StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	27880765	Gu S, Szafranski P, Akdemir ZC, Yuan B, Cooper ML, Magrina MA, Bacino CA, Lalani SR, Breman AM, Smith JL, Patel A, Song RH, Bi W, Cheung SW, Carvalho CM, Stankiewicz P, Lupski JR	Mechanisms for Complex Chromosomal Insertions	PLoS Genet	2016 Nov	6	Individuals with complex chromosome insertions	Array CGH	Homo sapiens	Cplex5	Agilent 4 x 180K oligonucleotide arrays	chr6:111061823-112340466):1;chr6:143001529-143306155):-1;chr6:151111676-159718163):-1			Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America	Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue, constituting ~2% of nonrecurrent copy-number gains. Little is known about the molecular mechanisms of their formation. We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on 10 individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing in 6 individuals to glean insights into potential mechanisms of formation. We observed microhomologies and templated insertions at the breakpoint junctions, resembling the breakpoint junction signatures found in complex genomic rearrangements generated by replication-based mechanism(s) with iterative template switches. In addition, we analyzed 5 families with apparently balanced insertion in one parent detected by FISH analysis and found that 3 parents had additional small copy-number variants (CNVs) at one or both sides of the inserting fragments as well as at the inserted sites. We propose that replicative repair can result in interchromosomal complex insertions generated through chromothripsis-like chromoanasynthesis involving two or three chromosomes, and cause a significant fraction of apparently balanced insertions harboring small flanking CNVs.	GRCh37/hg19	GSE89306			Unknow	
Research	27880765	Gu S, Szafranski P, Akdemir ZC, Yuan B, Cooper ML, Magrina MA, Bacino CA, Lalani SR, Breman AM, Smith JL, Patel A, Song RH, Bi W, Cheung SW, Carvalho CM, Stankiewicz P, Lupski JR	Mechanisms for Complex Chromosomal Insertions	PLoS Genet	2016 Nov	X	Individuals with complex chromosome insertions	Array CGH	Homo sapiens	Cplex6	Agilent 4 x 180K oligonucleotide arrays	chrX:0-153354257:0;chrX:153354258-153505599:1;chrX:153400494-153406246:2;chrX:153505600-155270560:0			Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America	Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue, constituting ~2% of nonrecurrent copy-number gains. Little is known about the molecular mechanisms of their formation. We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on 10 individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing in 6 individuals to glean insights into potential mechanisms of formation. We observed microhomologies and templated insertions at the breakpoint junctions, resembling the breakpoint junction signatures found in complex genomic rearrangements generated by replication-based mechanism(s) with iterative template switches. In addition, we analyzed 5 families with apparently balanced insertion in one parent detected by FISH analysis and found that 3 parents had additional small copy-number variants (CNVs) at one or both sides of the inserting fragments as well as at the inserted sites. We propose that replicative repair can result in interchromosomal complex insertions generated through chromothripsis-like chromoanasynthesis involving two or three chromosomes, and cause a significant fraction of apparently balanced insertions harboring small flanking CNVs.	GRCh37/hg19	GSE89306			Unknow	
Research	27880765	Gu S, Szafranski P, Akdemir ZC, Yuan B, Cooper ML, Magrina MA, Bacino CA, Lalani SR, Breman AM, Smith JL, Patel A, Song RH, Bi W, Cheung SW, Carvalho CM, Stankiewicz P, Lupski JR	Mechanisms for Complex Chromosomal Insertions	PLoS Genet	2016 Nov	13,X	Individuals with complex chromosome insertions	Array CGH	Homo sapiens	Cplex11	Agilent 4 x 180K oligonucleotide arrays	chr13:0-111923013:0;chr13:10617231-107784175:2;chr13:109760818-110923670:2;chr13:111923014-113766342:-1;chr13:113766343-115169878:0;chrX:0-79677006:0;chrX:79677007-80247351:1;chrX:80247352-81758343:0;chrX:81758344-84170318:1;chrX:82128724-82575149:2;chrX:84170319-155270560:0			Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America	Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue, constituting ~2% of nonrecurrent copy-number gains. Little is known about the molecular mechanisms of their formation. We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on 10 individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing in 6 individuals to glean insights into potential mechanisms of formation. We observed microhomologies and templated insertions at the breakpoint junctions, resembling the breakpoint junction signatures found in complex genomic rearrangements generated by replication-based mechanism(s) with iterative template switches. In addition, we analyzed 5 families with apparently balanced insertion in one parent detected by FISH analysis and found that 3 parents had additional small copy-number variants (CNVs) at one or both sides of the inserting fragments as well as at the inserted sites. We propose that replicative repair can result in interchromosomal complex insertions generated through chromothripsis-like chromoanasynthesis involving two or three chromosomes, and cause a significant fraction of apparently balanced insertions harboring small flanking CNVs.	GRCh37/hg19	GSE89306			Unknow