GEO DataSets

(Submitter supplied) Chromothripsis represents a novel phenomenon in the structural variation landscape of cancer genomes. Here, we analyzed the genomes of ten patients with congenital disease that were preselected to carry complex chromosomal rearrangements (CCRs) with more than two breakpoints. The rearrangements displayed unanticipated complexity resembling chromothripsis. We find that eight of them contain hallmarks of multiple clustered double-stranded DNA breaks (DSBs) on one or more chromosomes. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL8855 GPL6979 GPL6985

13 Samples

Download data: TXT

(Submitter supplied) Human eggs were fertilized with sperm carrying a homozygous mutation in the EYS gene at rs758109813 and treated with a Cas9 RNP targeting this mutation at either fertilization or at the 2-cell stage. The purpose of this analysis was to determine loss of heterozygosity due to CRISPR-induced chromosomal changes. We find that However, in half of the embryos, the break remains unrepaired throughout the first cell cycle, resulting in both segmental, as well as whole chromosome loss. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL28377

135 Samples

Download data: CEL, TXT

(Submitter supplied) Unbalanced translocations are a relatively common type of copy number variation and are a major contributor to neurodevelopmental disorders. We analyzed the breakpoints of 57 unique unbalanced translocations to investigate the mechanisms of how they form. 51 are simple unbalanced translocations between two different chromosome ends, and six rearrangements have more than three breakpoints involving two to five chromosomes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

7 related Platforms

57 Samples

Download data: TXT

(Submitter supplied) Structural rearrangements form a major class of somatic variation in cancer genomes. Local chromosome shattering, termed chromothripsis, is a mechanism proposed to be the cause of clustered chromosomal rearrangements and was recently described to occur in a small percentage of tumors. The significance of these clusters for tumor development or metastatic spread is largely unclear. We used genome-wide long mate-pair sequencing and SNP array profiling to reveal that chromothripsis is a widespread phenomenon in primary colorectal cancer and metastases. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL8855

16 Samples

Download data: TXT

(Submitter supplied) Small ~10 kb microhomology-mediated tandem duplications (“Group 1 TDs”) are abundant in BRCA1-linked but not BRCA2-linked breast cancer genomes. Here, we define the mechanism underlying this rearrangement signature. We show that BRCA1, but not BRCA2, suppresses TDs at a Tus/Ter site-specific chromosomal replication fork barrier in primary mammalian cells. BRCA1 has no equivalent role at chromosomal double strand breaks, indicating specificity for the stalled fork response. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

25 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16791

16 Samples

Download data: BED, NARROWPEAK, TXT

(Submitter supplied) Cancer genomes are characterized by accumulation of small-scale somatic mutations as well as large-scale chromosomal deletions, amplifications, and complex structural rearrangements. This characteristic is at least partially dependent on the ability of cancer cells to undergo recurrent chromosome breakage. In order to address to what extent chromosomal structural rearrangement breakpoints correlate with recurrent DNA double strand breaks (DSBs), we simultaneously mapped chromosome structural variation breakpoints by whole genome DNA-seq and spontaneous DSB formation by Break-seq in the breast cancer cell line MCF-7 and a non-cancer control cell line MCF-10A. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

10 Samples

Download data: NARROWPEAK

(Submitter supplied) Cancer genomes are characterized by accumulation of small-scale somatic mutations as well as large-scale chromosomal deletions, amplifications, and complex structural rearrangements. This characteristic is at least partially dependent on the ability of cancer cells to undergo recurrent chromosome breakage. In order to address to what extent chromosomal structural rearrangement breakpoints correlate with recurrent DNA double strand breaks (DSBs), we simultaneously mapped chromosome structural variation breakpoints by whole genome DNA-seq and spontaneous DSB formation by Break-seq in the breast cancer cell line MCF-7 and a non-cancer control cell line MCF-10A. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

2 Samples

Download data: BED, TXT

(Submitter supplied) Cancer genomes are characterized by accumulation of small-scale somatic mutations as well as large-scale chromosomal deletions, amplifications, and complex structural rearrangements. This characteristic is at least partially dependent on the ability of cancer cells to undergo recurrent chromosome breakage. In order to address to what extent chromosomal structural rearrangement breakpoints correlate with recurrent DNA double strand breaks (DSBs), we simultaneously mapped chromosome structural variation breakpoints by whole genome DNA-seq and spontaneous DSB formation by Break-seq in the breast cancer cell line MCF-7 and a non-cancer control cell line MCF-10A. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platforms:

GPL26057 GPL26058 GPL26059

126 Samples

Download data: TXT

(Submitter supplied) Human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used orthogonal long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. For non-recurrent events we found microhomology and microhomeology at the breakpoint junctions, an excess of deletion rearrangements on paternally-derived haplotypes, and elucidated recalcitrant breakpoints. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL26059

71 Samples

Download data: TXT

(Submitter supplied) Human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used orthogonal long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. For non-recurrent events we found microhomology and microhomeology at the breakpoint junctions, an excess of deletion rearrangements on paternally-derived haplotypes, and elucidated recalcitrant breakpoints. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL26058

24 Samples

Download data: TXT

(Submitter supplied) Human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used orthogonal long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. For non-recurrent events we found microhomology and microhomeology at the breakpoint junctions, an excess of deletion rearrangements on paternally-derived haplotypes, and elucidated recalcitrant breakpoints. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL26057

31 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array; Genome variation profiling by genome tiling array

Platforms:

GPL6985 GPL19718 GPL8693

10 Samples

Download data: TXT

(Submitter supplied) Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a mother to her child. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8693

3 Samples

Download data: TXT

(Submitter supplied) Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a female carrier to her child. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL6985

2 Samples

Download data: TXT

(Submitter supplied) Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a mother to her child. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL19718

5 Samples

Download data: TXT

(Submitter supplied) The structure of broken DNA ends is a critical determinant of the pathway used for DNA double strand break (DSB) repair. Here, we develop an approach, hairpin capture of DNA end structures (HCoDES), which elucidates chromosomal DNA end structures at single nucleotide resolution. HCoDES defines structures of physiologic DSBs generated by the RAG endonuclease, as well as those generated by nucleases widely used for genome editing. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

98 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL19705 GPL19706

12 Samples

Download data: TXT

(Submitter supplied) The goal of this experiment was to determine the size, genomic extent and gene content of complex rearrangements involving chromosome 9q

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19706

3 Samples

Download data: TXT