StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	24304937	MA Jacoby, RE De Jesus Pizarro, J Shao, DC Koboldt, RS Fulton, G Zhou, RK Wilson, MJ Walter	The DNA double-strand break response is abnormal in myeloblasts from patients with therapy-related acute myeloid leukemia	Leukemia	2013 Dec	3,7	Acute myeloid leukemia	Array CGH	Homo sapiens	189941	NimbleGen custom 2x720K array	chr12:11708326-22796431:-1;chr17:7517325-7518692:-1;chr3:103782198-106696566:-1;chr3:11079219-12582443:-1;chr3:113846696-114463826:-1;chr3:123948788-124132968:-1;chr3:169461120-170271699:-1;chr3:170375166-171616698:-1;chr3:171702102-173816191:-1;chr4:12024504-13146333:-1;chr5:105204558-180814163:-1;chr5:94263666-103717142:-1;chr7:18448564-19027294:-1;chr7:26521475-56468938:-1;chr7:62090285-70977718:-1;chr7:78426592-81535151:-1;chr7:81940100-87814558:-1;chr7:89133633-158816035:-1		TP53	Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO, USA	The complex chromosomal aberrations found in therapy-related acute myeloid leukemia (t-AML) suggest that the DNA double-strand break (DSB) response may be altered. In this study we examined the DNA DSB response of primary bone marrow cells from t-AML patients and performed next-generation sequencing of 37 canonical homologous recombination (HR) and non-homologous end-joining (NHEJ) DNA repair genes, and a subset of DNA damage response genes using tumor and paired normal DNA obtained from t-AML patients. Our results suggest that the majority of t-AML patients (11 of 15) have tumor-cell intrinsic, functional dysregulation of their DSB response. Distinct patterns of abnormal DNA damage response in myeloblasts correlated with acquired genetic alterations in TP53 and the presence of inferred chromothripsis. Furthermore, the presence of trisomy 8 in tumor cells was associated with persistently elevated levels of DSBs. Although tumor-acquired point mutations or small indels in canonical HR and NHEJ genes do not appear to be a dominant means by which t-AML leukemogenesis occurs, our functional studies suggest that an abnormal response to DNA damage is a common finding in t-AML.		GSE53250		PRJEB8343	Yes	NA
Research	24304937	MA Jacoby, RE De Jesus Pizarro, J Shao, DC Koboldt, RS Fulton, G Zhou, RK Wilson, MJ Walter	The DNA double-strand break response is abnormal in myeloblasts from patients with therapy-related acute myeloid leukemia	Leukemia	2013 Dec	3	Acute myeloid leukemia	Array CGH	Homo sapiens	530447	NimbleGen custom 2x720K array	chr21:31315314-46915712:1;chr22:14735065-49565939:1;chr3:142706131-150187585:-1;chr3:156299137-199381715:-1;chr3:20043408-31915861:-1;chr3:35197820-38538003:-1;chr3:41756417-48479360:-1;chr3:62156517-69781020:-1;chr3:69795134-75771557:-1;chr3:79933983-99089183:-1;chr5:55790692-67822695:-1;chr5:70841242-180593129:-1;chr7:22509353-57453201:-1;chr7:77985837-158816035:-1;chr9:28278165-29708951:-1		TP53	Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO, USA	The complex chromosomal aberrations found in therapy-related acute myeloid leukemia (t-AML) suggest that the DNA double-strand break (DSB) response may be altered. In this study we examined the DNA DSB response of primary bone marrow cells from t-AML patients and performed next-generation sequencing of 37 canonical homologous recombination (HR) and non-homologous end-joining (NHEJ) DNA repair genes, and a subset of DNA damage response genes using tumor and paired normal DNA obtained from t-AML patients. Our results suggest that the majority of t-AML patients (11 of 15) have tumor-cell intrinsic, functional dysregulation of their DSB response. Distinct patterns of abnormal DNA damage response in myeloblasts correlated with acquired genetic alterations in TP53 and the presence of inferred chromothripsis. Furthermore, the presence of trisomy 8 in tumor cells was associated with persistently elevated levels of DSBs. Although tumor-acquired point mutations or small indels in canonical HR and NHEJ genes do not appear to be a dominant means by which t-AML leukemogenesis occurs, our functional studies suggest that an abnormal response to DNA damage is a common finding in t-AML.		GSE53250		PRJEB8343	Yes	NA
Research	24304937	MA Jacoby, RE De Jesus Pizarro, J Shao, DC Koboldt, RS Fulton, G Zhou, RK Wilson, MJ Walter	The DNA double-strand break response is abnormal in myeloblasts from patients with therapy-related acute myeloid leukemia	Leukemia	2013 Dec	8	Acute myeloid leukemia	Array CGH	Homo sapiens	377512	NimbleGen custom 2x720K array	chr11:128800686-130257349:1;chr11:94227338-94952730:1;chr15:18422770-22846333:-1;chr2:236856627-241034230:-1;chr5:55540994-56620186:-1;chr5:93926699-158579837:-1;chr7:100907744-158816035:-1;chr8:110969199-116510809:1;chr8:116520326-120009329:-1;chr8:120983709-128749745:1;chr8:128750703-129002866:-1;chr8:129007972-129285458:1;chr8:129221549-130450443:-1;chr8:130456187-133444071:1;chr8:133476865-142859461:-1;chr8:16975-32351253:1;chr8:80504328-80762667:-1;chr8:80768366-84206585:1;chr8:86369737-87949326:1;chr8:90475849-108195805:1		TP53	Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO, USA	The complex chromosomal aberrations found in therapy-related acute myeloid leukemia (t-AML) suggest that the DNA double-strand break (DSB) response may be altered. In this study we examined the DNA DSB response of primary bone marrow cells from t-AML patients and performed next-generation sequencing of 37 canonical homologous recombination (HR) and non-homologous end-joining (NHEJ) DNA repair genes, and a subset of DNA damage response genes using tumor and paired normal DNA obtained from t-AML patients. Our results suggest that the majority of t-AML patients (11 of 15) have tumor-cell intrinsic, functional dysregulation of their DSB response. Distinct patterns of abnormal DNA damage response in myeloblasts correlated with acquired genetic alterations in TP53 and the presence of inferred chromothripsis. Furthermore, the presence of trisomy 8 in tumor cells was associated with persistently elevated levels of DSBs. Although tumor-acquired point mutations or small indels in canonical HR and NHEJ genes do not appear to be a dominant means by which t-AML leukemogenesis occurs, our functional studies suggest that an abnormal response to DNA damage is a common finding in t-AML.		GSE53250		PRJEB8343	Yes	NA