CTDB0040	Research	23716474	Iwakawa R, Takenaka M, Kohno T, Shimada Y, Totoki Y, Shibata T, Tsuta K, Nishikawa R, Noguchi M, Sato-Otsubo A, Ogawa S, Yokota J	Genome-wide identification of genes with amplification and/or fusion in small cell lung cancer	Genes Chromosomes Cancer	2013 May	1,20	Small cell lung cancer	SNP Array	Homo sapiens	H1963	Affymetrix human 250K Nsp SNP arrays			PPIE;BMP8B;TRIT1;MYCL1;MFSD2A;CAP1;PPT1;RLF;TMCO2;ZMPSTE24;COL9A2;SMAP2;ZNF643;ZNF642;DEM1;ZNF684;RIMS3	Division of Multistep Carcinogenesis, National Cancer Center Research Institute, Tokyo 104-0045, Japan	To obtain a landscape of gross genetic alterations in small cell lung cancer (SCLC), genome-wide copy number analysis and whole-transcriptome sequencing were performed in 58 and 42 SCLCs, respectively. Focal amplification of known oncogene loci, MYCL1 (1p34.2), MYCN (2p24.3), and MYC (8q24.21), was frequently and mutually exclusively detected. MYCL1 and MYC were co-amplified with other regions on either the same or the different chromosome in several cases. In addition, the 9p24.1 region was identified as being amplified in SCLCs without amplification of MYC family oncogenes. Notably, expression of the KIAA1432 gene in this region was significantly higher in KIAA1432 amplified cells than in non-amplified cells, and its mRNA expression showed strong correlations with the copy numbers. Thus, KIAA1432 is a novel gene activated by amplification in SCLCs. By whole-transcriptome sequencing, a total of 60 fusion transcripts, transcribed from 95 different genes, were identified as being expressed in SCLC cells. However, no in-frame fusion transcripts were recurrently detected in >=2 SCLCs, and genes in the amplified regions, such as PVT1 neighboring MYC and RLF in MYCL1 amplicons, were recurrently fused with genes in the same amplicons or with those in different amplicons on either the same or different chromosome. Thus, it was indicated that amplification and fusion of several genes on chromosomes 1 and 8 occur simultaneously but not sequentially through chromothripsis in the development of SCLC, and amplification rather than fusion of genes plays an important role in its development.					Yes	RLF,MYCL1;RLF,COL9A2;RLF,BCL2L1;RLF,HM13;RLF,SMAP2;TPX2,HM13;BCL2L1,HM13;BCL2L1,DEM1;BCL2L1,RIMS3;BCL2L1,ZNF684;ZMPSTE24,MFSD2A;SMAP2,MYCL1;BCL2L1,ZNF643;PPT1,BCL2L1;BCL2L1,BMP8B;BCL2L1,RLF
CTDB0050	Research	23630094	Stefan Nagel, Corinna Meyer, Hilmar Quentmeier, Maren Kaufmann, Hans G. Drexler, Roderick A. F. MacLeod	Chromothripsis in Hodgkin Lymphoma	Genes Chromosomes Cancer	2013 Apr	3,9	Hodgkin lymphoma	SNP Array	Homo sapiens	L-1236	Affymetrix SNP 6.0			ABL1;SHOX2	Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig,Germany	Chromosomal rearrangements are common features of most cancers, where they contribute to deregulated gene expression. Chromothripsis is a recently described oncogenic mechanism whereby small genomic pieces originating from one chromosomal region undergo massive rearrangements in a single step. Here, we document chromothripsis in Hodgkin lymphoma (HL) cell lines by genomic profiling, showing alternating amplicons of defined chromosomal regions. In L-1236 cells, fluorescent in situ hybridization analyses identified aberrations affecting amplified chromosomal segments that derived from the long arm regions of chromosomes 3 and 9 and that colocalized to a derivative chromosome 6, indicating the cataclysmic origin of this mutation. The ABL1 gene at 9q34 was targeted by these rearrangements leading to its overexpression in L-1236 cells, correlating with pharmacological resistance to treatment with the kinase inhibitor dasatinib. Collectively, we identified and characterized chromothriptic rearrangements in HL cell lines to serve as models for analyzing this novel oncogenomic mechanism.		GSE15264			Yes	NA
CTDB0074	Research	25836623	Tan L, Xu LH, Liu HB, Yang SJ	Small lymphocytic lymphoma/chronic lymphocytic leukemia with chromothripsis in an old woman.	Chin Med J (Engl)	2015 Apr	8,9,11,13,17,19,X	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	25836623_1					Center of Oncology and Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510230, China.	Cell karyotyping in patients with small lymphocytic lymphoma/chronic lymphocytic leukemia (SLL/CLL) is not easy to success, and small genomic lesions (<5 Mb) are not routinely detected by this method. It is likely that a complete genomic characterization of CLL requires a combination of fluorescence in situ hybridization (FISH), single nucleotide polymorphism (SNP) array profiling for comprehensive genome-wide analysis of acquired genomic copy number aberrations (aCNAs) and loss-of-heterozygosity (LOH) in dominant clones, and karyotyping for detection of balanced translocations, isochromosomes, and marker chromosomes. SNP array analysis can reveal chromothripsis, a phenomenon by which regions of the cancer genome are shattered and recombined to generate frequent oscillations between the lower and the higher DNA copy number states. This study provided cytogenetic findings in a CLL/SLL patient with v-myc avian myelocytomatosis viral oncogene homolog (C-MYC)-amplification by FISH, in which SNP arrays detected profound genomic upheaval due to chromothripsis that may lead to malignant transformation.	GRCh37/hg19				Yes	NA
CTDB0093	Research	25506394	Holzmann C, Markowski DN, Koczan D, Kupker W, Helmke BM, Bullerdiek J	Cytogenetically normal uterine leiomyomas without MED12-mutations - a source to identify unknown mechanisms of the development of uterine smooth muscle tumors.	Mol Cytogenet	2014 Nov	2,5,11,18	Uterine leiomyoma	SNP Array	Homo sapiens	My708	Affymetrix CytoScan HD Array				Institute of Medical Genetics, University Rostock Medical Center, Ernst-Heydemann-Strasse 8, D-18057 Rostock, Germany	BACKGROUND: Recent findings on genetic changes in uterine leiomyomas suggest these benign tumors being a heterogeneous group of diseases in terms of molecular pathogenesis with those showing karyotype alterations as well as those characterized only by cytogenetically invisible mutations of mediator subcomplex 12 (MED12). Herein, five uterine leiomyomas (UL) with an apparently normal karyotype that lacked MED12-mutations were investigated by copy number variation arrays along with their matching myometrium to search for small genomic imbalances. RESULTS: Of five tumors one showed chromothripsis-like phenomena with numerous gains and losses of small segments mainly clustered to five chromosomal regions i.e. 2p14-2pter, 2q33.1-2q37.3, 5q31.3-5qter,11q14.1-11qter, and 18p11.21-18q2.3. Apparently, these cells had escaped detection by classical cytogenetics. Histologically, the tumor presented as a cellular leiomyoma with extended hyalinization. Of the remaining four tumors, one had a small intragenic deletion of the HMGA2 gene that was lacking in the corresponding myometrium. The other three tumors did not show relevant copy number alterations at all. CONCLUSIONS: Overall, the results suggest that leiomyomas with an apparently normal karyotype based on classical cytogenetics and lacking MED12 mutations represent a heterogeneous group of diseases. While the HMGA2 deletion detected in one of the tumors likely represents the driver mutation and, due to its size, has escaped detection by classical cytogenetics, the extended genomic imbalances detected in one of the other cases cannot be overlooked by this method suggesting an inability of the affected cells to divide in vitro. Of particular interest in that case is the occurrence of so-called chromothripsis or firestorms without involvement of the loci of common chromosomal rearrangements in UL, as e.g. 12q14~15 and 6p21. While chromothripsis was initially described as a hallmark of malignancy, the etiology and significance of this phenomenon in benign tumors still remain obscure. In uterine smooth muscle tumors, these changes per se do not indicate malignancy.	GRCh37/hg19				Yes	NA
CTDB0126	Research	21628407	Magrangeas F, Avet-Loiseau H, Munshi NC, Minvielle S	Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients	Blood	2011 Jul	2	Multiple myeloma	SNP Array	Homo sapiens	MM_06358	Affymetrix SNP6 Array				Inserm U892, Universite de Nantes, Nantes, France	Multiple myeloma (MM) develops from a premalignant plasma cell proliferative disorder, and with time can progress to a more aggressive disease in extramedullary locations. The gradually clinical evolution is supported by clonal expansion of cells that acquire genetic lesions over years. This model of cancer evolution based on ongoing genomic instability mechanism may apply to development of most MM cases. However, in a small fraction of newly diagnosed MM who relapse quickly and finally die within 2 years, the gradual model appears to be untenable. Analysis of high resolution copy number profiles obtained using single nucleotide polymorphism array data from 764 newly diagnosed MM identified large numbers of genomic rearrangements with the hallmarks of chromothripsis in 1.3% of samples. Moreover, this catastrophic event confers a poor outcome. Because chromothripsis appears to occur in a single crisis, our results suggest that high-risk MM patients use this novel way of cancer evolution.	GRCh37/hg19	GSE27560			Yes	NA
CTDB0127	Research	21628407	Magrangeas F, Avet-Loiseau H, Munshi NC, Minvielle S	Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients	Blood	2011 Jul	1,3	Multiple myeloma	SNP Array	Homo sapiens	MM_07545	Affymetrix SNP6 Array				Inserm U892, Universite de Nantes, Nantes, France	Multiple myeloma (MM) develops from a premalignant plasma cell proliferative disorder, and with time can progress to a more aggressive disease in extramedullary locations. The gradually clinical evolution is supported by clonal expansion of cells that acquire genetic lesions over years. This model of cancer evolution based on ongoing genomic instability mechanism may apply to development of most MM cases. However, in a small fraction of newly diagnosed MM who relapse quickly and finally die within 2 years, the gradual model appears to be untenable. Analysis of high resolution copy number profiles obtained using single nucleotide polymorphism array data from 764 newly diagnosed MM identified large numbers of genomic rearrangements with the hallmarks of chromothripsis in 1.3% of samples. Moreover, this catastrophic event confers a poor outcome. Because chromothripsis appears to occur in a single crisis, our results suggest that high-risk MM patients use this novel way of cancer evolution.	GRCh37/hg19	GSE27560			Yes	NA
CTDB0128	Research	21628407	Magrangeas F, Avet-Loiseau H, Munshi NC, Minvielle S	Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients	Blood	2011 Jul	16,17	Multiple myeloma	SNP Array	Homo sapiens	MM_08186	Affymetrix SNP6 Array				Inserm U892, Universite de Nantes, Nantes, France	Multiple myeloma (MM) develops from a premalignant plasma cell proliferative disorder, and with time can progress to a more aggressive disease in extramedullary locations. The gradually clinical evolution is supported by clonal expansion of cells that acquire genetic lesions over years. This model of cancer evolution based on ongoing genomic instability mechanism may apply to development of most MM cases. However, in a small fraction of newly diagnosed MM who relapse quickly and finally die within 2 years, the gradual model appears to be untenable. Analysis of high resolution copy number profiles obtained using single nucleotide polymorphism array data from 764 newly diagnosed MM identified large numbers of genomic rearrangements with the hallmarks of chromothripsis in 1.3% of samples. Moreover, this catastrophic event confers a poor outcome. Because chromothripsis appears to occur in a single crisis, our results suggest that high-risk MM patients use this novel way of cancer evolution.	GRCh37/hg19	GSE27560			Yes	NA
CTDB0129	Research	21628407	Magrangeas F, Avet-Loiseau H, Munshi NC, Minvielle S	Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients	Blood	2011 Jul	3	Multiple myeloma	SNP Array	Homo sapiens	MM_09402	Affymetrix SNP6 Array				Inserm U892, Universite de Nantes, Nantes, France	Multiple myeloma (MM) develops from a premalignant plasma cell proliferative disorder, and with time can progress to a more aggressive disease in extramedullary locations. The gradually clinical evolution is supported by clonal expansion of cells that acquire genetic lesions over years. This model of cancer evolution based on ongoing genomic instability mechanism may apply to development of most MM cases. However, in a small fraction of newly diagnosed MM who relapse quickly and finally die within 2 years, the gradual model appears to be untenable. Analysis of high resolution copy number profiles obtained using single nucleotide polymorphism array data from 764 newly diagnosed MM identified large numbers of genomic rearrangements with the hallmarks of chromothripsis in 1.3% of samples. Moreover, this catastrophic event confers a poor outcome. Because chromothripsis appears to occur in a single crisis, our results suggest that high-risk MM patients use this novel way of cancer evolution.	GRCh37/hg19	GSE27560			Yes	NA
CTDB0130	Research	21628407	Magrangeas F, Avet-Loiseau H, Munshi NC, Minvielle S	Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients	Blood	2011 Jul	10,12	Multiple myeloma	SNP Array	Homo sapiens	MM_10217	Affymetrix SNP6 Array				Inserm U892, Universite de Nantes, Nantes, France	Multiple myeloma (MM) develops from a premalignant plasma cell proliferative disorder, and with time can progress to a more aggressive disease in extramedullary locations. The gradually clinical evolution is supported by clonal expansion of cells that acquire genetic lesions over years. This model of cancer evolution based on ongoing genomic instability mechanism may apply to development of most MM cases. However, in a small fraction of newly diagnosed MM who relapse quickly and finally die within 2 years, the gradual model appears to be untenable. Analysis of high resolution copy number profiles obtained using single nucleotide polymorphism array data from 764 newly diagnosed MM identified large numbers of genomic rearrangements with the hallmarks of chromothripsis in 1.3% of samples. Moreover, this catastrophic event confers a poor outcome. Because chromothripsis appears to occur in a single crisis, our results suggest that high-risk MM patients use this novel way of cancer evolution.	GRCh37/hg19	GSE27560			Yes	NA
CTDB0131	Research	21628407	Magrangeas F, Avet-Loiseau H, Munshi NC, Minvielle S	Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients	Blood	2011 Jul	8,18	Multiple myeloma	SNP Array	Homo sapiens	MM_10353	Affymetrix SNP6 Array				Inserm U892, Universite de Nantes, Nantes, France	Multiple myeloma (MM) develops from a premalignant plasma cell proliferative disorder, and with time can progress to a more aggressive disease in extramedullary locations. The gradually clinical evolution is supported by clonal expansion of cells that acquire genetic lesions over years. This model of cancer evolution based on ongoing genomic instability mechanism may apply to development of most MM cases. However, in a small fraction of newly diagnosed MM who relapse quickly and finally die within 2 years, the gradual model appears to be untenable. Analysis of high resolution copy number profiles obtained using single nucleotide polymorphism array data from 764 newly diagnosed MM identified large numbers of genomic rearrangements with the hallmarks of chromothripsis in 1.3% of samples. Moreover, this catastrophic event confers a poor outcome. Because chromothripsis appears to occur in a single crisis, our results suggest that high-risk MM patients use this novel way of cancer evolution.	GRCh37/hg19	GSE27560			Yes	NA
CTDB0132	Research	21628407	Magrangeas F, Avet-Loiseau H, Munshi NC, Minvielle S	Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients	Blood	2011 Jul	1	Multiple myeloma	SNP Array	Homo sapiens	MM_10389	Affymetrix SNP6 Array				Inserm U892, Universite de Nantes, Nantes, France	Multiple myeloma (MM) develops from a premalignant plasma cell proliferative disorder, and with time can progress to a more aggressive disease in extramedullary locations. The gradually clinical evolution is supported by clonal expansion of cells that acquire genetic lesions over years. This model of cancer evolution based on ongoing genomic instability mechanism may apply to development of most MM cases. However, in a small fraction of newly diagnosed MM who relapse quickly and finally die within 2 years, the gradual model appears to be untenable. Analysis of high resolution copy number profiles obtained using single nucleotide polymorphism array data from 764 newly diagnosed MM identified large numbers of genomic rearrangements with the hallmarks of chromothripsis in 1.3% of samples. Moreover, this catastrophic event confers a poor outcome. Because chromothripsis appears to occur in a single crisis, our results suggest that high-risk MM patients use this novel way of cancer evolution.	GRCh37/hg19	GSE27560			Yes	NA
CTDB0133	Research	21628407	Magrangeas F, Avet-Loiseau H, Munshi NC, Minvielle S	Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients	Blood	2011 Jul	16	Multiple myeloma	SNP Array	Homo sapiens	MM_11762	Affymetrix SNP6 Array				Inserm U892, Universite de Nantes, Nantes, France	Multiple myeloma (MM) develops from a premalignant plasma cell proliferative disorder, and with time can progress to a more aggressive disease in extramedullary locations. The gradually clinical evolution is supported by clonal expansion of cells that acquire genetic lesions over years. This model of cancer evolution based on ongoing genomic instability mechanism may apply to development of most MM cases. However, in a small fraction of newly diagnosed MM who relapse quickly and finally die within 2 years, the gradual model appears to be untenable. Analysis of high resolution copy number profiles obtained using single nucleotide polymorphism array data from 764 newly diagnosed MM identified large numbers of genomic rearrangements with the hallmarks of chromothripsis in 1.3% of samples. Moreover, this catastrophic event confers a poor outcome. Because chromothripsis appears to occur in a single crisis, our results suggest that high-risk MM patients use this novel way of cancer evolution.	GRCh37/hg19	GSE27560			Yes	NA
CTDB0134	Research	21628407	Magrangeas F, Avet-Loiseau H, Munshi NC, Minvielle S	Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients	Blood	2011 Jul	16	Multiple myeloma	SNP Array	Homo sapiens	MM_06415	Affymetrix SNP6 Array				Inserm U892, Universite de Nantes, Nantes, France	Multiple myeloma (MM) develops from a premalignant plasma cell proliferative disorder, and with time can progress to a more aggressive disease in extramedullary locations. The gradually clinical evolution is supported by clonal expansion of cells that acquire genetic lesions over years. This model of cancer evolution based on ongoing genomic instability mechanism may apply to development of most MM cases. However, in a small fraction of newly diagnosed MM who relapse quickly and finally die within 2 years, the gradual model appears to be untenable. Analysis of high resolution copy number profiles obtained using single nucleotide polymorphism array data from 764 newly diagnosed MM identified large numbers of genomic rearrangements with the hallmarks of chromothripsis in 1.3% of samples. Moreover, this catastrophic event confers a poor outcome. Because chromothripsis appears to occur in a single crisis, our results suggest that high-risk MM patients use this novel way of cancer evolution.	GRCh37/hg19	GSE27560			Yes	NA
CTDB0145	Research	24636338	Zemanova Z, Michalova K, Buryova H, Brezinova J, Kostylkova K, Bystricka D, Novakova M, Sarova I, Izakova S, Lizcova L, Ransdorfova S, Krejcik Z, Merkerova MD, Dohnalova A, Siskova M, Jonasova A, Neuwirtova R, Cermak J	Involvement of deleted chromosome 5 in complex chromosomal aberrations in newly diagnosed myelodysplastic syndromes (MDS) is correlated with extremely adverse prognosis.	Leuk Res	2014 May	2,14,17,18,19	Myelodysplastic syndrome	SNP Array	Homo sapiens	24636338_1	BlueGnome CytoChip Cancer SNP 180K + Illumina Human CytoSNP-12 array				Center of Oncocytogenetics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Czech Republic	MDS with complex chromosomal aberrations (CCA) are characterized by short survival and a high rate of transformation to AML. A comprehensive genome-wide analysis of bone-marrow cells of 157 adults with newly diagnosed MDS and CCA revealed a large spectrum of nonrandom genomic changes related to the advanced stages of MDS. Chromosome shattering, probably resulting from chromothripsis, was found in 47% of patients. Deleted chromosome 5 was unstable and often involved in different types of cryptic unbalanced rearrangements. No true monosomy 5 was observed. Patients with CCA involving deleted chromosome 5 had an extremely poor prognosis (median overall survival, 2 months).					No	NA
CTDB0146	Research	25128687	Plaisancie J, Kleinfinger P, Cances C, Bazin A, Julia S, Trost D, Lohmann L, Vigouroux A	Constitutional chromoanasynthesis: description of a rare chromosomal event in a patient.	Eur J Med Genet	2014 Oct	18	Congenital abnormality	SNP Array	Homo sapiens	25128687_1	Affymetrix CytoscanHD Array	chr18:11585369-12482080:1;chr18:30852180-36260132:1;chr18:44426209-44898600:1;chr18:46076777-46787156:1;chr18:52567865-58008305:1;chr18:60595227-60819311:1;chr18:63614315-66856964:1;chr18:73554500-77125545:1			Service de Genetique Medicale, Hopital Purpan, CHU Toulouse, France	Structural alterations in chromosomes are a frequent cause of cancers and congenital diseases. Recently, the phenomenon of chromosome crisis, consisting of a set of tens to hundreds of clustered genomic rearrangements, localized in one or a few chromosomes, was described in cancer cells under the term chromothripsis. Better knowledge and recognition of this catastrophic chromosome event has brought to light two distinct entities, chromothripsis and chromoanasynthesis. The complexity of these rearrangements and the original descriptions in tumor cells initially led to the thought that it was an acquired anomaly. In fact, a few patients have been reported with constitutional chromothripsis or chromoanasynthesis. Using microarray we identified a very complex chromosomal rearrangement in a patient who had a cytogenetically visible rearrangement of chromosome 18. The rearrangement contained more than 15 breakpoints localized on a single chromosome. Our patient displayed intellectual disability, behavioral troubles and craniofacial dysmorphism. Interestingly, the succession of duplications and triplications identified in our patient was not clustered on a single chromosomal region but spread over the entire chromosome 18. In the light of this new spectrum of chromosomal rearrangements, this report outlines the main features of these catastrophic events and discusses the underlying mechanism of the complex chromosomal rearrangement identified in our patient, which is strongly evocative of a chromoanasynthesis.	GRCh37/hg19				No	NA
CTDB0147	Research	24957271	Sarova I, Brezinova J, Lhotska H, Berkova A, Ransdorfova S, Zemanova Z, Soukupova J, Michalova K	Jumping-like translocation-a rare chromosomal rearrangement in a patient with Burkitt lymphoma/leukemia.	Cancer Genet	2014 May	11,15	Burkitt lymphoma/leukemia	SNP Array	Homo sapiens	24957271_1	BlueGnome CytoChip Cancer SNP 4 180K	chr13:90000000-98200000:1;chr13:98200000-115169878:-1;chr11:43500000-48800000:-1;chr15:44800000-59100000:-1;chr15:59100000-63700000:-1			Institute of Hematology and Blood Transfusion, Prague, Czech Republic	Chromosomal translocations are acquired genetic rearrangements in human cancers. Jumping translocations are rare nonreciprocal rearrangements involving the same donor chromosome segment translocated to two or more recipient chromosomes. In this report, we describe a patient with Burkitt lymphoma/leukemia (BL) and a complex karyotype including a t(2;8)(p12;q24), copy-neutral loss of heterozygosity at 17p13.1-p13.3 and 19q13.1-q13.2, trisomy 20, and two uncommon chromosomal aberrations. The first uncommon aberration was a complex rearrangement of chromosome 15 (probably the consequence of chromothripsis) masked by an apparently balanced reciprocal translocation, t(11;15)(p11.2;q21). The second one was a special type of unbalanced vice versa jumping translocation, which involved the same acceptor chromosome arm (13q) and various donor chromosome segments. It is unclear whether both atypical rearrangements are the consequence of the TP53 alteration or whether assumed chromothripsis influenced the development of the jumping-like translocation. However, the presence of the t(11;15)(p11.2;q21) in all pathological cells suggests that it occurred in the early stage of the disease, whereas the jumping-like translocation, as an additional change, subsequently accelerated the progression of the disease.	GRCh37/hg19				Yes	NA
CTDB0165	Research	25161957	Ambros IM, Brunner C, Abbasi R, Frech C, Ambros PF	Ultra-High Density SNParray in Neuroblastoma Molecular Diagnostics.	Front Oncol	2014 Aug	2	Neuroblastoma	SNP Array	Homo sapiens	25161957_1	Affymetrix CytoScan HD Array			MYCN;ALK;ATRX;ARID1A;ARID1B	Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria	Neuroblastoma serves as a paradigm for applying tumor genomic data for determining patient prognosis and thus for treatment allocation. MYCN status, i.e., amplified vs. non-amplified, was one of the very first biomarkers in oncology to discriminate aggressive from less aggressive or even favorable clinical courses of neuroblastoma. However, MYCN amplification is by far not the only genetic change associated with unfavorable clinical courses. So called segmental chromosomal aberrations, (SCAs) i.e., gains or losses of chromosomal fragments, can also indicate tumor aggressiveness. The clinical use of these genomic aberrations has, however, been hampered for many years by methodical and interpretational problems. Only after reaching worldwide consensus on markers, methodology, and data interpretation, information on SCAs has recently been implemented in clinical studies. Now, a number of collaborative studies within COG, GPOH, and SIOPEN use genomic information to stratify therapy for patients with localized and metastatic disease. Recently, new types of DNA based aberrations influencing the clinical behavior of neuroblastomas have been described. Deletions or mutations of genes like ATRX and a phenomenon referred to as chromothripsis are all assumed to correlate with an unfavorable clinical behavior. However, these genomic aberrations need to be scrutinized in larger studies applying the most appropriate techniques. Single nucleotide polymorphism arrays have proven successful in deciphering genomic aberrations of cancer cells; these techniques, however, are usually not applied in the daily routine. Here, we present an ultra-high density (UHD) SNParray technique which is, because of its high specificity and sensitivity and the combined copy number and allele information, highly appropriate for the genomic diagnosis of neuroblastoma and other malignancies.					Yes	NA
CTDB0239	Research	23930239	Jianming Pei, Suresh C. Jhanwar, Joseph R. Testa	Chromothripsis in a case of TP53-deficient chronic lymphocytic leukemia	Leukemia Research Reports	2012 Nov	2,5,6,7	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	23930239_1	Affymetrix CytoScan HD array			TP53;IGH	Cancer Biology Program and Clinical Cytogenomics Laboratory, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA	We describe genomic findings in a case of CLL with del(17p13.1) by FISH, in which SNP array analysis revealed chromothripsis, a phenomenon by which regions of the cancer genome are shattered and recombined to generate frequent oscillations between two DNA copy number states.The findings illustrate the value of SNP arrays for precise whole genome profiling in CLL and for the detection of alterations that would be overlooked with a standard FISH panel. This second report of chromothripsis in CLL indicates that this phenomenon is a recurrent change in this disease.					Yes	NA
CTDB0280	Research	22926521	Schepeler T, Lamy P, Hvidberg V, Laurberg JR, Fristrup N, Reinert T, Bartkova J, Tropia L, Bartek J, Halazonetis TD, Pan CC, Borre M, Dyrskjot L, Orntoft TF	A high resolution genomic portrait of bladder cancer: correlation between genomic aberrations and the DNA damage response	Oncogene	2013 Aug 	8	Bladder cancer	SNP Array	Homo sapiens	B1735	Affymetrix SNP 6.0	chr10:0-62759:0;chr10:135356696-135374737:0;chr10:28819363-135356695:-1;chr10:55106654-82886849:1;chr10:62760-42919144:1;chr10:84041293-84120682:1;chr11:0-188509:0;chr11:134449983-134452384:0;chr11:188510-134449982:-1;chr11:55844245-57208782:1;chr12:0-132349534:0;chr13:0-47869578:0;chr13:47869579-51359596:-1;chr13:51359597-56965032:0;chr13:56965033-64574504:-1;chr13:64574505-114142980:0;chr14:0-18072124:0;chr14:105952894-105989097:0;chr14:105989098-106356482:-1;chr14:106356483-106368585:0;chr14:18072125-105952893:-1;chr14:20981847-22390230:1;chr15:0-18846948:0;chr15:100286565-100338915:0;chr15:18846949-72101389:-1;chr15:62433956-100286564:1;chr15:89058903-100286564:-1;chr16:0-777:0;chr16:29769296-47443493:1;chr16:30536196-69429180:-1;chr16:69429181-69761496:0;chr16:69761497-88815037:-1;chr16:778-29917385:-1;chr16:88815038-88827254:0;chr17:0-526:0;chr17:22359448-78774742:0;chr17:527-22359447:-1;chr18:0-76117153:0;chr19:0-41910:0;chr19:41911-63789667:1;chr19:63789668-63811651:0;chr1:0-247249719:0;chr20:0-9305:0;chr20:62426599-62435964:0;chr20:9306-62426598:1;chr21:0-9965425:0;chr21:42848164-46921386:-1;chr21:46921387-46944323:0;chr21:9965426-46921386:1;chr22:0-14432528:0;chr22:14432529-15566422:-1;chr22:15566423-19174824:0;chr22:19174825-49581322:-1;chr22:49581323-49691432:0;chr2:0-242951149:0;chr3:0-199501827:0;chr4:0-191273063:0;chr5:0-6246866:0;chr5:180722928-180857866:0;chr5:49473152-180722927:-1;chr5:6246867-6629631:-1;chr5:6629632-9415932:0;chr5:9415933-9666220:-1;chr5:9666221-49473151:0;chr6:0-94661:0;chr6:13024644-13042233:-1;chr6:170892932-170899992:0;chr6:32173957-32294274:-1;chr6:32732822-46986613:-1;chr6:36760762-44020003:1;chr6:46986614-56641250:0;chr6:533262-1077236:-1;chr6:56641251-57419168:1;chr6:56900795-60414872:-1;chr6:58249221-61966190:1;chr6:61966190-170892931:-1;chr6:64720033-65084155:1;chr6:94662-36415922:1;chr7:0-52911:0;chr7:158819767-158821424:0;chr7:52912-158819766:1;chr8:0-21254:0;chr8:146268961-146274826:0;chr8:21255-43924583:-1;chr8:37244074-37709713:1;chr8:39600479-39633022:1;chr8:39988202-146268960:1;chr9:0-36430:0;chr9:13340082-16838616:1;chr9:140211217-140273252:0;chr9:26901712-37913961:1;chr9:36431-140211216:-1;chr9:36431-8471745:1;chr9:70136750-70160650:1;chrX:0-154913754:0;chrY:0-57772954:0		LRP1B	Department of Molecular Medicine, Aarhus University Hospital, Skejby, Aarhus N, Denmark	One major challenge in cancer research is to understand the complex interplay between the DNA damage response (DDR), genomic integrity, and tumor development. To address these issues, we analyzed 43 bladder tumor genomes from 22 patients using single nucleotide polymorphism (SNP) arrays, and tissue expression of multiple DDR proteins, including Timeless and its interaction partner Tipin. The SNP profiles confirmed and extended known copy number alterations (CNAs) at high resolution, showed clustering of CNAs at nine common fragile sites, and revealed that most metachronous tumors were clonally related. The occurrence of many novel uniparental disomy regions (UPDs) was of potential functional importance in some tumors because UPDs spanned mutated FGFR3 and PIK3CA alleles, and also homozygous deletion of the CDKN2A tumor suppressor locus. The DDR signaling as evaluated by phospho-epitope-specific antibodies against Ser139-phosphorylated H2A histone family member X (gama-H2AX), ataxia telangiectasia mutated (ATM), and ATM- and Rad3-related (ATR) was commonly activated in tumors with both moderate and high extent of accumulated genomic aberrations, the latter tumors showing a more frequent loss of ATM expression. Strikingly, the tumor genomes exhibiting the most complex alterations were associated with a high Ki67-proliferation index, abundant Timeless but not Tipin expression, aberrant p53 expression, and homozygous CDKN2A deletions. Of clinical relevance, evaluation of a tissue microarray (TMA; n=319) showed that abundant Timeless expression was associated with risk of progression to muscle-invasive disease (P<0.0005; hazard ratio, 2.4; 95% confidence interval, 1.6-3.8) and higher T stage (P<0.05). Univariate analysis confirmed this association (P=0.006) in an independent cohort (n=241) but statistical significance was not reached in a multivariate model. Overall, our results are consistent with DDR activation preceding the accumulation of genomic aberrations. Tumors with extensive genomic rearrangements were associated with inactivation of CDKN2A, excessive proliferation, and robust Timeless expression, the latter also correlating with the risk of disease progression. Moreover, we provide evidence to suggest that UPDs likely contribute to bladder tumorigenesis. 	NCBI 36/hg18				Yes	NA
CTDB0281	Research	22926521	Schepeler T, Lamy P, Hvidberg V, Laurberg JR, Fristrup N, Reinert T, Bartkova J, Tropia L, Bartek J, Halazonetis TD, Pan CC, Borre M, Dyrskjot L, Orntoft TF	A high resolution genomic portrait of bladder cancer: correlation between genomic aberrations and the DNA damage response	Oncogene	2013 Aug 	15	Bladder cancer	SNP Array	Homo sapiens	B2120	Affymetrix SNP 6.0	chr10:0-62759:0;chr10:135356696-135374737:0;chr10:28819363-135356695:-1;chr10:42942834-52884342:1;chr10:62760-42919144:1;chr11:0-188509:0;chr11:134449983-134452384:0;chr11:188510-134449982:-1;chr12:0-20703:0;chr12:132288264-132349534:0;chr12:20704-80221556:1;chr12:80221557-89016946:0;chr12:89016947-132288263:1;chr13:0-17924949:0;chr13:103350604-104079457:-1;chr13:104998316-105367736:-1;chr13:114076551-114126500:-1;chr13:114126501-114142980:0;chr13:17924950-114126500:1;chr13:39619501-40139362:-1;chr13:47869579-51359596:-1;chr13:56965033-64574504:-1;chr13:73176342-75200116:-1;chr13:77127934-81311465:-1;chr14:0-18072124:0;chr14:101148001-106356482:1;chr14:106356483-106368585:0;chr14:18072125-105952893:-1;chr14:20981847-22390230:1;chr14:22549488-22646058:1;chr14:32914815-32950451:1;chr14:44643030-44743518:1;chr14:44836032-46201834:1;chr14:55134198-64178550:1;chr14:65958113-67624680:1;chr14:67759880-67992179:1;chr14:70435216-77591627:1;chr15:0-18276341:0;chr15:100286565-100338915:0;chr15:18276342-18839951:-1;chr15:18276342-25501400:1;chr15:18846949-72101389:-1;chr15:26256457-26741881:1;chr15:45744994-51572163:1;chr15:59331351-62058525:1;chr15:62433956-100286564:1;chr15:72391771-78476143:-1;chr15:87323116-87996311:-1;chr15:89058903-100286564:-1;chr16:0-777:0;chr16:10239513-10553903:1;chr16:12926490-16537186:1;chr16:29917386-30536195:0;chr16:30536196-69429180:-1;chr16:69429181-69761496:0;chr16:69761497-88815037:-1;chr16:778-29917385:-1;chr16:88815038-88827254:0;chr16:9717766-9722139:1;chr17:0-21973579:0;chr17:21973580-78643088:1;chr17:27910816-33759421:-1;chr17:41101479-41501468:-1;chr17:45290083-45355051:-1;chr17:74341747-74431623:-1;chr17:76450575-77638327:-1;chr17:78153535-78643088:-1;chr17:78643089-78774742:0;chr18:0-1542:0;chr18:1543-218211:1;chr18:1543-76116029:-1;chr18:67812516-67815816:1;chr18:67943708-68000326:1;chr18:68867536-69174534:1;chr18:69222596-69369586:1;chr18:76116030-76117153:0;chr19:0-41910:0;chr19:41911-28414212:-1;chr19:41911-63789667:1;chr19:63789668-63811651:0;chr1:0-554559:0;chr1:110591317-247191012:1;chr1:247191013-247249719:0;chr1:554560-141577170:-1;chr20:0-9305:0;chr20:62426599-62435964:0;chr20:9306-62426598:1;chr21:0-9965425:0;chr21:42848164-46921386:-1;chr21:46921387-46944323:0;chr21:9965426-20877324:-1;chr21:9965426-46921386:1;chr22:0-15658264:0;chr22:15658265-15734134:-1;chr22:15734135-19174824:0;chr22:19174825-49581322:-1;chr22:31723725-37054519:1;chr22:49581323-49691432:0;chr2:0-2784:0;chr2:242738131-242951149:0;chr2:2785-141043480:1;chr2:2785-242738130:-1;chr3:0-35345:0;chr3:18965512-47731811:1;chr3:35346-18650563:1;chr3:35346-95002438:-1;chr3:95002439-199501827:0;chr4:0-2281:0;chr4:191261906-191273063:0;chr4:2282-191261905:-1;chr5:0-68532:0;chr5:180722928-180857866:0;chr5:49473152-180722927:-1;chr5:68533-49586994:1;chr6:0-94661:0;chr6:170892932-170899992:0;chr6:36415923-36760761:0;chr6:36760762-44020003:1;chr6:44020004-49037968:0;chr6:49037969-49108396:1;chr6:49108397-51068545:0;chr6:51068546-55876400:1;chr6:55876401-56641250:0;chr6:56641251-57419168:1;chr6:57419169-58249220:0;chr6:58249221-61966190:1;chr6:61966190-170892931:-1;chr6:62178982-62299803:1;chr6:64720033-65084155:1;chr6:94662-36415922:1;chr7:0-52911:0;chr7:11158045-11853724:-1;chr7:158819767-158821424:0;chr7:52912-158819766:1;chr7:9047113-10279718:-1;chr8:0-21254:0;chr8:146268961-146274826:0;chr8:21255-43924583:-1;chr8:2129727-2169873:1;chr8:39988202-146268960:1;chr9:0-36430:0;chr9:140211217-140273252:0;chr9:36431-140211216:-1;chrX:0-154913754:0;chrY:0-57772954:0			Department of Molecular Medicine, Aarhus University Hospital, Skejby, Aarhus N, Denmark	One major challenge in cancer research is to understand the complex interplay between the DNA damage response (DDR), genomic integrity, and tumor development. To address these issues, we analyzed 43 bladder tumor genomes from 22 patients using single nucleotide polymorphism (SNP) arrays, and tissue expression of multiple DDR proteins, including Timeless and its interaction partner Tipin. The SNP profiles confirmed and extended known copy number alterations (CNAs) at high resolution, showed clustering of CNAs at nine common fragile sites, and revealed that most metachronous tumors were clonally related. The occurrence of many novel uniparental disomy regions (UPDs) was of potential functional importance in some tumors because UPDs spanned mutated FGFR3 and PIK3CA alleles, and also homozygous deletion of the CDKN2A tumor suppressor locus. The DDR signaling as evaluated by phospho-epitope-specific antibodies against Ser139-phosphorylated H2A histone family member X (gama-H2AX), ataxia telangiectasia mutated (ATM), and ATM- and Rad3-related (ATR) was commonly activated in tumors with both moderate and high extent of accumulated genomic aberrations, the latter tumors showing a more frequent loss of ATM expression. Strikingly, the tumor genomes exhibiting the most complex alterations were associated with a high Ki67-proliferation index, abundant Timeless but not Tipin expression, aberrant p53 expression, and homozygous CDKN2A deletions. Of clinical relevance, evaluation of a tissue microarray (TMA; n=319) showed that abundant Timeless expression was associated with risk of progression to muscle-invasive disease (P<0.0005; hazard ratio, 2.4; 95% confidence interval, 1.6-3.8) and higher T stage (P<0.05). Univariate analysis confirmed this association (P=0.006) in an independent cohort (n=241) but statistical significance was not reached in a multivariate model. Overall, our results are consistent with DDR activation preceding the accumulation of genomic aberrations. Tumors with extensive genomic rearrangements were associated with inactivation of CDKN2A, excessive proliferation, and robust Timeless expression, the latter also correlating with the risk of disease progression. Moreover, we provide evidence to suggest that UPDs likely contribute to bladder tumorigenesis. 	NCBI 36/hg18				Yes	NA
CTDB0297	Research	24613276	Laurie CC, Laurie CA, Smoley SA, Carlson EE, Flinn I, Fridley BL, Greisman HA, Gribben JG, Jelinek DF, Nelson SC, Paietta E, Schaid D, Sun Z, Tallman MS, Weinshilboum R, Kay NE, Shanafelt TD	Acquired chromosomal anomalies in chronic lymphocytic leukemia patients compared with more than 50,000 quasi-normal participants	Cancer Genetics	2014 Jan	11	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	10	Illumina HumanOmni-Quad v1.0_B SNP microarray	chr10:0-88086:0;chr10:1333199-135374737:0;chr10:88087-1333198:-1;chr11:0-15590802:0;chr11:115677786-118336936:0;chr11:118336937-126720615:-1;chr11:126720616-128026677:0;chr11:128026678-134367886:-1;chr11:134367887-134452384:0;chr11:15590803-16626283:-1;chr11:16626284-34146998:0;chr11:34146999-34894477:-1;chr11:34894478-35227176:0;chr11:35227177-43341509:-1;chr11:43341510-48614745:0;chr11:48614746-51417246:-1;chr11:51417247-54508765:0;chr11:54508766-59693555:-1;chr11:59693556-77902555:0;chr11:77902556-83268891:-1;chr11:83268892-83735129:0;chr11:83735130-84917636:-1;chr11:84917637-86301560:0;chr11:86301561-88846159:-1;chr11:88846160-88994233:0;chr11:88994234-91701474:-1;chr11:91701475-95876561:0;chr11:95876562-115677785:-1;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;chr2:0-35281164:0;chr2:35281165-39625508:-1;chr2:39625509-53383060:0;chr2:53383061-54247074:-1;chr2:54247075-55473113:0;chr2:55473114-55837433:-1;chr2:55837434-56709282:0;chr2:56709283-59433830:-1;chr2:59433831-242951149:0;chr3:0-199501827:0;chr4:0-70092923:0;chr4:121277543-123877604:-1;chr4:123877605-191273063:0;chr4:70092924-73761895:-1;chr4:73761896-77315141:0;chr4:77315142-90447261:-1;chr4:90447262-121277542:0;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			Biostatistics Department, University of Washington, Seattle, WA, USA	Pretherapy patients with chronic lymphocytic leukemia (CLL) from US Intergroup trial E2997 were analyzed with single nucleotide polymorphism microarrays to detect acquired chromosomal anomalies. The four CLL-typical anomalies (11q-, +12, 13q-, and 17p-) were found at expected frequencies. Acquired anomalies in other regions account for 70% of the total detected anomalies, and their number per participant has a significant effect on progression-free survival after adjusting for the effects of 17p- (and other covariates). These results were compared with those from a previous study of more than 50,000 participants from the GENEVA consortium of genome-wide association studies, which analyzed individuals with a variety of medical conditions and healthy controls. The percentage of individuals with acquired anomalies is vastly different between the two studies (GENEVA 0.8%; E2997 80%). The composition of the anomalies also differs, with GENEVA having a higher percentage of acquired uniparental disomies and a lower percentage of deletions. The four common CLL anomalies are among the most frequent in GENEVA participants, some of whom may have CLL-precursor conditions or early stages of CLL. However, the patients from E2997 (and other studies of symptomatic CLL) have recurrent acquired anomalies that were not found in GENEVA participants, thus identifying genomic changes that may be unique to symptomatic stages of CLL. 	NCBI 36/hg18		phs000621		Yes	NA
CTDB0298	Research	24613276	Laurie CC, Laurie CA, Smoley SA, Carlson EE, Flinn I, Fridley BL, Greisman HA, Gribben JG, Jelinek DF, Nelson SC, Paietta E, Schaid D, Sun Z, Tallman MS, Weinshilboum R, Kay NE, Shanafelt TD	Acquired chromosomal anomalies in chronic lymphocytic leukemia patients compared with more than 50,000 quasi-normal participants	Cancer Genetics	2014 Jan	9	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	86	Illumina HumanOmni-Quad v1.0_B SNP microarray	chr10:0-135374737:0;chr11:0-129814088:0;chr11:129814089-134443680:-1;chr11:134443681-134452384:0;chr12:0-132349534:0;chr13:0-18086615:0;chr13:18086616-26402964:-1;chr13:26402965-114142980:0;chr14:0-67341733:0;chr14:67341734-92271752:-1;chr14:92271753-106368585:0;chr15:0-18421385:0;chr15:18421386-39191343:-1;chr15:39191344-39197996:0;chr15:39197997-41345866:-1;chr15:41345867-100338915:0;chr16:0-88827254:0;chr17:0-7213:0;chr17:19280415-78774742:0;chr17:7214-19280414:-1;chr18:0-76117153:0;chr19:0-63811651:0;chr1:0-247249719:0;chr20:0-62435964:0;chr21:0-13591801:0;chr21:13591802-23456930:-1;chr21:23456931-46944323:0;chr22:0-49691432:0;chr2:0-40813:0;chr2:208997028-231626311:-1;chr2:231626312-242951149:0;chr2:40814-88909336:1;chr2:88909337-208997027:0;chr3:0-199501827:0;chr4:0-191273063:0;chr5:0-180857866:0;chr6:0-9769250:0;chr6:45857783-57482074:-1;chr6:57482075-61949076:0;chr6:61949077-66859614:-1;chr6:66859615-66865882:0;chr6:66865883-67814410:-1;chr6:67814411-67827225:0;chr6:67827226-74890125:-1;chr6:74890126-74907772:0;chr6:74907773-75471929:-1;chr6:75471930-170899992:0;chr6:9769251-45857783:-1;chr7:0-158821424:0;chr8:0-185253:0;chr8:185254-38182392:-1;chr8:38182393-146274826:0;chr9:0-36586:0;chr9:105644055-109189988:0;chr9:109189989-110587420:-1;chr9:110587421-117495647:0;chr9:117495648-140186312:-1;chr9:140186313-140273252:0;chr9:14484389-16800346:0;chr9:16800347-22040873:-1;chr9:22040874-25320809:0;chr9:25320810-33808257:-1;chr9:33808258-67656949:0;chr9:36587-6530540:1;chr9:6530541-9876402:0;chr9:67656950-84950566:-1;chr9:84950567-91964998:0;chr9:91964999-92295939:-1;chr9:92295940-92675795:0;chr9:92675796-94618312:-1;chr9:94618313-96040218:0;chr9:96040219-96470652:-1;chr9:96470653-99476878:0;chr9:9876403-14484388:-1;chr9:99476879-105644054:-1;chrX:0-154913754:0;chrY:0-57772954:0			Biostatistics Department, University of Washington, Seattle, WA, USA	Pretherapy patients with chronic lymphocytic leukemia (CLL) from US Intergroup trial E2997 were analyzed with single nucleotide polymorphism microarrays to detect acquired chromosomal anomalies. The four CLL-typical anomalies (11q-, +12, 13q-, and 17p-) were found at expected frequencies. Acquired anomalies in other regions account for 70% of the total detected anomalies, and their number per participant has a significant effect on progression-free survival after adjusting for the effects of 17p- (and other covariates). These results were compared with those from a previous study of more than 50,000 participants from the GENEVA consortium of genome-wide association studies, which analyzed individuals with a variety of medical conditions and healthy controls. The percentage of individuals with acquired anomalies is vastly different between the two studies (GENEVA 0.8%; E2997 80%). The composition of the anomalies also differs, with GENEVA having a higher percentage of acquired uniparental disomies and a lower percentage of deletions. The four common CLL anomalies are among the most frequent in GENEVA participants, some of whom may have CLL-precursor conditions or early stages of CLL. However, the patients from E2997 (and other studies of symptomatic CLL) have recurrent acquired anomalies that were not found in GENEVA participants, thus identifying genomic changes that may be unique to symptomatic stages of CLL. 	NCBI 36/hg18		phs000621		Yes	NA
CTDB0299	Research	24613276	Laurie CC, Laurie CA, Smoley SA, Carlson EE, Flinn I, Fridley BL, Greisman HA, Gribben JG, Jelinek DF, Nelson SC, Paietta E, Schaid D, Sun Z, Tallman MS, Weinshilboum R, Kay NE, Shanafelt TD	Acquired chromosomal anomalies in chronic lymphocytic leukemia patients compared with more than 50,000 quasi-normal participants	Cancer Genetics	2014 Jan	9	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	203	Illumina HumanOmni-Quad v1.0_B SNP microarray	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;chr3:0-38410:0;chr3:17985707-38126735:-1;chr3:38126736-52498444:0;chr3:38411-9799651:-1;chr3:52498445-57909692:-1;chr3:57909693-71780450:0;chr3:71780451-90525615:-1;chr3:90525616-199501827:0;chr3:9799652-17985706:0;chr4:0-175186278:0;chr4:175186279-183245566:-1;chr4:183245567-184392508:0;chr4:184392509-191176659:-1;chr4:191176660-191273063:0;chr5:0-150543494:0;chr5:150543495-155946409:-1;chr5:155946410-180857866:0;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-21067715:0;chr9:113585700-114548976:0;chr9:114548977-115764223:-1;chr9:115764224-116210061:0;chr9:116210062-116488534:-1;chr9:116488535-118543174:0;chr9:118543175-121780706:-1;chr9:121780707-127831310:0;chr9:127831311-131697340:-1;chr9:131697341-140273252:0;chr9:21067716-21772164:-1;chr9:21772165-25430149:0;chr9:25430150-29024430:-1;chr9:29024431-29066690:0;chr9:29066691-29253492:-1;chr9:29253493-66579043:0;chr9:66579044-77281262:-1;chr9:77281263-77788424:0;chr9:77788425-93549966:-1;chr9:93549967-93557535:0;chr9:93557536-93911541:-1;chr9:93911542-99260626:0;chr9:99260627-113585699:-1;chrX:0-154913754:0;chrY:0-57772954:0			Biostatistics Department, University of Washington, Seattle, WA, USA	Pretherapy patients with chronic lymphocytic leukemia (CLL) from US Intergroup trial E2997 were analyzed with single nucleotide polymorphism microarrays to detect acquired chromosomal anomalies. The four CLL-typical anomalies (11q-, +12, 13q-, and 17p-) were found at expected frequencies. Acquired anomalies in other regions account for 70% of the total detected anomalies, and their number per participant has a significant effect on progression-free survival after adjusting for the effects of 17p- (and other covariates). These results were compared with those from a previous study of more than 50,000 participants from the GENEVA consortium of genome-wide association studies, which analyzed individuals with a variety of medical conditions and healthy controls. The percentage of individuals with acquired anomalies is vastly different between the two studies (GENEVA 0.8%; E2997 80%). The composition of the anomalies also differs, with GENEVA having a higher percentage of acquired uniparental disomies and a lower percentage of deletions. The four common CLL anomalies are among the most frequent in GENEVA participants, some of whom may have CLL-precursor conditions or early stages of CLL. However, the patients from E2997 (and other studies of symptomatic CLL) have recurrent acquired anomalies that were not found in GENEVA participants, thus identifying genomic changes that may be unique to symptomatic stages of CLL. 	NCBI 36/hg18		phs000621		Yes	NA
CTDB0302	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	11	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL060	Affymetrix Human SNPArray 6.0	chr10:0-135374737:0;chr11:0-60135986:0;chr11:102484994-105626485:-1;chr11:105626486-107429518:0;chr11:107429519-108827021:-1;chr11:108827022-109142986:0;chr11:109142987-114315496:-1;chr11:114315497-115772845:0;chr11:115772846-116519019:-1;chr11:116519020-119593663:0;chr11:119593664-120699800:-1;chr11:120699801-121840815:0;chr11:121840816-123275276:-1;chr11:123275277-134452384:0;chr11:60135987-60796999:-1;chr11:60797000-102484993:0;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;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0303	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	3	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL175up	Affymetrix Human SNPArray 6.0	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;chr3:0-106658335:0;chr3:106658336-108421254:-1;chr3:108421255-117982410:0;chr3:117982411-123699590:-1;chr3:123699591-132094098:0;chr3:132094099-132464500:-1;chr3:132464501-132664121:0;chr3:132664122-146476071:-1;chr3:146476072-199501827:0;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			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0304	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	9,15	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL259up	Affymetrix Human SNPArray 6.0	chr10:0-135374737:0;chr11:0-134452384:0;chr12:0-132349534:0;chr13:0-114142980:0;chr14:0-106368585:0;chr15:0-18276341:0;chr15:100286565-100338915:0;chr15:18276342-30905963:-1;chr15:30905964-32887157:0;chr15:32887158-46449080:-1;chr15:46449081-51938390:0;chr15:51938391-55169874:-1;chr15:55169875-98156853:0;chr15:98156854-100286564:-1;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;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-2172289:0;chr9:101714048-101724151:0;chr9:101724152-111739097:-1;chr9:111739098-140273252:0;chr9:14572421-20553798:0;chr9:20553799-32860406:-1;chr9:2172290-4329207:-1;chr9:32860407-32860854:0;chr9:32860855-36874813:1;chr9:36874814-70130415:0;chr9:4329208-5119013:0;chr9:5119014-14572420:-1;chr9:70130416-81358290:-1;chr9:81358291-81358421:0;chr9:81358422-101714047:1;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0305	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	2,8	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL269up	Affymetrix Human SNPArray 6.0	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;chr2:0-59565606:0;chr2:111149065-112828328:-1;chr2:112828329-165284219:0;chr2:165284220-166919690:-1;chr2:166919691-171468527:0;chr2:171468528-172046546:-1;chr2:172046547-176248648:0;chr2:176248649-176824870:-1;chr2:176824871-178272553:0;chr2:178272554-180127517:-1;chr2:180127518-182667909:0;chr2:182667910-183995267:-1;chr2:183995268-185551104:0;chr2:185551105-189536072:-1;chr2:189536073-200288762:0;chr2:200288763-201948900:-1;chr2:201948901-204367611:0;chr2:204367612-209066946:-1;chr2:209066947-209802628:0;chr2:209802629-210858261:-1;chr2:210858262-223396325:0;chr2:223396326-226389803:-1;chr2:226389804-242951149:0;chr2:59565607-63157944:1;chr2:63157945-63163576:0;chr2:63163577-75819642:1;chr2:75819643-111149064:0;chr3:0-199501827:0;chr4:0-191273063:0;chr5:0-180857866:0;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-38162914:0;chr8:38162915-40264829:-1;chr8:40264830-48463332:0;chr8:48463333-48752079:-1;chr8:48752080-58390943:0;chr8:58390944-64602899:-1;chr8:64602900-70645031:0;chr8:70645032-72011812:-1;chr8:72011813-77954414:0;chr8:77954415-80170682:-1;chr8:80170683-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0306	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	2	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL287up	Affymetrix Human SNPArray 6.0	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;chr2:0-2771:0;chr2:18968900-34493565:0;chr2:2772-18968899:-1;chr2:34493566-52456236:-1;chr2:52456237-55689565:0;chr2:55689566-58397402:-1;chr2:58397403-66744891:0;chr2:66744892-86807366:-1;chr2:86807367-242951149:0;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			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0307	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	1	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL293up	Affymetrix Human SNPArray 6.0	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;chr1:0-6181716:0;chr1:108545037-110478611:-1;chr1:110478612-115474186:0;chr1:115474187-117860862:-1;chr1:117860863-247249719:0;chr1:41776339-42476711:-1;chr1:42476712-76587476:0;chr1:6181717-9105521:-1;chr1:76587477-77290475:-1;chr1:77290476-77790158:0;chr1:77790159-78745998:-1;chr1:78745999-81170853:0;chr1:81170854-85012152:-1;chr1:85012153-89058530:0;chr1:89058531-95482527:-1;chr1:9105522-41776338:0;chr1:95482528-108545036:0;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;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0308	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	6	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL300up	Affymetrix Human SNPArray 6.0	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;chr6:0-13130713:0;chr6:13130714-30368961:-1;chr6:141550230-142146472:-1;chr6:142146473-170899992:0;chr6:30368962-38572563:0;chr6:38572564-74660435:-1;chr6:74660436-141550229:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0309	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	6	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL066	Affymetrix Human SNPArray 6.0	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;chr6:0-94648:0;chr6:104456117-131403627:0;chr6:131403628-135722572:-1;chr6:135722573-158212103:0;chr6:1485308-21598311:0;chr6:158212104-158256190:-1;chr6:158256191-170899992:0;chr6:21598312-30559883:-1;chr6:30559884-43419066:0;chr6:43419067-74537921:-1;chr6:74537922-96392731:0;chr6:94649-1485307:1;chr6:96392732-104456116:-1;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0310	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	9	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL067	Affymetrix Human SNPArray 6.0	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;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-6229927:0;chr9:134464983-135623426:0;chr9:135623427-140211203:1;chr9:140211204-140273252:0;chr9:16649260-70133637:0;chr9:6229928-6291157:-1;chr9:6291158-6534765:0;chr9:6534766-16649259:-1;chr9:70133638-70788159:-1;chr9:70788160-71007979:0;chr9:71007980-79558276:-1;chr9:79558277-92605773:0;chr9:92605774-134464982:-1;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0311	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	17	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL077	Affymetrix Human SNPArray 6.0	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;chr17:0-513:0;chr17:2180649-3765470:0;chr17:23747045-78774742:0;chr17:3765471-5803018:-1;chr17:514-2180648:-1;chr17:5803019-7006097:0;chr17:7006098-7946630:-1;chr17:7946631-8703256:0;chr17:8703257-23747044:-1;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;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0312	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	13	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL104	Affymetrix Human SNPArray 6.0	chr10:0-135374737:0;chr11:0-134452384:0;chr12:0-132349534:0;chr13:0-40350248:0;chr13:40350249-40807123:-1;chr13:40807124-45814699:0;chr13:45814700-46261011:-1;chr13:46261012-47441703:0;chr13:47441704-48167674:-1;chr13:48167675-48401438:0;chr13:48401439-50271572:-1;chr13:50271573-50350855:0;chr13:50350856-50394321:-1;chr13:50394322-114142980:0;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;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0313	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	15	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL173up	Affymetrix Human SNPArray 6.0	chr10:0-135374737:0;chr11:0-134452384:0;chr12:0-132349534:0;chr13:0-114142980:0;chr14:0-106368585:0;chr15:0-32451386:0;chr15:32451387-39315978:-1;chr15:39315979-50042146:0;chr15:50042147-54732740:-1;chr15:54732741-83956290:0;chr15:83956291-87312981:-1;chr15:87312982-100338915:0;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;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0314	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	14	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL182up	Affymetrix Human SNPArray 6.0	chr10:0-135374737:0;chr11:0-134452384:0;chr12:0-132349534:0;chr13:0-114142980:0;chr14:0-62916329:0;chr14:62916330-64451324:-1;chr14:64451325-66924574:0;chr14:66924575-67349109:-1;chr14:67349110-68774305:0;chr14:68774306-70635712:-1;chr14:70635713-71420608:0;chr14:71420609-73782090:-1;chr14:73782091-106368585:0;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;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0315	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	11	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL210up	Affymetrix Human SNPArray 6.0	chr10:0-135374737:0;chr11:0-60213474:0;chr11:117469701-120284568:0;chr11:120284569-122491536:-1;chr11:122491537-122545917:0;chr11:122545918-122900680:-1;chr11:122900681-134452384:0;chr11:60213475-63748377:-1;chr11:63748378-76186932:0;chr11:76186933-117469700:-1;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;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0316	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	2	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL236up	Affymetrix Human SNPArray 6.0	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;chr2:0-42506337:0;chr2:100948167-111159725:0;chr2:111159726-112194596:-1;chr2:112194597-113366646:0;chr2:113366647-115093496:-1;chr2:115093497-135157627:0;chr2:135157628-136837001:-1;chr2:136837002-171514115:0;chr2:171514116-172077646:-1;chr2:172077647-201421698:0;chr2:201421699-204439764:-1;chr2:204439765-242951149:0;chr2:42506338-48582437:-1;chr2:48582438-96099906:0;chr2:96099907-100948166:-1;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			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0317	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	9,13	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL263up	Affymetrix Human SNPArray 6.0	chr10:0-135374737:0;chr11:0-134452384:0;chr12:0-132349534:0;chr13:0-43576588:0;chr13:106878224-114126500:-1;chr13:114126501-114142980:0;chr13:43576589-44695858:-1;chr13:44695859-47237563:0;chr13:47237564-48828370:-1;chr13:48828371-48828643:0;chr13:48828644-50691845:-1;chr13:50691846-51974706:0;chr13:51974707-55476935:-1;chr13:55476936-80419771:0;chr13:80419772-85048205:-1;chr13:85048206-85638599:0;chr13:85638600-90543572:-1;chr13:90543573-106878223:0;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;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0318	Research	23047824	Edelmann J, Holzmann K, Miller F, Winkler D, Buhler A, Zenz T, Bullinger L, Kuhn MW, Gerhardinger A, Bloehdorn J, Radtke I, Su X, Ma J, Pounds S, Hallek M, Lichter P, Korbel J, Busch R, Mertens D, Downing JR, Stilgenbauer S, Dohner H	High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations	Blood	2012 Dec	2,5	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	CLL267up	Affymetrix Human SNPArray 6.0	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;chr2:0-167124683:0;chr2:167124684-170891195:-1;chr2:170891196-178272540:0;chr2:178272541-180648285:-1;chr2:180648286-182257504:0;chr2:182257505-183959860:-1;chr2:183959861-208884588:0;chr2:208884589-210984140:-1;chr2:210984141-242951149:0;chr3:0-199501827:0;chr4:0-191273063:0;chr5:0-5448825:0;chr5:113020008-113424277:-1;chr5:113424278-113699666:0;chr5:113699667-113743974:-1;chr5:113743975-114158359:0;chr5:114158360-116586372:-1;chr5:116586373-120729373:0;chr5:120729374-127600968:-1;chr5:127600969-180857866:0;chr5:5448826-6695426:-1;chr5:6695427-113020007:0;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0			Department of Internal Medicine III, Ulm University, Ulm, Germany	To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.	NCBI 36/hg18	GSE36908			Yes	NA
CTDB0328	Research	25903014	Karrman K, Castor A, Behrendtz M, Forestier E, Olsson L, Ehinger M, Biloglav A, Fioretos T, Paulsson K, Johansson B	Deep sequencing and SNP array analyses of pediatric T-cell acute lymphoblastic leukemia reveal NOTCH1 mutations in minor subclones and a high incidence of uniparental isodisomies affecting CDKN2A	Journal of Hematology & Oncology	2015 Apr 	6	Acute lymphoblastic leukemia	SNP Array	Homo sapiens	U1	Illumina Humancnv370-Duo BeadChip	chr10:0-135534747:0;chr11:0-135006516:0;chr12:0-133851895:0;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-198022430:0;chr4:0-191154276:0;chr5:0-180915260:0;chr6:0-21884494:0;chr6:113895050-115470638:0;chr6:115470639-115965140:-1;chr6:115965141-117079874:0;chr6:117079875-119696844:-1;chr6:119696845-124344876:0;chr6:124344877-125649002:-1;chr6:125649003-128702993:0;chr6:128702994-129171964:-1;chr6:129171965-131033847:0;chr6:131033848-134133659:-1;chr6:134133660-137059441:0;chr6:137059442-140181508:-1;chr6:140181509-142439352:0;chr6:142439353-143807471:-1;chr6:143807472-143977499:0;chr6:143977500-151238363:-1;chr6:151238364-151523056:0;chr6:151523057-151988351:-1;chr6:151988352-152813956:0;chr6:152813957-156481213:-1;chr6:156481214-157274780:0;chr6:157274781-160952471:-1;chr6:160952472-161512963:0;chr6:161512964-167752761:-1;chr6:167752762-169723044:0;chr6:169723045-170507358:-1;chr6:170507359-171115067:0;chr6:21884495-21951866:-1;chr6:21951867-21964217:0;chr6:21964218-21974661:-1;chr6:21974662-70201286:0;chr6:70201287-70512716:1;chr6:70512717-79477494:0;chr6:79477495-113895049:-1;chr7:0-159138663:0;chr8:0-146364022:0;chr9:0-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0		CASP8AP2;	Department of Clinical Genetics, University and Regional Laboratories, Region Skane, SE-221 85, Lund, Sweden	BACKGROUND: Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease that arises in a multistep fashion through acquisition of several genetic aberrations, subsequently giving rise to a malignant, clonal expansion of T-lymphoblasts. The aim of the present study was to identify additional as well as cooperative genetic events in T-ALL. METHODS: A population-based pediatric T-ALL series comprising 47 cases was investigated by SNP array and deep sequencing analyses of 75 genes, in order to ascertain pathogenetically pertinent aberrations and to identify cooperative events. RESULTS: The majority (92%) of cases harbored copy number aberrations/uniparental isodisomies (UPIDs), with a median of three changes (range 0-11) per case. The genes recurrently deleted comprised CDKN2A, CDKN2B, LEF1, PTEN, RBI, and STIL. No case had a whole chromosome UPID; in fact, literature data show that this is a rare phenomenon in T-ALL. However, segmental UPIDs (sUPIDs) were seen in 42% of our cases, with most being sUPID9p that always were associated with homozygous CDKN2A deletions, with a heterozygous deletion occurring prior to the sUPID9p in all instances. Among the 75 genes sequenced, 14 (19%) were mutated in 28 (72%) of 39 analyzed cases. The genes targeted are involved in signaling transduction, epigenetic regulation, and transcription. In some cases, NOTCH1 mutations were seen in minor subclones and lost at relapse; thus, such mutations can be secondary events. CONCLUSIONS: Deep sequencing and SNP array analyses of T-ALL revealed lack of wUPIDs, a high proportion of sUPID9p targeting CDKN2A, NOTCH1 mutations in subclones, and recurrent mutations of genes involved in signaling transduction, epigenetic regulation, and transcription.	GRCh37/hg19				Yes	NA
CTDB0330	Research	24550227	Messina M, Del Giudice I, Khiabanian H, Rossi D, Chiaretti S, Rasi S, Spina V, Holmes AB, Marinelli M, Fabbri G, Piciocchi A, Mauro FR, Guarini A, Gaidano G, Dalla-Favera R, Pasqualucci L, Rabadan R, Foa R	Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness	Blood	2014 Apr 	6,8,9,13	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	7228	Affymetrix Human SNP Array 6.0				Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy	Fludarabine refractoriness (FR) represents an unsolved clinical problem of chronic lymphocytic leukemia (CLL) management. Although next-generation sequencing studies have led to the identification of a number of genes frequently mutated in FR-CLL, a comprehensive evaluation of the FR-CLL genome has not been reported. Toward this end, we studied 10 FR-CLLs by combining whole-exome sequencing and copy number aberration (CNA) analysis, which showed an average of 16.3 somatic mutations and 4 CNAs per sample. Screening of recurrently mutated genes in 48 additional FR-CLLs revealed that ~70% of FR-CLLs carry >=1 mutation in genes previously associated with CLL clinical course, including TP53 (27.5%), NOTCH1 (24.1%), SF3B1 (18.9%), and BIRC3 (15.5%). In addition, this analysis showed that 10.3% of FR-CLL cases display mutations of the FAT1 gene, which encodes for a cadherin-like protein that negatively regulates Wnt signaling, consistent with a tumor suppressor role. The frequency of FAT1-mutated cases was significantly higher in FR-CLL than in unselected CLLs at diagnosis (10.3% vs 1.1%, P = .004), suggesting a role in the development of a high-risk phenotype. These findings have general implications for the mechanisms leading to FR and point to Wnt signaling as a potential therapeutic target in FR-CLL.	NCBI 36/hg18	GSE51711			Yes	NA
CTDB0331	Research	24550227	Messina M, Del Giudice I, Khiabanian H, Rossi D, Chiaretti S, Rasi S, Spina V, Holmes AB, Marinelli M, Fabbri G, Piciocchi A, Mauro FR, Guarini A, Gaidano G, Dalla-Favera R, Pasqualucci L, Rabadan R, Foa R	Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness	Blood	2014 Apr 	8,9,13	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	4845	Affymetrix Human SNP Array 6.0				Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy	Fludarabine refractoriness (FR) represents an unsolved clinical problem of chronic lymphocytic leukemia (CLL) management. Although next-generation sequencing studies have led to the identification of a number of genes frequently mutated in FR-CLL, a comprehensive evaluation of the FR-CLL genome has not been reported. Toward this end, we studied 10 FR-CLLs by combining whole-exome sequencing and copy number aberration (CNA) analysis, which showed an average of 16.3 somatic mutations and 4 CNAs per sample. Screening of recurrently mutated genes in 48 additional FR-CLLs revealed that ~70% of FR-CLLs carry >=1 mutation in genes previously associated with CLL clinical course, including TP53 (27.5%), NOTCH1 (24.1%), SF3B1 (18.9%), and BIRC3 (15.5%). In addition, this analysis showed that 10.3% of FR-CLL cases display mutations of the FAT1 gene, which encodes for a cadherin-like protein that negatively regulates Wnt signaling, consistent with a tumor suppressor role. The frequency of FAT1-mutated cases was significantly higher in FR-CLL than in unselected CLLs at diagnosis (10.3% vs 1.1%, P = .004), suggesting a role in the development of a high-risk phenotype. These findings have general implications for the mechanisms leading to FR and point to Wnt signaling as a potential therapeutic target in FR-CLL.	NCBI 36/hg18	GSE51711			Yes	NA
CTDB0332	Research	24550227	Messina M, Del Giudice I, Khiabanian H, Rossi D, Chiaretti S, Rasi S, Spina V, Holmes AB, Marinelli M, Fabbri G, Piciocchi A, Mauro FR, Guarini A, Gaidano G, Dalla-Favera R, Pasqualucci L, Rabadan R, Foa R	Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness	Blood	2014 Apr 	8,9,13	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	6012	Affymetrix Human SNP Array 6.0				Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy	Fludarabine refractoriness (FR) represents an unsolved clinical problem of chronic lymphocytic leukemia (CLL) management. Although next-generation sequencing studies have led to the identification of a number of genes frequently mutated in FR-CLL, a comprehensive evaluation of the FR-CLL genome has not been reported. Toward this end, we studied 10 FR-CLLs by combining whole-exome sequencing and copy number aberration (CNA) analysis, which showed an average of 16.3 somatic mutations and 4 CNAs per sample. Screening of recurrently mutated genes in 48 additional FR-CLLs revealed that ~70% of FR-CLLs carry >=1 mutation in genes previously associated with CLL clinical course, including TP53 (27.5%), NOTCH1 (24.1%), SF3B1 (18.9%), and BIRC3 (15.5%). In addition, this analysis showed that 10.3% of FR-CLL cases display mutations of the FAT1 gene, which encodes for a cadherin-like protein that negatively regulates Wnt signaling, consistent with a tumor suppressor role. The frequency of FAT1-mutated cases was significantly higher in FR-CLL than in unselected CLLs at diagnosis (10.3% vs 1.1%, P = .004), suggesting a role in the development of a high-risk phenotype. These findings have general implications for the mechanisms leading to FR and point to Wnt signaling as a potential therapeutic target in FR-CLL.	NCBI 36/hg18	GSE51711			Yes	NA
CTDB0333	Research	24550227	Messina M, Del Giudice I, Khiabanian H, Rossi D, Chiaretti S, Rasi S, Spina V, Holmes AB, Marinelli M, Fabbri G, Piciocchi A, Mauro FR, Guarini A, Gaidano G, Dalla-Favera R, Pasqualucci L, Rabadan R, Foa R	Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness	Blood	2014 Apr 	3,12	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	4380	Affymetrix Human SNP Array 6.0				Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy	Fludarabine refractoriness (FR) represents an unsolved clinical problem of chronic lymphocytic leukemia (CLL) management. Although next-generation sequencing studies have led to the identification of a number of genes frequently mutated in FR-CLL, a comprehensive evaluation of the FR-CLL genome has not been reported. Toward this end, we studied 10 FR-CLLs by combining whole-exome sequencing and copy number aberration (CNA) analysis, which showed an average of 16.3 somatic mutations and 4 CNAs per sample. Screening of recurrently mutated genes in 48 additional FR-CLLs revealed that ~70% of FR-CLLs carry >=1 mutation in genes previously associated with CLL clinical course, including TP53 (27.5%), NOTCH1 (24.1%), SF3B1 (18.9%), and BIRC3 (15.5%). In addition, this analysis showed that 10.3% of FR-CLL cases display mutations of the FAT1 gene, which encodes for a cadherin-like protein that negatively regulates Wnt signaling, consistent with a tumor suppressor role. The frequency of FAT1-mutated cases was significantly higher in FR-CLL than in unselected CLLs at diagnosis (10.3% vs 1.1%, P = .004), suggesting a role in the development of a high-risk phenotype. These findings have general implications for the mechanisms leading to FR and point to Wnt signaling as a potential therapeutic target in FR-CLL.	NCBI 36/hg18	GSE51711			Yes	NA
CTDB0334	Research	24550227	Messina M, Del Giudice I, Khiabanian H, Rossi D, Chiaretti S, Rasi S, Spina V, Holmes AB, Marinelli M, Fabbri G, Piciocchi A, Mauro FR, Guarini A, Gaidano G, Dalla-Favera R, Pasqualucci L, Rabadan R, Foa R	Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness	Blood	2014 Apr 	14	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	9311	Affymetrix Human SNP Array 6.0				Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy	Fludarabine refractoriness (FR) represents an unsolved clinical problem of chronic lymphocytic leukemia (CLL) management. Although next-generation sequencing studies have led to the identification of a number of genes frequently mutated in FR-CLL, a comprehensive evaluation of the FR-CLL genome has not been reported. Toward this end, we studied 10 FR-CLLs by combining whole-exome sequencing and copy number aberration (CNA) analysis, which showed an average of 16.3 somatic mutations and 4 CNAs per sample. Screening of recurrently mutated genes in 48 additional FR-CLLs revealed that ~70% of FR-CLLs carry >=1 mutation in genes previously associated with CLL clinical course, including TP53 (27.5%), NOTCH1 (24.1%), SF3B1 (18.9%), and BIRC3 (15.5%). In addition, this analysis showed that 10.3% of FR-CLL cases display mutations of the FAT1 gene, which encodes for a cadherin-like protein that negatively regulates Wnt signaling, consistent with a tumor suppressor role. The frequency of FAT1-mutated cases was significantly higher in FR-CLL than in unselected CLLs at diagnosis (10.3% vs 1.1%, P = .004), suggesting a role in the development of a high-risk phenotype. These findings have general implications for the mechanisms leading to FR and point to Wnt signaling as a potential therapeutic target in FR-CLL.	NCBI 36/hg18	GSE51711			Yes	NA
CTDB0335	Research	24550227	Messina M, Del Giudice I, Khiabanian H, Rossi D, Chiaretti S, Rasi S, Spina V, Holmes AB, Marinelli M, Fabbri G, Piciocchi A, Mauro FR, Guarini A, Gaidano G, Dalla-Favera R, Pasqualucci L, Rabadan R, Foa R	Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness	Blood	2014 Apr 	3,12	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	9244	Affymetrix Human SNP Array 6.0				Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy	Fludarabine refractoriness (FR) represents an unsolved clinical problem of chronic lymphocytic leukemia (CLL) management. Although next-generation sequencing studies have led to the identification of a number of genes frequently mutated in FR-CLL, a comprehensive evaluation of the FR-CLL genome has not been reported. Toward this end, we studied 10 FR-CLLs by combining whole-exome sequencing and copy number aberration (CNA) analysis, which showed an average of 16.3 somatic mutations and 4 CNAs per sample. Screening of recurrently mutated genes in 48 additional FR-CLLs revealed that ~70% of FR-CLLs carry >=1 mutation in genes previously associated with CLL clinical course, including TP53 (27.5%), NOTCH1 (24.1%), SF3B1 (18.9%), and BIRC3 (15.5%). In addition, this analysis showed that 10.3% of FR-CLL cases display mutations of the FAT1 gene, which encodes for a cadherin-like protein that negatively regulates Wnt signaling, consistent with a tumor suppressor role. The frequency of FAT1-mutated cases was significantly higher in FR-CLL than in unselected CLLs at diagnosis (10.3% vs 1.1%, P = .004), suggesting a role in the development of a high-risk phenotype. These findings have general implications for the mechanisms leading to FR and point to Wnt signaling as a potential therapeutic target in FR-CLL.	NCBI 36/hg18	GSE51711			Yes	NA
CTDB0337	Research	24401281	Stevens-Kroef MJ, van den Berg E, Olde Weghuis D, Geurts van Kessel A, Pfundt R, Linssen-Wiersma M, Benjamins M, Dijkhuizen T, Groenen PJ, Simons A	Identification of prognostic relevant chromosomal abnormalities in chronic lymphocytic leukemia using microarray-based genomic profiling	Molecular Cytogenetics	2014 Jan 	11	Chronic lymphocytic leukemia	SNP Array	Homo sapiens	case 11	CytoSan HD array and HumanOmniExpress12v1.0 array				Department of Human Genetics, Radboud university medical center, P,O, Box 9101, Nijmegen 6500 HB, The Netherlands. Marian	BACKGROUND: Characteristic genomic abnormalities in patients with B cell chronic lymphocytic leukemia (CLL) have been shown to provide important prognostic information. Fluorescence in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA), currently used in clinical diagnostics of CLL, are targeted tests aimed at specific genomic loci. Microarray-based genomic profiling is a new high-resolution tool that enables genome-wide analyses. The aim of this study was to compare two recently launched genomic microarray platforms, i.e., the CytoScan HD Array (Affymetrix) and the HumanOmniExpress Array (Illumina), with FISH and MLPA to ascertain whether these latter tests can be replaced by either one of the microarray platforms in a clinical diagnostic setting. RESULT: Microarray-based genomic profiling and FISH were performed in all 28 CLL patients. For an unbiased comparison of the performance of both microarray platforms 9 patients were evaluated on both platforms, resulting in the identification of exactly identical genomic aberrations. To evaluate the detection limit of the microarray platforms we included 7 patients in which the genomic abnormalities were present in a relatively low percentage of the cells (range 5-28%) as previously determined by FISH. We found that both microarray platforms allowed the detection of copy number abnormalities present in as few as 16% of the cells. In addition, we found that microarray-based genomic profiling allowed the identification of genomic abnormalities that could not be detected by FISH and/or MLPA, including a focal TP53 loss and copy neutral losses of heterozygosity of chromosome 17p. CONCLUSION: From our results we conclude that although the microarray platforms exhibit a somewhat lower limit of detection compared to FISH, they still allow the detection of copy number abnormalities present in as few as 16% of the cells. By applying similar interpretation criteria, the results obtained from both platforms were comparable. In addition, we conclude that both microarray platforms allow the identification of additional potential prognostic relevant abnormalities such as focal TP53 deletions and copy neutral losses of heterozygosity of chromosome 17p, which would have remained undetected by FISH or MLPA. The prognostic relevance of these novel genomic alterations requires further evaluation in prospective clinical trials. 	GRCh37/hg19				Yes	NA
CTDB0342	Research	24819516	Iannelli F, Collino A, Sinha S, Radaelli E, Nicoli P, D'Antiga L, Sonzogni A, Faivre J, Buendia MA, Sturm E, Thompson RJ, Knisely AS, Natoli G, Ghisletti S, Ciccarelli FD	Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency	Nature Communications	2014 May 	4,6	Hepatocellular carcinoma	SNP Array	Homo sapiens	UKT	Illumina HumanOmniExpress-12 v1.0	chr10:0-4431609:0;chr10:10185316-10228683:0;chr10:10228684-10586371:1;chr10:10586372-47681956:0;chr10:117395006-117727166:1;chr10:117727167-135534747:0;chr10:4431610-4944816:1;chr10:47681957-47940417:1;chr10:47940418-52451271:0;chr10:4944817-8563174:0;chr10:52451272-58121201:1;chr10:58121202-58249478:0;chr10:58249479-60590203:1;chr10:60590204-66827629:0;chr10:66827630-67780727:1;chr10:67780728-67780897:0;chr10:67780898-70455490:1;chr10:70455491-82653859:0;chr10:82653860-85210888:1;chr10:85210889-85210945:0;chr10:85210946-85241941:-1;chr10:85241942-117395005:0;chr10:8563175-10185315:1;chr11:0-135006516:0;chr12:0-85071585:0;chr12:85071586-85091700:1;chr12:85091701-133851895:0;chr13:0-51542208:0;chr13:115103530-115169878:0;chr13:51542209-115103529:1;chr14:0-25281567:0;chr14:25281568-30102025:1;chr14:30102026-40314469:0;chr14:40314470-49384358:1;chr14:49384359-71092255:0;chr14:71092256-71117483:-1;chr14:71117484-79399654:0;chr14:79399655-85693853:1;chr14:85693854-85709381:0;chr14:85709382-88494613:1;chr14:88494614-107349540:0;chr15:0-26824731:0;chr15:26824732-26865632:1;chr15:26865633-80315415:0;chr15:80315416-80331233:-1;chr15:80331234-102531392:0;chr16:0-46450036:0;chr16:46450037-58900866:-1;chr16:58900867-65596701:0;chr16:65596702-72147186:-1;chr16:72147187-80913668:0;chr16:80913669-82181608:-1;chr16:82181609-82181976:0;chr16:82181977-82182229:1;chr16:82182230-90354753:0;chr17:0-32354752:0;chr17:32354753-32501774:-1;chr17:32501775-50577943:0;chr17:50577944-53248927:1;chr17:53248928-77365872:0;chr17:77365873-77368132:1;chr17:77368133-81195210:0;chr18:0-24384539:0;chr18:24384540-29146918:1;chr18:29146919-37707850:0;chr18:37707851-42306884:1;chr18:42306885-56872177:0;chr18:56872178-56878274:1;chr18:56878275-62191652:0;chr18:62191653-67718688:1;chr18:67718689-68585023:0;chr18:68585024-71412693:1;chr18:71412694-78077248:0;chr19:0-260911:0;chr19:11879420-18502835:1;chr19:18502836-19902915:0;chr19:19902916-29343037:1;chr19:260912-7266944:1;chr19:29343038-29347038:0;chr19:29347039-34309277:1;chr19:34309278-34333500:0;chr19:34333501-36856251:1;chr19:36856252-36856378:0;chr19:36856379-38702777:1;chr19:38702778-50741569:0;chr19:50741570-53518747:1;chr19:53518748-53554239:0;chr19:53554240-54720958:1;chr19:54720959-55859438:0;chr19:55859439-58141281:1;chr19:58141282-58153576:0;chr19:58153577-59097160:1;chr19:59097161-59128983:0;chr19:7266945-11879419:0;chr1:0-7811960:0;chr1:100043790-102297844:0;chr1:102297845-108421058:1;chr1:108421059-165646757:0;chr1:165646758-165650616:1;chr1:165650617-184527030:0;chr1:184527031-193700387:1;chr1:193700388-193715322:0;chr1:193715323-197521877:1;chr1:197521878-214751785:0;chr1:214751786-217088584:1;chr1:217088585-237773426:0;chr1:237773427-242158192:1;chr1:242158193-249250621:0;chr1:46989742-46990681:-1;chr1:46990682-68407583:0;chr1:68407584-76499313:1;chr1:76499314-79174954:0;chr1:7811961-7829107:1;chr1:7829108-46989741:0;chr1:79174955-84917707:1;chr1:84917708-96339893:0;chr1:96339894-100043789:1;chr20:0-63243:0;chr20:13954880-14031391:0;chr20:14031392-17459584:1;chr20:1726904-1727506:0;chr20:1727507-1729560:1;chr20:1729561-1748125:0;chr20:17459585-17463916:0;chr20:17463917-24639916:1;chr20:1748126-6087162:1;chr20:24639917-24666099:0;chr20:24666100-26293985:1;chr20:26293986-29445643:0;chr20:29445644-52845398:1;chr20:52845399-52851118:0;chr20:52851119-54784952:1;chr20:54784953-54795922:0;chr20:54795923-56965708:1;chr20:56965709-57032712:0;chr20:57032713-57357395:1;chr20:57357396-57374242:0;chr20:57374243-59971800:1;chr20:59971801-59988068:0;chr20:59988069-62764435:1;chr20:6087163-6089740:0;chr20:6089741-9051482:1;chr20:62764436-63025520:0;chr20:63244-1726903:1;chr20:9051483-9055819:0;chr20:9055820-9088624:1;chr20:9088625-9109892:0;chr20:9109893-13954879:1;chr21:0-10827532:0;chr21:10827533-23250041:1;chr21:23250042-23264429:0;chr21:23264430-26699228:1;chr21:26699229-26706355:0;chr21:26706356-27922192:1;chr21:27922193-27924202:0;chr21:27924203-32485200:1;chr21:32485201-32486882:0;chr21:32486883-46926551:1;chr21:46926552-46934860:0;chr21:46934861-48100155:1;chr21:48100156-48129895:0;chr22:0-51304566:0;chr2:0-4237883:0;chr2:14255030-14255040:0;chr2:14255041-14286717:1;chr2:14286718-81313892:0;chr2:209140046-243199373:0;chr2:4237884-5488456:1;chr2:5488457-5488518:0;chr2:5488519-14255029:1;chr2:81313893-81440526:1;chr2:81440527-81444319:0;chr2:81444320-209140045:1;chr3:0-3191812:0;chr3:3191813-3207754:1;chr3:3207755-198022430:0;chr4:0-27268341:0;chr4:113782927-113784481:0;chr4:113784482-113924858:-1;chr4:113924859-113927364:0;chr4:113927365-138609462:1;chr4:138609463-141410250:0;chr4:141410251-143421175:1;chr4:143421176-143426030:0;chr4:143426031-143452535:1;chr4:143452536-177360668:0;chr4:177360669-178803423:1;chr4:178803424-178805082:0;chr4:178805083-178821372:-1;chr4:178821373-178827896:0;chr4:178827897-183574838:1;chr4:183574839-191154276:0;chr4:27268342-29314598:1;chr4:29314599-29317917:0;chr4:29317918-29330467:1;chr4:29330468-29331116:0;chr4:29331117-31071934:1;chr4:31071935-31077544:0;chr4:31077545-31104796:-1;chr4:31104797-31110336:0;chr4:31110337-36325988:1;chr4:36325989-43232758:0;chr4:43232759-47181795:1;chr4:47181796-58121588:0;chr4:58121589-69822928:1;chr4:69822929-69901662:0;chr4:69901663-70521159:1;chr4:70521160-91046718:0;chr4:91046719-113782926:1;chr5:0-81979165:0;chr5:106276533-115885573:0;chr5:115885574-122514588:1;chr5:122514589-124188886:0;chr5:124188887-124245657:1;chr5:124245658-127740575:0;chr5:127740576-130164900:1;chr5:130164901-162652826:0;chr5:162652827-167070649:1;chr5:167070650-180915260:0;chr5:81979166-84163069:1;chr5:84163070-84167823:0;chr5:84167824-89439105:1;chr5:89439106-89456354:0;chr5:89456355-92141172:1;chr5:92141173-98593452:0;chr5:98593453-106276532:1;chr6:0-7979532:0;chr6:10155288-23978217:0;chr6:104559149-120222328:0;chr6:120222329-123897071:1;chr6:123897072-140219413:0;chr6:140219414-142024463:1;chr6:142024464-148940807:0;chr6:148940808-148997371:-1;chr6:148997372-166287777:0;chr6:166287778-166308198:1;chr6:166308199-171115067:0;chr6:23978218-23984030:-1;chr6:23984031-33110833:0;chr6:33110834-33115762:-1;chr6:33115763-61891117:0;chr6:61891118-65289746:1;chr6:65289747-65317294:0;chr6:65317295-69743528:1;chr6:69743529-91210593:0;chr6:7979533-10155287:1;chr6:91210594-104559148:1;chr7:0-77818151:0;chr7:144137137-147277640:1;chr7:147277641-159138663:0;chr7:77818152-97463961:1;chr7:97463962-144137136:0;chr8:0-164983:0;chr8:105810398-105815144:0;chr8:105815145-115448234:1;chr8:11147124-11406592:0;chr8:11406593-12933568:1;chr8:115448235-115923991:0;chr8:115923992-123537857:1;chr8:123537858-123537947:0;chr8:123537948-126798409:1;chr8:126798410-126799010:0;chr8:126799011-127306602:1;chr8:127306603-127308156:0;chr8:127308157-129043582:1;chr8:129043583-129059109:0;chr8:129059110-134660741:1;chr8:12933569-12933580:0;chr8:12933581-15037929:1;chr8:134660742-134673367:0;chr8:134673368-135792825:1;chr8:135792826-135793641:0;chr8:135793642-135794496:1;chr8:135794497-135796965:0;chr8:135796966-138209669:1;chr8:138209670-138243038:0;chr8:138243039-139101291:1;chr8:139101292-139102266:0;chr8:139102267-146293414:1;chr8:146293415-146364022:0;chr8:15037930-15051871:0;chr8:15051872-15258706:1;chr8:15258707-15265900:0;chr8:15265901-16823648:1;chr8:164984-2290039:1;chr8:16823649-17780035:0;chr8:17780036-19113393:1;chr8:19113394-19121923:0;chr8:19121924-20274088:1;chr8:20274089-20280941:0;chr8:20280942-27856331:1;chr8:2290040-2292023:0;chr8:2292024-4219116:1;chr8:27856332-27858736:0;chr8:27858737-27875050:-1;chr8:27875051-27875619:0;chr8:27875620-30455200:1;chr8:30455201-30462148:0;chr8:30462149-50115532:1;chr8:4219117-4225232:0;chr8:4225233-5172992:1;chr8:50115533-50125077:0;chr8:50125078-51988578:1;chr8:5172993-5182238:0;chr8:5182239-5818128:1;chr8:51988579-51996074:0;chr8:51996075-61979873:1;chr8:5818129-5823185:0;chr8:5823186-11147123:1;chr8:61979874-62000238:0;chr8:62000239-69996372:1;chr8:69996373-70049903:0;chr8:70049904-75239978:1;chr8:75239979-75242410:0;chr8:75242411-77539322:1;chr8:77539323-77718818:0;chr8:77718819-79654145:1;chr8:79654146-80519540:0;chr8:80519541-83265571:1;chr8:83265572-83292294:0;chr8:83292295-90372173:1;chr8:90372174-90520648:0;chr8:90520649-105810397:1;chr9:0-8227100:0;chr9:104443319-107760227:1;chr9:107760228-119939388:0;chr9:119939389-119955982:-1;chr9:119955983-125254954:0;chr9:125254955-125257838:-1;chr9:125257839-141213431:0;chr9:13458524-22159981:0;chr9:22159982-26178732:1;chr9:26178733-28420019:0;chr9:28420020-31856797:1;chr9:31856798-31868611:0;chr9:31868612-31892857:1;chr9:31892858-90051390:0;chr9:8227101-13458523:1;chr9:90051391-90095024:1;chr9:90095025-104443318:0;chrX:0-155270560:0;chrY:0-59373566:0		ADAD1;ADH1A;ADH1B;ADH1C;ADH4;ADH5;ADH6;ADH7;AGA;AGXT2L1;AIMP1;ALPK1;ANKRD50;ANXA5;AP1AR;ARAP2;ARHGEF38;ARSJ;ASCC3;ATOH1;BANK1;BBS12;BBS7;BDH2;BMPR1B;C4orf17;C4orf21;C4orf29;C4orf3;C4orf32;C4orf33;C4orf37;C6orf168;C6orf170;CAMK2D;CASP6;CCDC109B;CCNA2;CCNC;CENPC1;CENPE;CEP170P1;CFI;CISD2;CLVS2;COL25A1;COQ3;COX7B2;CXXC4;CYP2U1;DAPP1;DDIT4L;DKK2;DNAJB14;EEF1E1;EEF1E1-MUTED;EGF;EIF4E;ELMOD2;ELOVL6;EMCN;ENPEP;EPHA5;EPHA7;EXOSC9;FABP2;FABP7;FAM190A;FAT4;FBXL4;FGF2;FHL5;FLJ20021;FTLP10;FUT9;GABRA2;GABRA4;GABRG1;GAR1;GJA1;GNPDA2;GNRHR;GPR63;GRID2;GRIK2;GSTCD;GUF1;H2AFZ;HADH;HPGDS;HSF2;HSPA4L;IL15;IL2;IL21;INPP4B;INTS12;INTU;KCTD8;KHDRBS2;KIAA1109;KLHL32;LAMTOR3;LARP1B;LARP7;LEF1;LGSN;LOC100130890;LOC100507096;LOC285456;LOC285501;LOC550112;LOC641518;LPHN3;LRIT3;MAD2L1;MANBA;MANEA;MAP3K7;MCHR2;METAP1;METTL14;MFSD8;MIR1243;MIR1305;MIR2054;MIR2113;MIR302A;MIR302B;MIR302C;MIR302D;MIR3668;MIR367;MIR3684;MIR4275;MIR4465;MIR4643;MIR577;MMS22L;MTRNR2L9;MTTP;MUTED;MYOZ2;NDNF;NDST3;NDST4;NDUFAF4;NEIL3;NEUROG2;NFKB1;NPNT;NUDT6;OSTC;PABPC4L;PAPSS1;PCDH10;PCDH18;PCDH7;PDE5A;PDHA2;PDLIM5;PGRMC2;PHF17;PHF3;PIP5K1P1;PITX2;PKIB;PLA2G12A;PLK4;PNISR;POU3F2;PP12613;PPA2;PPP3CA;PRDM13;PRDM5;PRSS12;PTP4A1;QRFPR;RAP1GDS1;RG9MTD2;RNF150;RPL34;RRH;SCLT1;SEC24B;SEC24D;SERINC1;SGMS2;SIM1;SLC25A31;SLC35B3;SLC39A8;SLC9B1;SLC9B2;SMARCAD1;SMPDL3A;SNHG8;SPATA5;SPRY1;STAP1;SYNPO2;SYT14L;TACR3;TBC1D9;TBCK;TECRL;TET2;TMEM155;TMPRSS11A;TMPRSS11B;TMPRSS11BNL;TMPRSS11D;TMPRSS11F;TNIP3;TRAM1L1;TRDN;TRPC3;TSPAN5;UBA6;UBE2D3;UCP1;UFL1;UGT2A1;UGT2A2;UGT2A3;UGT2B15;UGT2B17;UGT2B4;UGT2B7;UGT8;UNC5C;USP45;USP53;VEGFC;YIPF7;YTHDC1;ZNF330;	European Institute of Oncology (IEO), Department of Experimental Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy 	Hepatocellular carcinoma (HCC) is almost invariably associated with an underlying inflammatory state, whose direct contribution to the acquisition of critical genomic changes is unclear. Here we map acquired genomic alterations in human and mouse HCCs induced by defects in hepatocyte biliary transporters, which expose hepatocytes to bile salts and cause chronic inflammation that develops into cancer. In both human and mouse cancer genomes, we find few somatic point mutations with no impairment of cancer genes, but massive gene amplification and rearrangements. This genomic landscape differs from that of virus- and alcohol-associated liver cancer. Copy-number gains preferentially occur at late stages of cancer development and frequently target the MAPK signalling pathway, and in particular direct regulators of JNK. The pharmacological inhibition of JNK retards cancer progression in the mouse. Our study demonstrates that intrahepatic cholestasis leading to hepatocyte exposure to bile acids and inflammation promotes cancer through genomic modifications that can be distinguished from those determined by other aetiological factors. 	GRCh37/hg19				Yes	NA
CTDB0355	Research	25625332	Castro-Vega LJ, Letouze E, Burnichon N, Buffet A, Disderot PH, Khalifa E, Loriot C, Elarouci N, Morin A, Menara M, Lepoutre-Lussey C, Badoual C, Sibony M, Dousset B, Libe R, Zinzindohoue F, Plouin PF, Bertherat J, Amar L, de Reynies A, Favier J, Gimenez-Roqueplo AP	Multi-omics analysis defines core genomic alterations in pheochromocytomas and paragangliomas	Nature Communications	2015 Jan 	1,5,17	Pheochromocytomas and paragangliomas	SNP Array	Homo sapiens	37	Illumina HumanCNV610-Quad v1.0. Hybridization				INSERM, UMR970, Paris-Cardiovascular Research Center, F-75015 Paris, France 	Pheochromocytomas and paragangliomas (PCCs/PGLs) are neural crest-derived tumours with a very strong genetic component. Here we report the first integrated genomic examination of a large collection of PCC/PGL. SNP array analysis reveals distinct copy-number patterns associated with genetic background. Whole-exome sequencing shows a low mutation rate of 0.3 mutations per megabase, with few recurrent somatic mutations in genes not previously associated with PCC/PGL. DNA methylation arrays and miRNA sequencing identify DNA methylation changes and miRNA expression clusters strongly associated with messenger RNA expression profiling. Overexpression of the miRNA cluster 182/96/183 is specific in SDHB-mutated tumours and induces malignant traits, whereas silencing of the imprinted DLK1-MEG3 miRNA cluster appears as a potential driver in a subgroup of sporadic tumours. Altogether, the complete genomic landscape of PCC/PGL is mainly driven by distinct germline and/or somatic mutations in susceptibility genes and reveals different molecular entities, characterized by a set of unique genomic alterations. 	GRCh37/hg19				Yes	NA
CTDB0356	Research	25625332	Castro-Vega LJ, Letouze E, Burnichon N, Buffet A, Disderot PH, Khalifa E, Loriot C, Elarouci N, Morin A, Menara M, Lepoutre-Lussey C, Badoual C, Sibony M, Dousset B, Libe R, Zinzindohoue F, Plouin PF, Bertherat J, Amar L, de Reynies A, Favier J, Gimenez-Roqueplo AP	Multi-omics analysis defines core genomic alterations in pheochromocytomas and paragangliomas	Nature Communications	2015 Jan 	1,5,17	Pheochromocytomas and paragangliomas	SNP Array	Homo sapiens	49	Illumina HumanCNV610-Quad v1.0. Hybridization				INSERM, UMR970, Paris-Cardiovascular Research Center, F-75015 Paris, France 	Pheochromocytomas and paragangliomas (PCCs/PGLs) are neural crest-derived tumours with a very strong genetic component. Here we report the first integrated genomic examination of a large collection of PCC/PGL. SNP array analysis reveals distinct copy-number patterns associated with genetic background. Whole-exome sequencing shows a low mutation rate of 0.3 mutations per megabase, with few recurrent somatic mutations in genes not previously associated with PCC/PGL. DNA methylation arrays and miRNA sequencing identify DNA methylation changes and miRNA expression clusters strongly associated with messenger RNA expression profiling. Overexpression of the miRNA cluster 182/96/183 is specific in SDHB-mutated tumours and induces malignant traits, whereas silencing of the imprinted DLK1-MEG3 miRNA cluster appears as a potential driver in a subgroup of sporadic tumours. Altogether, the complete genomic landscape of PCC/PGL is mainly driven by distinct germline and/or somatic mutations in susceptibility genes and reveals different molecular entities, characterized by a set of unique genomic alterations. 	GRCh37/hg19				Yes	NA
CTDB0357	Research	25625332	Castro-Vega LJ, Letouze E, Burnichon N, Buffet A, Disderot PH, Khalifa E, Loriot C, Elarouci N, Morin A, Menara M, Lepoutre-Lussey C, Badoual C, Sibony M, Dousset B, Libe R, Zinzindohoue F, Plouin PF, Bertherat J, Amar L, de Reynies A, Favier J, Gimenez-Roqueplo AP	Multi-omics analysis defines core genomic alterations in pheochromocytomas and paragangliomas	Nature Communications	2015 Jan 	1,5,17	Pheochromocytomas and paragangliomas	SNP Array	Homo sapiens	188	Illumina HumanCNV610-Quad v1.0. Hybridization				INSERM, UMR970, Paris-Cardiovascular Research Center, F-75015 Paris, France 	Pheochromocytomas and paragangliomas (PCCs/PGLs) are neural crest-derived tumours with a very strong genetic component. Here we report the first integrated genomic examination of a large collection of PCC/PGL. SNP array analysis reveals distinct copy-number patterns associated with genetic background. Whole-exome sequencing shows a low mutation rate of 0.3 mutations per megabase, with few recurrent somatic mutations in genes not previously associated with PCC/PGL. DNA methylation arrays and miRNA sequencing identify DNA methylation changes and miRNA expression clusters strongly associated with messenger RNA expression profiling. Overexpression of the miRNA cluster 182/96/183 is specific in SDHB-mutated tumours and induces malignant traits, whereas silencing of the imprinted DLK1-MEG3 miRNA cluster appears as a potential driver in a subgroup of sporadic tumours. Altogether, the complete genomic landscape of PCC/PGL is mainly driven by distinct germline and/or somatic mutations in susceptibility genes and reveals different molecular entities, characterized by a set of unique genomic alterations. 	GRCh37/hg19				Yes	NA
CTDB0372	Research	26031834	Norris AL, Kamiyama H, Makohon-Moore A, Pallavajjala A, Morsberger LA, Lee K, Batista D, Iacobuzio-Donahue CA, Lin MT, Klein AP, Hruban RH, Wheelan SJ, Eshleman JR	Transflip mutations produce deletions in pancreatic cancer	Genes, Chromosomes & Cancer	2015 May 	9,18	Pancreatic cancer	SNP Array	Homo sapiens	Pa102C	Illumina Omni2.5 array			C18orf54;CCDC68;DCC;DYNAP;ELAC1;FAM75D1;LINC01539;LOC101927273;MAPK4;MBD2;ME2;MEX3C;MIR4529;MRO;POLI;RAB27B;SMAD4;SNORA37;STARD6;TCF4;	Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, 21231	Pancreatic ductal adenocarcinoma (PDAC) is driven by the inactivation of the tumor suppressor genes (TSGs), CDKN2A (P16) and SMAD4 (DPC4), commonly by homozygous deletions (HDs). Using a combination of high density single-nucleotide polymorphism (SNP) microarray and whole genome sequencing (WGS), we fine-mapped novel breakpoints surrounding deletions of CDKN2A and SMAD4 and characterized them by their underlying structural variants (SVs). Only one third of CDKN2A and SMAD4 deletions (6 of 18) were simple interstitial deletions, rather, the majority of deletions were caused by complex rearrangements, specifically, a translocation on one side of the TSG in combination with an inversion on the other side. We designate these as TransFlip mutations. Characteristics of TransFlip mutations are: (1) a propensity to target the TSGs CDKN2A and SMAD4 (P < 0.005), (2) not present in the germline of the examined samples, (3) non-recurrent breakpoints, (4) relatively small (47 bp to 3.4 kb) inversions, (5) inversions can be either telomeric or centromeric to the TSG, and (6) non-reciprocal, and non-recurrent translocations. TransFlip mutations are novel complex genomic rearrangements with unique breakpoint signatures in pancreatic cancer. We hypothesize that they are a common but poorly understood mechanism of TSG inactivation in human cancer.	GRCh37/hg19				Yes	NA
CTDB0373	Research	26031834	Norris AL, Kamiyama H, Makohon-Moore A, Pallavajjala A, Morsberger LA, Lee K, Batista D, Iacobuzio-Donahue CA, Lin MT, Klein AP, Hruban RH, Wheelan SJ, Eshleman JR	Transflip mutations produce deletions in pancreatic cancer	Genes, Chromosomes & Cancer	2015 May 	18	Pancreatic cancer	SNP Array	Homo sapiens	Pa227C	Illumina Omni2.5 array			C18orf54;CCDC68;DCC;DYNAP;ELAC1;MBD2;ME2;MEX3C;POLI;RAB27B;SMAD4;SNORA37;STARD6;TCF4;	Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, 21231	Pancreatic ductal adenocarcinoma (PDAC) is driven by the inactivation of the tumor suppressor genes (TSGs), CDKN2A (P16) and SMAD4 (DPC4), commonly by homozygous deletions (HDs). Using a combination of high density single-nucleotide polymorphism (SNP) microarray and whole genome sequencing (WGS), we fine-mapped novel breakpoints surrounding deletions of CDKN2A and SMAD4 and characterized them by their underlying structural variants (SVs). Only one third of CDKN2A and SMAD4 deletions (6 of 18) were simple interstitial deletions, rather, the majority of deletions were caused by complex rearrangements, specifically, a translocation on one side of the TSG in combination with an inversion on the other side. We designate these as TransFlip mutations. Characteristics of TransFlip mutations are: (1) a propensity to target the TSGs CDKN2A and SMAD4 (P < 0.005), (2) not present in the germline of the examined samples, (3) non-recurrent breakpoints, (4) relatively small (47 bp to 3.4 kb) inversions, (5) inversions can be either telomeric or centromeric to the TSG, and (6) non-reciprocal, and non-recurrent translocations. TransFlip mutations are novel complex genomic rearrangements with unique breakpoint signatures in pancreatic cancer. We hypothesize that they are a common but poorly understood mechanism of TSG inactivation in human cancer.	GRCh37/hg19				Yes	NA
CTDB0383	Research	22833442	Stevens-Kroef M, Weghuis DO, Croockewit S, Derksen L, Hooijer J, Elidrissi-Zaynoun N, Siepman A, Simons A, Kessel AG	High detection rate of clinically relevant genomic abnormalities in plasma cells enriched from patients with multiple myeloma	Genes, Chromosomes & Cancer	2012 Nov	13	Multiple myeloma	SNP Array	Homo sapiens	case 34	Affymetrix GeneChip 250k				Department of Human Genetics, Radboud University Nijmegen Medical Centre, The Netherlands	Multiple myeloma is a heterogeneous disease, which is characterized by the occurrence of specific genomic abnormalities that are both of diagnostic and prognostic relevance. Since the detection of these abnormalities through molecular-genetic techniques is hampered by the overall low percentage of plasma cells present in primary bone marrow aspirates, we assessed the efficacy of these techniques in enriched plasma cell fractions from 61 multiple myeloma patients. Using interphase FISH, genomic abnormalities could be detected in 96% of the enriched samples as compared to 61% in the cultured whole bone marrow samples. We also found that microarray-based genomic profiling of enriched plasma samples facilitates the detection of additional, possibly clinically relevant, genomic abnormalities. We conclude that the genomic delineation of enriched plasma cells from multiple myeloma patients results in a significantly increased detection rate of clinically relevant genomic abnormalities. In order to facilitate molecular-genetic data interpretation, we recommend morphological assessment of plasma cell purity after enrichment.					Yes	NA
CTDB0400	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_100246	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0401	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_100221	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0402	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_100171	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0403	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_100161	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0404	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_100229	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0405	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_100241	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0406	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_90150	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0407	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_90892	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0408	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_90769	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0409	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_90779	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0410	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_100187	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0411	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_90123	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA
CTDB0412	Research	25770156	Watkins J, Weekes D, Shah V, Gazinska P, Joshi S, Sidhu B, Gillett C, Pinder S, Vanoli F, Jasin M, Mayrhofer M, Isaksson A, Cheang MC, Mirza H, Frankum J, Lord CJ, Ashworth A, Vinayak S, Ford JM, Telli ML, Grigoriadis A, Tutt AN	Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers	Cancer Discovery	2015 May	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X	Breast cancer	SNP Array	Homo sapiens	P_90178	Affymetrix SNP6.0				Breakthrough Breast Cancer Research Unit, King's College London, London, United Kingdom	Triple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC. SIGNIFICANCE: Previous studies have shown correlation between mutational scars and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such scars and expression of meiotic genes as predictive biomarkers. 		GSE40267			Yes	NA