;SUFU	Hematopathology Unit, Hospital Clinic Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain	Chronic lymphocytic leukemia (CLL) is a common disease with highly variable clinical course. Several recurrent chromosomal alterations are associated with prognosis and may guide risk-adapted therapy. We have developed a targeted genome-wide array to provide a robust tool for ascertaining abnormalities in CLL and to overcome limitations of the 4-marker fluorescence in situ hybridization (FISH). DNA from 180 CLL patients were hybridized to the qChip Hemo array with a high density of probes covering commonly altered loci in CLL (11q22-q23, 13q14, and 17p13), nine focal regions (2p15-p16.1, 2p24.3, 2q13, 2q36.3-q37.1, 3p21.31, 8q24.21, 9p21.3, 10q24.32, and 18q21.32-q21.33) and two larger regions (6q14.1-q22.31 and 7q31.33-q33). Overall, 86% of the cases presented copy number alterations (CNA) by array. There was a high concordance of array findings with FISH (84% sensitivity, 100% specificity); all discrepancies corresponded to subclonal alterations detected only by FISH. A chromothripsis-like pattern was detected in eight cases. Three showed concomitant shattered 5p with gain of TERT along with isochromosome 17q. Presence of 11q loss was associated with shorter time to first treatment (P = 0.003), whereas 17p loss, increased genomic complexity, and chromothripsis were associated with shorter overall survival (P < 0.001, P = 0.001, and P = 0.02, respectively). In conclusion, we have validated a targeted array for the diagnosis of CLL that accurately detects, in a single experiment, all relevant CNAs, genomic complexity, chromothripsis, copy number neutral loss of heterozygosity, and CNAs not covered by the FISH panel. This test may be used as a practical tool to stratify CLL patients for routine diagnostics or clinical trials.	GRCh37/hg19	GSE66923			Yes	NA
CTDB0424	Research	26305789	Salaverria I, Martin-Garcia D, Lopez C, Clot G, Garcia-Aragones M, Navarro A, Delgado J, Baumann T, Pinyol M, Martin-Guerrero I, Carrio A, Costa D, Queiros AC, Jayne S, Aymerich M, Villamor N, Colomer D, Gonzalez M, Lopez-Guillermo A, Campo E, Dyer MJ, Siebert R, Armengol L, Bea S	Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia	Genes Chromosomes Cancer	2015 Nov	5	Chronic lymphocytic leukemia	Array CGH	Homo sapiens	94	qChip Hemo array	chr5:0-1635135:1;chr5:1635135-16113045:-1;chr5:16113045-21741262:1;chr5:21741262-22716680:-1;chr5:22716680-23640589:1;chr5:23640589-24563866:-1;chr5:24563866-29286182:1;chr5:29286182-30221099:-1;chr5:30221099-33065344:1;chr5:33065344-180915260:0		TERT	Hematopathology Unit, Hospital Clinic Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain	Chronic lymphocytic leukemia (CLL) is a common disease with highly variable clinical course. Several recurrent chromosomal alterations are associated with prognosis and may guide risk-adapted therapy. We have developed a targeted genome-wide array to provide a robust tool for ascertaining abnormalities in CLL and to overcome limitations of the 4-marker fluorescence in situ hybridization (FISH). DNA from 180 CLL patients were hybridized to the qChip Hemo array with a high density of probes covering commonly altered loci in CLL (11q22-q23, 13q14, and 17p13), nine focal regions (2p15-p16.1, 2p24.3, 2q13, 2q36.3-q37.1, 3p21.31, 8q24.21, 9p21.3, 10q24.32, and 18q21.32-q21.33) and two larger regions (6q14.1-q22.31 and 7q31.33-q33). Overall, 86% of the cases presented copy number alterations (CNA) by array. There was a high concordance of array findings with FISH (84% sensitivity, 100% specificity); all discrepancies corresponded to subclonal alterations detected only by FISH. A chromothripsis-like pattern was detected in eight cases. Three showed concomitant shattered 5p with gain of TERT along with isochromosome 17q. Presence of 11q loss was associated with shorter time to first treatment (P = 0.003), whereas 17p loss, increased genomic complexity, and chromothripsis were associated with shorter overall survival (P < 0.001, P = 0.001, and P = 0.02, respectively). In conclusion, we have validated a targeted array for the diagnosis of CLL that accurately detects, in a single experiment, all relevant CNAs, genomic complexity, chromothripsis, copy number neutral loss of heterozygosity, and CNAs not covered by the FISH panel. This test may be used as a practical tool to stratify CLL patients for routine diagnostics or clinical trials.	GRCh37/hg19	GSE66923			Yes	NA
CTDB0425	Research	26305789	Salaverria I, Martin-Garcia D, Lopez C, Clot G, Garcia-Aragones M, Navarro A, Delgado J, Baumann T, Pinyol M, Martin-Guerrero I, Carrio A, Costa D, Queiros AC, Jayne S, Aymerich M, Villamor N, Colomer D, Gonzalez M, Lopez-Guillermo A, Campo E, Dyer MJ, Siebert R, Armengol L, Bea S	Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia	Genes Chromosomes Cancer	2015 Nov	5,12	Chronic lymphocytic leukemia	Array CGH	Homo sapiens	D1016	qChip Hemo array	chr5:0-4932247:1;chr5:4932248-10467303:0;chr5:10467304-24206970:-1;chr5:24206971-40463864:1;chr5:40463865-40549635:0;chr5:40549636-46350808:-1;chr5:46350807-71514596:0;chr5:71514597-87578797:-1;chr5:87578798-89720410:1;chr5:89720409-89725809:0;chr5:89725810-107092989:-1;chr5:107092989-108797097:1;chr5:108797098-109788754:0;chr5:109788755-111844602:-1;chr5:111844603-113899732:0;chr5:113899733-119403621:-1;chr5:119403622-180915260:0;chr12:0-3916043:1;chr12:3916043-6894818:1;chr12:6894818-7074306:1;chr12:7074306-7266926:0;chr12:7266927-8246697:-1;chr12:8246698-8566721:0;chr12:8566722-16265843:-1;chr12:16265843-16441845:1;chr12:16441845-17785834:1;chr12:17785834-17998159:1;chr12:17998160-18506525:0;chr12:18506526-20500890:-1;chr12:20500890-21052802:1;chr12:21052803-22316053:0;chr12:22316054-22846206:1;chr12:22846206-25044343:1;chr12:25044344-133851895:0		TERT	Hematopathology Unit, Hospital Clinic Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain	Chronic lymphocytic leukemia (CLL) is a common disease with highly variable clinical course. Several recurrent chromosomal alterations are associated with prognosis and may guide risk-adapted therapy. We have developed a targeted genome-wide array to provide a robust tool for ascertaining abnormalities in CLL and to overcome limitations of the 4-marker fluorescence in situ hybridization (FISH). DNA from 180 CLL patients were hybridized to the qChip Hemo array with a high density of probes covering commonly altered loci in CLL (11q22-q23, 13q14, and 17p13), nine focal regions (2p15-p16.1, 2p24.3, 2q13, 2q36.3-q37.1, 3p21.31, 8q24.21, 9p21.3, 10q24.32, and 18q21.32-q21.33) and two larger regions (6q14.1-q22.31 and 7q31.33-q33). Overall, 86% of the cases presented copy number alterations (CNA) by array. There was a high concordance of array findings with FISH (84% sensitivity, 100% specificity); all discrepancies corresponded to subclonal alterations detected only by FISH. A chromothripsis-like pattern was detected in eight cases. Three showed concomitant shattered 5p with gain of TERT along with isochromosome 17q. Presence of 11q loss was associated with shorter time to first treatment (P = 0.003), whereas 17p loss, increased genomic complexity, and chromothripsis were associated with shorter overall survival (P < 0.001, P = 0.001, and P = 0.02, respectively). In conclusion, we have validated a targeted array for the diagnosis of CLL that accurately detects, in a single experiment, all relevant CNAs, genomic complexity, chromothripsis, copy number neutral loss of heterozygosity, and CNAs not covered by the FISH panel. This test may be used as a practical tool to stratify CLL patients for routine diagnostics or clinical trials.	GRCh37/hg19	GSE66923			Yes	NA
CTDB0426	Research	26305789	Salaverria I, Martin-Garcia D, Lopez C, Clot G, Garcia-Aragones M, Navarro A, Delgado J, Baumann T, Pinyol M, Martin-Guerrero I, Carrio A, Costa D, Queiros AC, Jayne S, Aymerich M, Villamor N, Colomer D, Gonzalez M, Lopez-Guillermo A, Campo E, Dyer MJ, Siebert R, Armengol L, Bea S	Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia	Genes Chromosomes Cancer	2015 Nov	5	Chronic lymphocytic leukemia	Array CGH	Homo sapiens	D1089	qChip Hemo array	chr5:0-1473747:1;chr5:1473747-10467304:-1;chr5:10467304-11923754:1;chr5:11923754-14080860:-1;chr5:14080860-17066497:1;chr5:17066498-18571708:0;chr5:18571709-20893807:-1;chr5:20893807-24247917:1;chr5:24247917-25034495:-1;chr5:25034496-27272147:0;chr5:27272148-31572967:-1;chr5:31572968-42882592:0;chr5:42882593-46350808:-1;chr5:46350809-180915260:0		TERT	Hematopathology Unit, Hospital Clinic Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain	Chronic lymphocytic leukemia (CLL) is a common disease with highly variable clinical course. Several recurrent chromosomal alterations are associated with prognosis and may guide risk-adapted therapy. We have developed a targeted genome-wide array to provide a robust tool for ascertaining abnormalities in CLL and to overcome limitations of the 4-marker fluorescence in situ hybridization (FISH). DNA from 180 CLL patients were hybridized to the qChip Hemo array with a high density of probes covering commonly altered loci in CLL (11q22-q23, 13q14, and 17p13), nine focal regions (2p15-p16.1, 2p24.3, 2q13, 2q36.3-q37.1, 3p21.31, 8q24.21, 9p21.3, 10q24.32, and 18q21.32-q21.33) and two larger regions (6q14.1-q22.31 and 7q31.33-q33). Overall, 86% of the cases presented copy number alterations (CNA) by array. There was a high concordance of array findings with FISH (84% sensitivity, 100% specificity); all discrepancies corresponded to subclonal alterations detected only by FISH. A chromothripsis-like pattern was detected in eight cases. Three showed concomitant shattered 5p with gain of TERT along with isochromosome 17q. Presence of 11q loss was associated with shorter time to first treatment (P = 0.003), whereas 17p loss, increased genomic complexity, and chromothripsis were associated with shorter overall survival (P < 0.001, P = 0.001, and P = 0.02, respectively). In conclusion, we have validated a targeted array for the diagnosis of CLL that accurately detects, in a single experiment, all relevant CNAs, genomic complexity, chromothripsis, copy number neutral loss of heterozygosity, and CNAs not covered by the FISH panel. This test may be used as a practical tool to stratify CLL patients for routine diagnostics or clinical trials.	GRCh37/hg19	GSE66923			Yes	NA
CTDB0496	Research	28787462	Rozenblum E, Sotelo-Silveira JR, Kim GY, Zhu JY, Lau CC, McNeil N, Korolevich S, Liao H,, Cherry JM, Munroe DJ,, Ried T, Meltzer PS, Kuehl WM, Roschke AV	Novel near-diploid ovarian cancer cell line derived from a highly aneuploid metastatic ovarian tumor	PLoS One	2017 Aug	18	Ovarian cancer	Array CGH	Homo sapiens	OVDM1-P18	Agilent CGH Microarray Kit 244A 				Genetics Branch, CCR, NCI, NIH, Bethesda, Maryland, United States of America	A new ovarian near-diploid cell line, OVDM1, was derived from a highly aneuploid serous ovarian metastatic adenocarcinoma. A metastatic tumor was obtained from a 47-year-old Ashkenazi Jewish patient three years after the first surgery removed the primary tumor, both ovaries, and the remaining reproductive organs. OVDM1 was characterized by cell morphology, genotyping, tumorigenic assay, mycoplasma testing, spectral karyotyping (SKY), and molecular profiling of the whole genome by aCGH and gene expression microarray. Targeted sequencing of a panel of cancer-related genes was also performed. Hierarchical clustering of gene expression data clearly confirmed the ovarian origin of the cell line. OVDM1 has a near-diploid karyotype with a low-level aneuploidy, but samples of the original metastatic tumor were grossly aneuploid. A number of single nucleotide variations (SNVs)/mutations were detected in OVDM1 and the metastatic tumor samples. Some of them were cancer-related according to COSMIC and HGMD databases (no founder mutations in BRCA1 and BRCA2 have been found). A large number of focal copy number alterations (FCNAs) were detected, including homozygous deletions (HDs) targeting WWOX and GATA4. Progression of OVDM1 from early to late passages was accompanied by preservation of the near-diploid status, acquisition of only few additional large chromosomal rearrangements and more than 100 new small FCNAs. Most of newly acquired FCNAs seem to be related to localized but massive DNA fragmentation (chromothripsis-like rearrangements). Newly developed near-diploid OVDM1 cell line offers an opportunity to evaluate tumorigenesis pathways/events in a minor clone of metastatic ovarian adenocarcinoma as well as mechanisms of chromothripsis.	GRCh35/hg17	GSE70264			Yes	NA
CTDB0497	Research	28787462	Rozenblum E, Sotelo-Silveira JR, Kim GY, Zhu JY, Lau CC, McNeil N, Korolevich S, Liao H,, Cherry JM, Munroe DJ,, Ried T, Meltzer PS, Kuehl WM, Roschke AV	Novel near-diploid ovarian cancer cell line derived from a highly aneuploid metastatic ovarian tumor	PLoS One	2017 Aug	18	Ovarian cancer	Array CGH	Homo sapiens	OVDM1-P30	Agilent CGH Microarray Kit 244A 				Genetics Branch, CCR, NCI, NIH, Bethesda, Maryland, United States of America	A new ovarian near-diploid cell line, OVDM1, was derived from a highly aneuploid serous ovarian metastatic adenocarcinoma. A metastatic tumor was obtained from a 47-year-old Ashkenazi Jewish patient three years after the first surgery removed the primary tumor, both ovaries, and the remaining reproductive organs. OVDM1 was characterized by cell morphology, genotyping, tumorigenic assay, mycoplasma testing, spectral karyotyping (SKY), and molecular profiling of the whole genome by aCGH and gene expression microarray. Targeted sequencing of a panel of cancer-related genes was also performed. Hierarchical clustering of gene expression data clearly confirmed the ovarian origin of the cell line. OVDM1 has a near-diploid karyotype with a low-level aneuploidy, but samples of the original metastatic tumor were grossly aneuploid. A number of single nucleotide variations (SNVs)/mutations were detected in OVDM1 and the metastatic tumor samples. Some of them were cancer-related according to COSMIC and HGMD databases (no founder mutations in BRCA1 and BRCA2 have been found). A large number of focal copy number alterations (FCNAs) were detected, including homozygous deletions (HDs) targeting WWOX and GATA4. Progression of OVDM1 from early to late passages was accompanied by preservation of the near-diploid status, acquisition of only few additional large chromosomal rearrangements and more than 100 new small FCNAs. Most of newly acquired FCNAs seem to be related to localized but massive DNA fragmentation (chromothripsis-like rearrangements). Newly developed near-diploid OVDM1 cell line offers an opportunity to evaluate tumorigenesis pathways/events in a minor clone of metastatic ovarian adenocarcinoma as well as mechanisms of chromothripsis.	GRCh35/hg17	GSE70264			Yes	NA
CTDB0503	Research	28201779	Abou-El-Ardat K, Seifert M, Becker K, Eisenreich S, Lehmann M, Hackmann K, Rump A, Meijer G, Carvalho B, Temme A, Schackert G, Schrock E, Krex D, Klink B	Comprehensive molecular characterization of multifocal glioblastoma proves its monoclonal origin and reveals novel insights into clonal evolution and heterogeneity of glioblastomas	Neuro Oncol	2017 Apr	2,12	Glioblastoma	Array CGH	Homo sapiens	patient_2	Agilent SurePrint G3 Human CGH Microarray Kit 2x400K 			MYCN; CDK4; MDM2	Institut fur Klinische Genetik, Medizinische Fakultat Carl Gustav Carus, Technische Universitat Dresden, Dresden, Germany	The evolution of primary glioblastoma (GBM) is poorly understood. Multifocal GBM (ie, multiple synchronous lesions in one patient) could elucidate GBM development. METHODS: We present the first comprehensive study of 12 GBM foci from 6 patients using array-CGH, spectral karyotyping, gene expression arrays, and next-generation sequencing. RESULTS: Multifocal GBMs genetically resemble primary GBMs. Comparing foci from the same patient proved their monoclonal origin. All tumors harbored alterations in the 3 GBM core pathways: RTK/PI3K, p53, and RB regulatory pathways with aberrations of EGFR and CDKN2A/B in all (100%) patients. This unexpected high frequency reflects a distinct genetic signature of multifocal GBMs and might account for their highly malignant and invasive phenotype. Surprisingly, the types of mutations in these genes/pathways were different in tumor foci from the same patients. For example, we found distinct mutations/aberrations in PTEN, TP53, EGFR, and CDKN2A/B, which therefore must have occurred independently and late during tumor development. We also identified chromothripsis as a late event and in tumors with wild-type TP53. Only 2 events were found to be early in all patients: single copy loss of PTEN and TERT promoter point mutations. CONCLUSIONS: Multifocal GBMs develop through parallel genetic evolution. The high frequency of alterations in 3 main pathways suggests that these are essential steps in GBM evolution; however, their late occurrence indicates that they are not founder events but rather subclonal drivers. This might account for the marked genetic heterogeneity seen in primary GBM and therefore has important implications for GBM therapy.	GRCh36/hg18				Yes	
CTDB0504	Research	28201779	Abou-El-Ardat K, Seifert M, Becker K, Eisenreich S, Lehmann M, Hackmann K, Rump A, Meijer G, Carvalho B, Temme A, Schackert G, Schrock E, Krex D, Klink B	Comprehensive molecular characterization of multifocal glioblastoma proves its monoclonal origin and reveals novel insights into clonal evolution and heterogeneity of glioblastomas	Neuro Oncol	2017 Apr	10	Glioblastoma	Array CGH	Homo sapiens	patient_6	Agilent SurePrint G3 Human CGH Microarray Kit 2x400K 				Institut fur Klinische Genetik, Medizinische Fakultat Carl Gustav Carus, Technische Universitat Dresden, Dresden, Germany	The evolution of primary glioblastoma (GBM) is poorly understood. Multifocal GBM (ie, multiple synchronous lesions in one patient) could elucidate GBM development. METHODS: We present the first comprehensive study of 12 GBM foci from 6 patients using array-CGH, spectral karyotyping, gene expression arrays, and next-generation sequencing. RESULTS: Multifocal GBMs genetically resemble primary GBMs. Comparing foci from the same patient proved their monoclonal origin. All tumors harbored alterations in the 3 GBM core pathways: RTK/PI3K, p53, and RB regulatory pathways with aberrations of EGFR and CDKN2A/B in all (100%) patients. This unexpected high frequency reflects a distinct genetic signature of multifocal GBMs and might account for their highly malignant and invasive phenotype. Surprisingly, the types of mutations in these genes/pathways were different in tumor foci from the same patients. For example, we found distinct mutations/aberrations in PTEN, TP53, EGFR, and CDKN2A/B, which therefore must have occurred independently and late during tumor development. We also identified chromothripsis as a late event and in tumors with wild-type TP53. Only 2 events were found to be early in all patients: single copy loss of PTEN and TERT promoter point mutations. CONCLUSIONS: Multifocal GBMs develop through parallel genetic evolution. The high frequency of alterations in 3 main pathways suggests that these are essential steps in GBM evolution; however, their late occurrence indicates that they are not founder events but rather subclonal drivers. This might account for the marked genetic heterogeneity seen in primary GBM and therefore has important implications for GBM therapy.	GRCh36/hg18				Yes	
CTDB0511	Research	28099951	Suzuki E, Shima H, Toki M, Hanew K, Matsubara K, Kurahashi H, Narumi S, Ogata T, Kamimaki T, Fukami M	Complex X-Chromosomal Rearrangements in Two Women with Ovarian Dysfunction: Implications of Chromothripsis/Chromoanasynthesis-Dependent and -Independent Origins of Complex Genomic Alterations	Cytogenet Genome Res	2016	X	Ovarian Dysfunction	Array CGH	Homo sapiens	patient_1	Agilent SurePrint G3 Human Catalog 2x400K			SHOX;POF1B;DIAPH2;PGRMC1	Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan	Our current understanding of the phenotypic consequences and the molecular basis of germline complex chromosomal rearrangements remains fragmentary. Here, we report the clinical and molecular characteristics of 2 women with germline complex X-chromosomal rearrangements. Patient 1 presented with nonsyndromic ovarian dysfunction and hyperthyroidism; patient 2 exhibited various Turner syndrome- associated symptoms including ovarian dysfunction, short stature, and autoimmune hypothyroidism. The genomic abnormalities of the patients were characterized by array-based comparative genomic hybridization, high-resolution karyotyping, microsatellite genotyping, X-inactivation analysis, and bisulfite sequencing. Patient 1 carried a rearrangement of unknown parental origin with a 46,X,der(X)(pter->p22.1::p11.23->q24::q21.3->q24::p11.4->pter) karyotype, indicative of a catastrophic chromosomal reconstruction due to chromothripsis/chromoanasynthesis. Patient 2 had a paternally derived isochromosome with a 46,X,der(X)(pter->p22.31::q22.1->q10::q10->q22.1::p22.31->pter) karyotype, which likely resulted from 2 independent, sequential events. Both patients showed completely skewed X inactivation. CpG sites at Xp22.3 were hypermethylated in patient 2. The results indicate that germline complex X-chromosomal rearrangements underlie nonsyndromic ovarian dysfunction and Turner syndrome. Disease-causative mechanisms of these rearrangements likely include aberrant DNA methylation, in addition to X-chromosomal mispairing and haploinsufficiency of genes escaping X inactivation. Notably, our data imply that germline complex X-chromosomal rearrangements are created through both chromothripsis/chromoanasynthesis-dependent and -independent processes.	GRCh37/hg19				No	
CTDB0512	Research	28085746	Koduru PR, Wilson K, Wen J, Garcia R, Patel S, Monaghan SA	Cytogenetic and Cytogenomic Microarray Characterization of Chromothripsis in Chromosome 8 Affecting MOZ/NCOA2 (TIF2), FGFR1, RUNX1T1, and RUNX1 in a Pediatric Acute Myeloid Leukemia	J Pediatr Hematol Oncol	2017 May	8	Pediatric Acute Myeloid Leukemia	Array CGH	Homo sapiens	28085746_patient	Unknow			MOZ/NCOA2;FGFR1;RUNX1T1;RUNX1	Department of Pathology, UT Southwestern Medical Center, Dallas, TX	Concurrent perturbations in different driver genes have been reported primarily in lymphoma. In acute myeloid leukemia (AML), cases with concurrent alterations in 2 driver genes are infrequently reported. In contrast to pathogenetic pathways in lymphoma with concurrently perturbed genes, the initial gene alteration in AML arrests maturation and the alteration in the second gene promote self-renewal of the blasts. Here, we report a unique case of infantile leukemia in which chromothripsis in chromosome 8 completely altered the G-band structure and resulted in concurrent changes in MOZ/NCOA2, FGFR1, RUNX1T1, and RUNX1. These multiple-hit abnormalities in AML have not been reported previously.	GRCh37/hg19				Yes	FGFR1,RUNX1; RUNX1T1,RUNX1
CTDB0514	Research	27880765	Gu S, Szafranski P, Akdemir ZC, Yuan B, Cooper ML, Magrina MA, Bacino CA, Lalani SR, Breman AM, Smith JL, Patel A, Song RH, Bi W, Cheung SW, Carvalho CM, Stankiewicz P, Lupski JR	Mechanisms for Complex Chromosomal Insertions	PLoS Genet	2016 Nov	6	Individuals with complex chromosome insertions	Array CGH	Homo sapiens	Cplex5	Agilent 4 x 180K oligonucleotide arrays	chr6:111061823-112340466):1;chr6:143001529-143306155):-1;chr6:151111676-159718163):-1			Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America	Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue, constituting ~2% of nonrecurrent copy-number gains. Little is known about the molecular mechanisms of their formation. We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on 10 individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing in 6 individuals to glean insights into potential mechanisms of formation. We observed microhomologies and templated insertions at the breakpoint junctions, resembling the breakpoint junction signatures found in complex genomic rearrangements generated by replication-based mechanism(s) with iterative template switches. In addition, we analyzed 5 families with apparently balanced insertion in one parent detected by FISH analysis and found that 3 parents had additional small copy-number variants (CNVs) at one or both sides of the inserting fragments as well as at the inserted sites. We propose that replicative repair can result in interchromosomal complex insertions generated through chromothripsis-like chromoanasynthesis involving two or three chromosomes, and cause a significant fraction of apparently balanced insertions harboring small flanking CNVs.	GRCh37/hg19	GSE89306			Unknow	
CTDB0515	Research	27880765	Gu S, Szafranski P, Akdemir ZC, Yuan B, Cooper ML, Magrina MA, Bacino CA, Lalani SR, Breman AM, Smith JL, Patel A, Song RH, Bi W, Cheung SW, Carvalho CM, Stankiewicz P, Lupski JR	Mechanisms for Complex Chromosomal Insertions	PLoS Genet	2016 Nov	X	Individuals with complex chromosome insertions	Array CGH	Homo sapiens	Cplex6	Agilent 4 x 180K oligonucleotide arrays	chrX:0-153354257:0;chrX:153354258-153505599:1;chrX:153400494-153406246:2;chrX:153505600-155270560:0			Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America	Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue, constituting ~2% of nonrecurrent copy-number gains. Little is known about the molecular mechanisms of their formation. We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on 10 individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing in 6 individuals to glean insights into potential mechanisms of formation. We observed microhomologies and templated insertions at the breakpoint junctions, resembling the breakpoint junction signatures found in complex genomic rearrangements generated by replication-based mechanism(s) with iterative template switches. In addition, we analyzed 5 families with apparently balanced insertion in one parent detected by FISH analysis and found that 3 parents had additional small copy-number variants (CNVs) at one or both sides of the inserting fragments as well as at the inserted sites. We propose that replicative repair can result in interchromosomal complex insertions generated through chromothripsis-like chromoanasynthesis involving two or three chromosomes, and cause a significant fraction of apparently balanced insertions harboring small flanking CNVs.	GRCh37/hg19	GSE89306			Unknow	
CTDB0516	Research	27880765	Gu S, Szafranski P, Akdemir ZC, Yuan B, Cooper ML, Magrina MA, Bacino CA, Lalani SR, Breman AM, Smith JL, Patel A, Song RH, Bi W, Cheung SW, Carvalho CM, Stankiewicz P, Lupski JR	Mechanisms for Complex Chromosomal Insertions	PLoS Genet	2016 Nov	13,X	Individuals with complex chromosome insertions	Array CGH	Homo sapiens	Cplex11	Agilent 4 x 180K oligonucleotide arrays	chr13:0-111923013:0;chr13:10617231-107784175:2;chr13:109760818-110923670:2;chr13:111923014-113766342:-1;chr13:113766343-115169878:0;chrX:0-79677006:0;chrX:79677007-80247351:1;chrX:80247352-81758343:0;chrX:81758344-84170318:1;chrX:82128724-82575149:2;chrX:84170319-155270560:0			Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America	Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue, constituting ~2% of nonrecurrent copy-number gains. Little is known about the molecular mechanisms of their formation. We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on 10 individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing in 6 individuals to glean insights into potential mechanisms of formation. We observed microhomologies and templated insertions at the breakpoint junctions, resembling the breakpoint junction signatures found in complex genomic rearrangements generated by replication-based mechanism(s) with iterative template switches. In addition, we analyzed 5 families with apparently balanced insertion in one parent detected by FISH analysis and found that 3 parents had additional small copy-number variants (CNVs) at one or both sides of the inserting fragments as well as at the inserted sites. We propose that replicative repair can result in interchromosomal complex insertions generated through chromothripsis-like chromoanasynthesis involving two or three chromosomes, and cause a significant fraction of apparently balanced insertions harboring small flanking CNVs.	GRCh37/hg19	GSE89306			Unknow	
CTDB0589	Research	27741277	Abaigar M, Robledo C, Benito R, Ramos F, Diez-Campelo M, Hermosin L, Sanchez-Del-Real J, Alonso JM, Cuello R, Megido M, Rodriguez JN, Martin-Nunez G, Aguilar C, Vargas M, Martin AA, Garcia JL, Kohlmann A, Del Canizo MC, Hernandez-Rivas JM	Chromothripsis Is a Recurrent Genomic Abnormality in High-Risk Myelodysplastic Syndromes	PLoS One	2016 Oct	13	Myelodysplastic syndromes	Array CGH	Homo sapiens	27741277_026	NimbleGen 12x135K Whole-Genome Tiling v3.0 Array	chr13:0-18544844:0;chr13:100224902-102938165:-1;chr13:102938166-103453456:0;chr13:103453457-104094273:-1;chr13:104094274-107995454:0;chr13:107995455-110269932:1;chr13:110269933-110284511:0;chr13:110284512-114302034:-1;chr13:114302035-114142980:0;chr13:18544845-20440119:1;chr13:20440120-20511838:0;chr13:20511839-24763687:1;chr13:24763688-24824898:0;chr13:24824899-25847533:1;chr13:25847534-25849288:0;chr13:25849289-30835598:1;chr13:30835599-31664375:0;chr13:31664376-32572721:-1;chr13:32572722-34556708:0;chr13:34556709-35149194:-1;chr13:35149195-35190755:0;chr13:35190756-35198796:1;chr13:35198797-35287334:0;chr13:35287335-49555063:-1;chr13:49555064-53646644:0;chr13:53646645-56086252:-1;chr13:56086253-59126704:0;chr13:59126705-59531321:-1;chr13:59531322-61887290:0;chr13:61887291-89466951:-1;chr13:89466952-89658313:0;chr13:89658314-93680622:1;chr13:93680623-93699130:0;chr13:93699131-95541444:-1;chr13:95541445-98460263:0;chr13:98460264-98747948:-1;chr13:98747949-100224901:0		LINC00417;ANKRD20A9P;RNU6-55P;RNU6-76P;LINC00408;LINC00442;RNU6-52P;TUBA3C;LOC101928697;ANKRD26P3;LINC00421;TPTE2;MPHOSPH8;PSPC1;ZMYM5;ZMYM2;LINC01072;GJA3;GJB2;GJB6;CRYL1;MIR4499;CRYL1;IFT88;IL17D;N6AMT2;XPO4;LINC00367;LATS2;SAP18;SKA3;MRPL57;LINC01046;MIPEPP3;LINC00539;ZDHHC20;MICU2;RNU6-59P;FGF9;LINC00424;LINC00540;BASP1P1;SGCG;RNU6-58P;SACS;SACS-AS1;LINC00327;TNFRSF19;MIPEP;C1QTNF9B-AS1;C1QTNF9B;ANKRD20A19P;SPATA13;MIR2276;SPATA13-AS1;C1QTNF9;PARP4;TPTE2P6;ATP12A;RNF17;CENPJ;TPTE2P1;PABPC3;AMER2;LINC00463;LINC01053;MTMR6;NUPL1;ATP8A2;RNU6-78P;ATP8A2;SHISA2;RNF6;CDK8;WASF3;GPR12;USP12;USP12-AS1;USP12-AS2;LINC00412;RPL21;SNORD102;SNORA27;RASL11A;GTF3A;MTIF3;RNU6-63P;LNX2;POLR1D;GSX1;PDX1-AS1;PDX1;ATP5EP2;CDX2;URAD;FLT3;PAN3-AS1;PAN3;RNU6-82P;FLT1;POMP;SLC46A3;RNU6-53P;MTUS2;MTUS2-AS1;SLC7A1;UBL3;LINC00297;LINC00572;LINC00544;KATNAL1;RNU6-64P;LINC00426;LINC01058;HMGB1;USPL1;ALOX5AP;LINC00398;RXFP2;EEF1DP3;FRY-AS1;FRY;ZAR1L;BRCA2;N4BP2L1;N4BP2L2;MINOS1P1;N4BP2L2-IT2;LINC00457;NBEA;NBEA;NBEA;MAB21L1;DCLK1;CCDC169-SOHLH2;SOHLH2;CCDC169;RNU6-71P;SPG20;SPG20-AS1;CCNA1;SERTM1;RFXAP;SMAD9;ALG5;EXOSC8;SUPT20H;CSNK1A1L;LINC01048;LINC00547;POSTN;TRPC4;LINC00571;UFM1;LINC00437;LINC00366;FREM2;RNU6-56P;STOML3;PROSER1;NHLRC3;LHFP;COG6;MIR4305;LINC00332;LINC00548;LINC00598;FOXO1;MIR320D1;MRPS31;SLC25A15;TPTE2P5;MIR621;SUGT1P3;ELF1;WBP4;MIR3168;KBTBD6;LOC101929140;KBTBD7;MTRF1;NAA16;RNU6-57P;OR7E37P;RGCC;VWA8;MIR5006;VWA8-AS1;DGKH;AKAP11;TNFSF11;FAM216B;LINC01050;LINC00428;EPSTI1;DNAJC15;LINC00400;ENOX1;ENOX1-AS2;CCDC122;LACC1;LINC00284;SMIM2-AS1;SMIM2;SMIM2-IT1;MIR8079;SERP2;TUSC8;TSC22D1;TSC22D1-AS1;LINC00330;NUFIP1;GPALPP1;LOC101929259;GTF2F2;RNU6-69P;KCTD4;TPT1;SNORA31;TPT1-AS1;SLC25A30;SLC25A30-AS1;COG3;ERICH6B;LINC01055;SPERT;SIAH3;ZC3H13;CPB2-AS1;CPB2;LCP1;LRRC63;LINC00563;KIAA0226L;RNU6-68P;LINC01198;LRCH1;ESD;HTR2A;HTR2A-AS1;LINC00562;SUCLA2;NUDT15;MED4;MED4-AS1;ITM2B;LINC00441;RB1;LPAR6;RCBTB2;LINC00462;CYSLTR2;FNDC3A;MLNR;CDADC1;CAB39L;SETDB2;PHF11;RCBTB1;LINC00458;MIR1297;MIR5007;LINC00358;LINC01075;LINC00448;LINC00376;LINC00395;OR7E156P;RNU6-81P;LOC102723968;MIR548X2;MIR4704;PCDH9;PCDH9-AS2;PCDH9-AS3;PCDH9-AS4;LINC00364;LINC00550;LINC00383;KLHL1;ATXN8OS;LINC00348;DACH1;MZT1;BORA;DIS3;PIBF1;RNU6-79P;KLF5;RNU6-66P;LINC00392;KLF12;LINC00381;LINC00347;CTAGE11P;TBC1D4;COMMD6;UCHL3;LMO7-AS1;LMO7;LMO7DN;LMO7DN-IT1;KCTD12;BTF3P11;IRG1;CLN5;FBXL3;MYCBP2;MYCBP2-AS1;SCEL;SCEL-AS1;SLAIN1;MIR3665;EDNRB-AS1;EDNRB;LINC01069;LINC00446;RNF219-AS1;POU4F1;RNF219;LINC00331;RBM26;RBM26-AS1;NDFIP2-AS1;NDFIP2;LINC01068;LINC01038;LINC00382;LINC01080;SPRY2;LINC00377;LINC00564;RNU6-67P;SLITRK1;LINC00333;LINC00375;LINC00351;RNU6-72P;SLITRK6;MIR4500HG;MIR4500;SLITRK5;LINC00397;LINC00433;LINC00440;LINC00559;MIR622;LIN01049;RNU-75P;LINC00410;LINC00380;LINC00379;MIR17HG;MIR17;MIR18A;MIR19A;MIR20A;MIR19B1;MIR92A1;GPC5;GPC5-AS2;MIR48AS;GPC5-AS1;LIN00363;GPC6;GPC6-AS2;GPC6-AS1;DCT;TGDS;GPR180;LOC101927248;SOX21;SOX21-AS1;LINC00557;ABCC4;CLDN10;CLDN10-AS1;STK24;SLC15A1;PCCA;PCCA-AS1;GGACT;TMTC4;NALCN-AS1;LINC00411;NALCN;ITGBL1;FGF14;MIR2681;MIR4705;FGF14-IT1;FGF14-AS1;FGF14-AS2;TPP2;METTL21C;CCDC168;TEX30;KDELC1;BIVM;BIVM-ERCC5;ERCC5;METTL21EP;LIG4;ABHD13;TNFSF13B;MYO16;MYO16-AS1;LINC00399;LINC00676;IRS2;LINC00396;COL4A1;COL4A1;COL4A2;MIR8073;COL4A2-AS1;RAB20;CARKD;CARS2;ING1;LINC00346;ANKRD10;LINC00431;LINC00368;ARHGEF7;ARHGEF7-AS1;LOC101060553;TEX29;LINC00354;LINC00403;SOX1;LINC01070;LOC101928730;LINC01044;SPACA7;TUBGCP3;ATP11AUN;ATP11A;ATP11A-AS1;MCF2L-AS1;MCF2L;F7;F10;F10-AS1;PROZ;PCID2;CUL4A;MIR8075;LAMP1;GRTP1;GRTP1-AS1;LOC101928841;ADPRHL1;DCUN1D2;TMCO3;TFDP1;ATP4B;GRK1;LINC00552;TMEM255B;GAS6-AS1;GAS6;GAS6-AS2;LINC00452;LINC00565;RASA3;CDC16;MIR548AR;MIR4502;UPF3A	Unidad de Diagnostico Molecular y Celular del Cancer, Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain	comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) in a series of MDS and MDS/myeloproliferative neoplasms (MPN) patients. 301 patients diagnosed with MDS (n = 240) or MDS/MPN (n = 61) were studied at the time of diagnosis. A genome-wide analysis of DNA copy number abnormalities was performed. In addition, a mutational analysis of DNMT3A, TET2, RUNX1, TP53 and BCOR genes was performed by NGS in selected cases. 285 abnormalities were identified in 71 patients (23.6%). Three high-risk MDS cases (1.2%) displayed chromothripsis involving exclusively chromosome 13 and affecting some cancer genes: FLT3, BRCA2 and RB1. All three cases carried TP53 mutations as revealed by NGS. Moreover, in the whole series, the integrative analysis of aCGH and NGS enabled the identification of cryptic recurrent deletions in 2p23.3 (DNMT3A; n = 2.8%), 4q24 (TET2; n = 10%) 17p13 (TP53; n = 8.5%), 21q22 (RUNX1; n = 7%), and Xp11.4 (BCOR; n = 2.8%), while mutations in the non-deleted allele where found only in DNMT3A (n = 1), TET2 (n = 3), and TP53 (n = 4). These cryptic abnormalities were detected mainly in patients with normal (45%) or non-informative (15%) karyotype by conventional cytogenetics, except for those with TP53 deletion and mutation (15%), which had a complex karyotype. In addition to well-known copy number defects, the presence of chromothripsis involving chromosome 13 was a novel recurrent change in high-risk MDS patients. Array CGH analysis revealed the presence of cryptic abnormalities in genomic regions where MDS-related genes, such as TET2, DNMT3A, RUNX1 and BCOR, are located.	GRCh36/hg18	GSE67682			Yes	
CTDB0590	Research	27741277	Abaigar M, Robledo C, Benito R, Ramos F, Diez-Campelo M, Hermosin L, Sanchez-Del-Real J, Alonso JM, Cuello R, Megido M, Rodriguez JN, Martin-Nunez G, Aguilar C, Vargas M, Martin AA, Garcia JL, Kohlmann A, Del Canizo MC, Hernandez-Rivas JM	Chromothripsis Is a Recurrent Genomic Abnormality in High-Risk Myelodysplastic Syndromes	PLoS One	2016 Oct	13	Myelodysplastic syndromes	Array CGH	Homo sapiens	27741277_027	NimbleGen 12x135K Whole-Genome Tiling v3.0 Array	chr13:0-18544844:0;chr13:111268759-114302034:1;chr13:114302035-114142980:0;chr13:18544845-28026673:1;chr13:28026674-28092710:0;chr13:28092711-31753393:1;chr13:31753394-31778817:0;chr13:31778818-31923805:-1;chr13:31923806-31934278:0;chr13:31934279-32178937:1;chr13:32178938-32205508:0;chr13:32205509-34693503:-1;chr13:34693504-34738108:0;chr13:34738109-40773999:1;chr13:40774000-40964446:0;chr13:40964447-41385529:-1;chr13:41385530-41393215:0;chr13:41393216-46380250:1;chr13:46380251-46419481:0;chr13:46419482-51739755:-1;chr13:51739756-95471065:0;chr13:95471066-95645135:1;chr13:95645136-111268758:0		LINC00417;ANKRD20A9P;RNU6-55P;RNU6-76P;LINC00408;LINC00442;RNU6-52P;TUBA3C;LOC101928697;ANKRD26P3;LINC00421;TPTE2;MPHOSPH8;PSPC1;ZMYM5;ZMYM2;LINC01072;GJA3;GJB2;GJB6;CRYL1;MIR4499;IFT88;IL17D;N6AMT2;XPO4;LINC00367;LATS2;SAP18;SKA3;MRPL57;LINC01046;MIPEPP3;LINC00539;ZDHHC20;MICU2;RNU6-59P;FGF9;LINC00424;LINC00540;BASP1P1;SGCG;RNU6-58P;SACS;SACS-AS1;LINC00327;TNFRSF19;MIPEP;C1QTNF9B-AS1;C1QTNF9B;ANKRD20A19P;SPATA13;MIR2276;SPATA13-AS1;C1QTNF9;PARP4;TPTE2P6;ATP12A;RNF17;CENPJ;TPTE2P1;PABPC3;AMER2;LINC00463;LINC01053;MTMR6;NUPL1;ATP8A2;RNU6-78P;SHISA2;RNF6;CDK8;WASF3;GPR12;USP12;USP12-AS1;USP12-AS2;LINC00412;RPL21;SNORD102;SNORA27;RASL11A;GTF3A;MTIF3;RNU6-63P;LNX2;POLR1D;GSX1;PDX1-AS1;PDX1;ATP5EP2;CDX2;URAD;FLT3;FLT3;PAN3-AS1;PAN3;RNU6-82P;FLT1;POMP;SLC46A3;RNU6-53P;MTUS2;MTUS2-AS1;SLC7A1;UBL3;LINC00297;LINC00572;LINC00544;KATNAL1;RNU6-64P;LINC00426;LINC01058;HMGB1;USPL1;ALOX5AP;LINC00398;LINC00545;TEX26-AS1;MEDAG;TEX26;HSPH1;B3GALTL;RXFP2;RXFP2;EEF1DP3;EEF1DP3;FRY-AS1;FRY;FRY;ZAR1L;BRCA2;N4BP2L1;N4BP2L2;MINOS1P1;N4BP2L2-IT2;N4BP2L2;PDS5B;LINC00423;KL;STARD13;STARD13-AS;RFC3;LINC00457;NBEA;MAB21L1;DCLK1;SOHLH2;CCDC169-SOHLH2;CCDC169;RNU6-71P;SPG20;SPG20-AS1;CCNA1;SERTM1;RFXAP;SMAD9;ALG5;EXOSC8;SUPT20H;CSNK1A1L;LINC01048;LINC00547;POSTN;TRPC4;LINC00571;UFM1;LINC00437;LINC00366;FREM2;RNU6-56P;STOML3;PROSER1;NHLRC3;LHFP;COG6;MIR4305;LINC00332;LINC00548;LINC00598;FOXO1;MIR320D1;MRPS31;ELF1;WBP4;MIR3168;KBTBD6;LOC101929140;KBTBD7;MTRF1;NAA16;RNU6-57P;OR7E37P;RGCC;VWA8;MIR5006;VWA8-AS1;DGKH;AKAP11;TNFSF11;FAM216B;LINC01050;LINC00428;EPSTI1;DNAJC15;LINC00400;ENOX1;ENOX1-AS2;CCDC122;LACC1;LINC00284;SMIM2-AS1;SMIM2;SMIM2-IT1;MIR8079;SERP2;TUSC8;TSC22D1;TSC22D1-AS1;LINC00330;NUFIP1;GPALPP1;LOC101929259;GTF2F2;RNU6-69P;KCTD4;TPT1;SNORA31;TPT1-AS1;SLC25A30;SLC25A30-AS1;COG3;ERICH6B;LINC01055;SPERT;SIAH3;ZC3H13;CPB2-AS1;CPB2;LCP1;LRRC63;LINC00563;KIAA0226L;LINC01198;LRCH1;ESD;HTR2A;HTR2A-AS1;LINC00562;SUCLA2;NUDT15;MED4;MED4-AS1;ITM2B;LINC00441;RB1;LPAR6;RCBTB2;LINC00462;CYSLTR2;FNDC3A;MLNR;CDADC1;CAB39L;SETDB2;PHF11;RCBTB1;ARL11;EBPL;KPNA3;CTAGE10P;SPRYD7;DLEU2;MIR3613;TRIM13;KCNRG;MIR16-1;MIR15A;DLEU1;ST13P4;DLEU1-AS1;DLEU7;DLEU7-AS1;RNASEH2B-AS1;RNASEH2B;GUCY1B2;LINC00371;FAM124A;SERPINE3;MIR5693;INTS6;INTS6-AS1;MIR4703;WDFY2;CLDN10;CLDN10-AS1;DZIP1;ARHGEF7;TEX29;LINC00354;LINC00403;SOX1;LINC01070;LOC101928730;LINC01044;SPACA7;TUBGCP3;ATP11AUN;ATP11A;ATP11A-AS1;MCF2L-AS1;MCF2L;F7;F10;F10-AS1;PROZ;PCID2;CUL4A;MIR8075;LAMP1;GRTP1;GRTP1-AS1;LOC101928841;ADPRHL1;DCUN1D2;TMCO3;TFDP1;ATP4B;GRK1;LINC00552;TMEM255B;GAS6-AS1;GAS6;GAS6-AS2;LINC00452;LINC00565;RASA3;CDC16;MIR548AR;MIR4502;UPF3A	Unidad de Diagnostico Molecular y Celular del Cancer, Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain	comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) in a series of MDS and MDS/myeloproliferative neoplasms (MPN) patients. 301 patients diagnosed with MDS (n = 240) or MDS/MPN (n = 61) were studied at the time of diagnosis. A genome-wide analysis of DNA copy number abnormalities was performed. In addition, a mutational analysis of DNMT3A, TET2, RUNX1, TP53 and BCOR genes was performed by NGS in selected cases. 285 abnormalities were identified in 71 patients (23.6%). Three high-risk MDS cases (1.2%) displayed chromothripsis involving exclusively chromosome 13 and affecting some cancer genes: FLT3, BRCA2 and RB1. All three cases carried TP53 mutations as revealed by NGS. Moreover, in the whole series, the integrative analysis of aCGH and NGS enabled the identification of cryptic recurrent deletions in 2p23.3 (DNMT3A; n = 2.8%), 4q24 (TET2; n = 10%) 17p13 (TP53; n = 8.5%), 21q22 (RUNX1; n = 7%), and Xp11.4 (BCOR; n = 2.8%), while mutations in the non-deleted allele where found only in DNMT3A (n = 1), TET2 (n = 3), and TP53 (n = 4). These cryptic abnormalities were detected mainly in patients with normal (45%) or non-informative (15%) karyotype by conventional cytogenetics, except for those with TP53 deletion and mutation (15%), which had a complex karyotype. In addition to well-known copy number defects, the presence of chromothripsis involving chromosome 13 was a novel recurrent change in high-risk MDS patients. Array CGH analysis revealed the presence of cryptic abnormalities in genomic regions where MDS-related genes, such as TET2, DNMT3A, RUNX1 and BCOR, are located.	GRCh36/hg18	GSE67682			Yes	
CTDB0591	Research	27741277	Abaigar M, Robledo C, Benito R, Ramos F, Diez-Campelo M, Hermosin L, Sanchez-Del-Real J, Alonso JM, Cuello R, Megido M, Rodriguez JN, Martin-Nunez G, Aguilar C, Vargas M, Martin AA, Garcia JL, Kohlmann A, Del Canizo MC, Hernandez-Rivas JM	Chromothripsis Is a Recurrent Genomic Abnormality in High-Risk Myelodysplastic Syndromes	PLoS One	2016 Oct	13	Myelodysplastic syndromes	Array CGH	Homo sapiens	27741277_072	NimbleGen 12x135K Whole-Genome Tiling v3.0 Array	chr13:0-20223376:0;chr13:105600013-114142980:0;chr13:20223377-21774751:1;chr13:21774752-26008549:0;chr13:26008550-26823821:-1;chr13:26823822-26843551:0;chr13:26843552-29141245:1;chr13:29141246-29153048:0;chr13:29153049-29574970:-1;chr13:29574971-29598385:0;chr13:29598386-31092176:1;chr13:31092177-31109870:0;chr13:31109871-31349780:-1;chr13:31349781-31421871:0;chr13:31421872-31860544:1;chr13:31860545-31902741:0;chr13:31902742-35957157:-1;chr13:35957158-38324761:0;chr13:38324762-38995506:-1;chr13:38995507-39018272:0;chr13:39018273-42380430:1;chr13:42380431-43688279:0;chr13:43688280-45546500:1;chr13:45546501-45555481:0;chr13:45555482-82820718:-1;chr13:82820719-82942589:0;chr13:82942590-83487314:1;chr13:83487315-83666678:0;chr13:83666679-88672589:-1;chr13:88672590-89658313:0;chr13:89658314-92345411:1;chr13:92345412-92419919:0;chr13:92419920-105600012:-1		GJB6;CRYL1;MIR4499;IFT88;IL17D;N6AMT2;XPO4;LINC00367;LATS2;SAP18;SKA3;MRPL57;LINC01046;MIPEPP3;LINC00539;ZDHHC20;MICU2;RNU6-59P;FGF9;ATP8A2;SHISA2;RNF6;CDK8;WASF3;GPR12;USP12;USP12-AS1;USP12-AS2;LINC00412;RPL21;SNORD102;SNORA27;RASL11A;GTF3A;MTIF3;RNU6-63P;LNX2;POLR1D;GSX1;PDX1-AS1;PDX1;ATP5EP2;CDX2;URAD;FLT3;PAN3-AS1;PAN3;RNU6-82P;FLT1;POMP;SLC46A3;RNU6-53P;MTUS2;MTUS2;MTUS2-AS1;SLC7A1;UBL3;LINC00297;LINC00572;LINC00544;KATNAL1;RNU6-64P;LINC00426;LINC01058;HMGB1;USPL1;ALOX5AP;LINC00398;LINC00545;TEX26-AS1;MEDAG;TEX26;HSPH1;B3GALTL;RXFP2;EEF1DP3;EEF1DP3;FRY-AS1;FRY;ZAR1L;BRCA2;N4BP2L1;N4BP2L2;MINOS1P1;N4BP2L2-IT2;N4BP2L2;PDS5B;LINC00423;KL;STARD13;STARD13-AS;RFC3;LINC00457;NBEA;MAB21L1;DCLK1;UFM1;LIN00437;LINC00366;FREM2;RNU6-56P;STOML3;PROSER1;NHLRC3;LHFP;COG6;MIR4305;LINC00332;LINC00548;LINC00598;FOXO1;MIR320D1;MRPS31;SLC25A15;TPTE2P5;MIR621;SUGT1P3;ELF1;WBP4;MIR3168;KBTBD6;LOC101929140;KBTBD7;MTRF1;NAA16;RNU6-57P;OR7E37P;RGCC;VWA8;MIR5006;VWA8-AS1;DGKH;AKAP11;ENOX1;CCDC122;LACC1;LINC00284;SMIM2-AS1;SMIM2;SMIM2-IT1;MIR8079;SERP2;TUSC8;TSC22D1;TSC22D1-AS1;LINC00330;NUFIP1;GPALPP1;LOC101929259;GTF2F2;RNU6-69P;KCTD4;TPT1;SNORA31;TPT1-AS1;SLC25A30;SLC25A30-AS1;COG3;ERICH6B;ERICH6B;LINC01055;SPERT;SIAH3;ZC3H13;CPB2-AS1;CPB2;LCP1;LRRC63;LINC00563;KIAA0226L;RNU6-68P;LINC01198;LRCH1;ESD;HTR2A;HTR2A-AS1;LINC00562;SUCLA2;NUDT15;MED4;MED4-AS1;ITM2B;LINC00441;RB1;LPAR6;RCBTB2;LINC00462;CYSLTR2;FNDC3A;MLNR;CDADC1;CAB39L;SETDB2;PHF11;RCBTB1;ARL11;EBPL;KPNA3;CTAGE10P;SPRYD7;DLEU2;MIR3613;TRIM13;KCNRG;MIR16-1;MIR15A;DLEU1;ST13P4;DLEU1-AS1;DLEU7;DLEU7-AS1;RNASEH2B-AS1;RNASEH2B;GUCY1B2;LINC00371;FAM124A;SERPINE3;MIR5693;INTS6;INTS6-AS1;MIR4703;WDFY2;DHRS12;LINC00282;CCDC70;ATP7B;ALG11;UTP14C;NEK5;LOC101929657;NEK3;MRPS31P5;LOC103191607;THSD1;VPS36;CKAP2;TPTE2P3;HNRNPA1L2;SUGT1;LECT1;MIR759;PCDH8;OLFM4;LINC01065;LINC00558;LINC00458;MIR1297;MIR5007;PRR20C;PRR20B;PRR20A;PRR20D;PRR20E;PCDH17;LOC101926897;DIAPH3;DIAPH3-AS1;DIAPH3-AS2;LINC00434;TDRD3;LINC00378;MIR3169;PCDH20;LINC00358;LINC01075;LINC00448;LINC00376;LINC00395;OR7E156P;RNU6-81P;LOC102723968;MIR548X2;MIR4704;PCDH9;PCDH9-AS2;PCDH9-AS3;PCDH9-AS4;LINC00364;LINC00550;LINC00383;KLHL1;ATXN8OS;LINC00348;DACH1;MZT1;BORA;DIS3;PIBF1;RNU6-79P;KLF5;RNU6-66P;LINC00392;KLF12;LINC00381;LINC00347;CTAGE11P;TBC1D4;COMMD6;UCHL3;LMO7-AS1;LMO7;LMO7DN;LMO7DN-IT1;KCTD12;BTF3P11;IRG1;CLN5;FBXL3;MYCBP2;MYCBP2-AS1;SCEL;SCEL-AS1;SLAIN1;MIR3665;EDNRB-AS1;EDNRB;LINC01069;LINC00446;RNF219-AS1;POU4F1;RNF219;LINC00331;RBM26;RBM26-AS1;NDFIP2-AS1;NDFIP2;LINC01068;LINC01038;LINC00382;LINC01080;SPRY2;LINC00377;LINC00564;RNU6-67P;SLITRK1;LINC00333;LIN00375;LINC00351;RNU6-72P;SLITRK6;MIR4500HG;MIR4500;SLITRK5;LINC00397;LINC00433;LINC00559;MIR622;LINC01049;RNU6-75P;LINC00410;LINC00380;LINC00379;MIR17HG;MIR17;MIR18A;MIR19A;MIR20A;MIR19B1;MIR92A1;GPC5;GPC5-AS2;GPC5;MIR548AS;GPC5-AS1;LINC00363;GPC6;GPC6-AS2;GPC6-AS1;DCT;TGDS;GPR180;LOC101927248;SOX21;SOX21-AS1;LOC101927284;LINC00557;ABCC4;CLDN10;CLDN10-AS1;DZIP1;DNAJC3;UGGT2;HS6ST3;MIR4501;LINC00359;OXGR1;LINC00456;MBNL2;RAP2A;IPO5;FARP1;RNF113B;MIR3170;STK24;SLC15A1;DOCK9;DOCK9-AS1;RNU6-83P;DOCK9-AS2;UBAC2-AS1;UBAC2;GPR18;GPR183;FKSG29;MIR623;LINC01232;TM9SF2;LINC01039;CLYBL;MIR4306;CLYBL-AS2;CLYBL-AS1;LOC101927437;ZIC5;ZIC2;LINC00554;PCCA;PCCA-AS1;GGACT;TMTC4;NALCN-AS1;LINC00411;NALCN;ITGBL1;FGF14;MIR2681;MIR4705;FGF14-IT1;FGF14-AS1;FGF14-AS2;TPP2;METTL21C;CCDC168;TEX30;KDELC1;BIVM;BIVM-ERCC5;ERCC5;METTL21EP;SLC10A2;LINC01309;DAOA-AS1;DAOA	Unidad de Diagnostico Molecular y Celular del Cancer, Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain	comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) in a series of MDS and MDS/myeloproliferative neoplasms (MPN) patients. 301 patients diagnosed with MDS (n = 240) or MDS/MPN (n = 61) were studied at the time of diagnosis. A genome-wide analysis of DNA copy number abnormalities was performed. In addition, a mutational analysis of DNMT3A, TET2, RUNX1, TP53 and BCOR genes was performed by NGS in selected cases. 285 abnormalities were identified in 71 patients (23.6%). Three high-risk MDS cases (1.2%) displayed chromothripsis involving exclusively chromosome 13 and affecting some cancer genes: FLT3, BRCA2 and RB1. All three cases carried TP53 mutations as revealed by NGS. Moreover, in the whole series, the integrative analysis of aCGH and NGS enabled the identification of cryptic recurrent deletions in 2p23.3 (DNMT3A; n = 2.8%), 4q24 (TET2; n = 10%) 17p13 (TP53; n = 8.5%), 21q22 (RUNX1; n = 7%), and Xp11.4 (BCOR; n = 2.8%), while mutations in the non-deleted allele where found only in DNMT3A (n = 1), TET2 (n = 3), and TP53 (n = 4). These cryptic abnormalities were detected mainly in patients with normal (45%) or non-informative (15%) karyotype by conventional cytogenetics, except for those with TP53 deletion and mutation (15%), which had a complex karyotype. In addition to well-known copy number defects, the presence of chromothripsis involving chromosome 13 was a novel recurrent change in high-risk MDS patients. Array CGH analysis revealed the presence of cryptic abnormalities in genomic regions where MDS-related genes, such as TET2, DNMT3A, RUNX1 and BCOR, are located.	GRCh36/hg18	GSE67682			Yes	
CTDB0595	Research	27216161	Del Rey J, Santos M, Gonzalez-Meneses A, Mila M, Fuster C	Heterogeneity of a Constitutional Complex Chromosomal Rearrangement in 2q	Cytogenet Genome Res	2016	2	Congenital abnormality	Array CGH	Homo sapiens	27216161_case					Unitat de Biologia Celx00B7;lular i Genx00E8;tica Mx00E8;dica, Facultat de Medicina, Universitat Autx00F2;noma de Barcelona, Barcelona, Spain	Complex chromosome rearrangements (CCRs) are unusual structural chromosome alterations found in humans, and to date only a few have been characterized molecularly. New mechanisms, such as chromothripsis, have been proposed to explain the presence of the CCRs in cancer cells and in patients with congenital disorders and/or mental retardation. The aim of the present study was the molecular characterization of a constitutional CCR in a girl with multiple congenital disorders and intellectual disability in order to determine the genotype-phenotype relation and to clarify whether the CCR could have been caused by chromosomal catastrophic events. The present CCR was characterized by G-banding, high-resolution CGH, multiplex ligation-dependent probe amplification and subtelomeric  q-FISH analyses. Preliminary results indicate that the de novo CCR is unbalanced showing a  q .  deletion and  q q .  partial trisomy. Our patient shows some of the typical traits and intellectual disability described in patients with  q  deletion and also in carriers of  q q .  partial trisomy; thus, the clinical disorders could be explained by additional effects of both chromosome alterations (deletions and duplications). A posterior, sequential FISH study using BAC probes revealed the unexpected presence of at least   different reorganizations affecting  q q . , suggesting the existence of chromosome instability in this region. The present CCR is the first case described in the literature of heterogeneity of unbalanced CCRs affecting a small region of  q, indicating that the mechanisms involved in constitutional chromosome rearrangement may be more complex than previously thought.	GRCh37/hg19				No	
CTDB0596	Research	26543079	Kjeldsen E	Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies	Cancer Genomics Proteomics	2015 Nov-Dec	19	Acute myeloid leukemia	Array CGH	Homo sapiens	case174	4x180K Cancer Cytochip array				HaemoDiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Aarhus, Denmark Eigil	BACKGROUND: The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. MATERIALS AND METHODS: The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. RESULTS: Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. CONCLUSION: oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies.	GRCh36/hg18				Yes	
CTDB0597	Research	26543079	Kjeldsen E	Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies	Cancer Genomics Proteomics	2015 Nov-Dec	11	Acute myeloid leukemia	Array CGH	Homo sapiens	case127	4x180K Cancer Cytochip array				HaemoDiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Aarhus, Denmark Eigil	BACKGROUND: The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. MATERIALS AND METHODS: The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. RESULTS: Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. CONCLUSION: oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies.	GRCh36/hg18				Yes	
CTDB0598	Research	26543079	Kjeldsen E	Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies	Cancer Genomics Proteomics	2015 Nov-Dec	16,17	Acute myeloid leukemia	Array CGH	Homo sapiens	case228	4x180K Cancer Cytochip array				HaemoDiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Aarhus, Denmark Eigil	BACKGROUND: The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. MATERIALS AND METHODS: The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. RESULTS: Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. CONCLUSION: oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies.	GRCh36/hg18				Yes	
CTDB0599	Research	26543079	Kjeldsen E	Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies	Cancer Genomics Proteomics	2015 Nov-Dec	5,6,11	Acute myeloid leukemia	Array CGH	Homo sapiens	case146	4x180K Cancer Cytochip array				HaemoDiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Aarhus, Denmark Eigil	BACKGROUND: The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. MATERIALS AND METHODS: The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. RESULTS: Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. CONCLUSION: oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies.	GRCh36/hg18				Yes	
CTDB0600	Research	26543079	Kjeldsen E	Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies	Cancer Genomics Proteomics	2015 Nov-Dec	7,X	Acute myeloid leukemia	Array CGH	Homo sapiens	case170	4x180K Cancer Cytochip array				HaemoDiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Aarhus, Denmark Eigil	BACKGROUND: The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. MATERIALS AND METHODS: The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. RESULTS: Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. CONCLUSION: oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies.	GRCh36/hg18				Yes	
CTDB0601	Research	26543079	Kjeldsen E	Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies	Cancer Genomics Proteomics	2015 Nov-Dec	3	Acute myeloid leukemia	Array CGH	Homo sapiens	case173	4x180K Cancer Cytochip array				HaemoDiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Aarhus, Denmark Eigil	BACKGROUND: The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. MATERIALS AND METHODS: The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. RESULTS: Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. CONCLUSION: oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies.	GRCh36/hg18				Yes	
CTDB0602	Research	26543079	Kjeldsen E	Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies	Cancer Genomics Proteomics	2015 Nov-Dec	8,9,13,16,19,21	Acute myeloid leukemia	Array CGH	Homo sapiens	case179	4x180K Cancer Cytochip array				HaemoDiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Aarhus, Denmark Eigil	BACKGROUND: The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. MATERIALS AND METHODS: The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. RESULTS: Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. CONCLUSION: oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies.	GRCh36/hg18				Yes	
CTDB0603	Research	26543079	Kjeldsen E	Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies	Cancer Genomics Proteomics	2015 Nov-Dec	3	Acute myeloid leukemia	Array CGH	Homo sapiens	case186	4x180K Cancer Cytochip array				HaemoDiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Aarhus, Denmark Eigil	BACKGROUND: The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. MATERIALS AND METHODS: The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. RESULTS: Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. CONCLUSION: oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies.	GRCh36/hg18				Yes	
CTDB0604	Research	26543079	Kjeldsen E	Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies	Cancer Genomics Proteomics	2015 Nov-Dec	11	Acute myeloid leukemia	Array CGH	Homo sapiens	case226	4x180K Cancer Cytochip array				HaemoDiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Aarhus, Denmark Eigil	BACKGROUND: The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. MATERIALS AND METHODS: The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. RESULTS: Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. CONCLUSION: oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies.	GRCh36/hg18				Yes	
CTDB0605	Research	26543079	Kjeldsen E	Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies	Cancer Genomics Proteomics	2015 Nov-Dec	11,22	Acute myeloid leukemia	Array CGH	Homo sapiens	case206	4x180K Cancer Cytochip array				HaemoDiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Aarhus, Denmark Eigil	BACKGROUND: The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. MATERIALS AND METHODS: The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. RESULTS: Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. CONCLUSION: oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies.	GRCh36/hg18				Yes	
CTDB0606	Research	26543079	Kjeldsen E	Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies	Cancer Genomics Proteomics	2015 Nov-Dec	4,6,11,13	Acute myeloid leukemia	Array CGH	Homo sapiens	case218	4x180K Cancer Cytochip array				HaemoDiagnostic Laboratory, Cancer Cytogenetics Section, Department of Hematology, Aarhus University Hospital, Aarhus, Denmark Eigil	BACKGROUND: The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. MATERIALS AND METHODS: The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. RESULTS: Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. CONCLUSION: oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies.	GRCh36/hg18				Yes