StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	22388000	Chiang C, Jacobsen JC, Ernst C, Hanscom C, Heilbut A, Blumenthal I, Mills RE, Kirby A, Lindgren AM, Rudiger SR, McLaughlan CJ, Bawden CS, Reid SJ, Faull RL, Snell RG, Hall IM, Shen Y, Ohsumi TK, Borowsky ML, Daly MJ, Lee C, Morton CC, MacDonald ME, Gusella JF, Talkowski ME	Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration.	Nat Genet	2012 Mar	5,X	Germline	Next Generation Sequencing	Homo sapiens	BSID42	Illumina HiSeq 2000		hsX:110368673-110368673,hs5:90466028-90466028;hs5:90502468-90502468,hsX:130567294-130567294;hs5:90711091-90711091,hs5:90892029-90892029;hs5:90892144-90892144,hsX:131442883-131442883;hsX:110368663-110368663,hs5:90719199-90719199;hsX:131438029-131438029,hs5:92483810-92483810;hs5:90494025-90494025,hs5:90892027-90892027;hs5:90494024-90494024,hs5:90502468-90502468;hs5:90691787-90691787,hs5:90886192-90886192;hs5:92932823-92932823,hs5:90693163-90693163;hs5:92483805-92483805,hs5:90719148-90719148;hs5:90892142-90892142,hs5:90466010-90466010;hs5:90886193-90886193,hs5:92932823-92932823;hsX:130567294-130567294,hs5:90711016-90711016		Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA	We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations.	GRCh37/hg19				No	NA
Research	22388000	Chiang C, Jacobsen JC, Ernst C, Hanscom C, Heilbut A, Blumenthal I, Mills RE, Kirby A, Lindgren AM, Rudiger SR, McLaughlan CJ, Bawden CS, Reid SJ, Faull RL, Snell RG, Hall IM, Shen Y, Ohsumi TK, Borowsky ML, Daly MJ, Lee C, Morton CC, MacDonald ME, Gusella JF, Talkowski ME	Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration.	Nat Genet	2012 Mar	3,5,7	Germline	Next Generation Sequencing	Homo sapiens	BSID43	Illumina HiSeq 2000		hs3:155627600-155627600,hs7:120004011-120004011;hs7:119889673-119889673,hs3:155627601-155627601;hs3:152159406-152159406,hs7:119999922-119999922;hs7:120765008-120765008,hs3:152159406-152159406;hs7:119646830-119646830,hs7:120254239-120254239;hs7:119889690-119889690,hs7:119646829-119646829;hs7:119995774-119995774,hs7:119999919-119999919;hs7:122606556-122606556,hs7:120254240-120254240;hs5:87073891-87073891,hs7:119995778-119995778;hs7:122606486-122606486,hs5:87073908-87073908;hs7:120004010-120004010,hs7:120766450-120766450		Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA	We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations.	GRCh37/hg19				No	NA