GEO DataSets

(Submitter supplied) We describe a multiple de novo CNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional de novo CNVs. Five such families are studied, which consists of four trios and one singleton. Various array platforms are used to interogate these families to identify de novo CNVs.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL8882 GPL21135

13 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

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

8 related Platforms

52 Samples

Download data: CEL, CYCHP, GFF, IDAT, PAIR, TXT

(Submitter supplied) We describe a multiple de novo CNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional de novo CNVs. Five such families are studied, which consists of four trios and one singleton. Various array platforms are used to interogate these families to identify de novo CNVs.

Organism:

Homo sapiens

Type:

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

4 related Platforms

25 Samples

Download data: TXT

(Submitter supplied) We describe a multiple de novo CNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional de novo CNVs. Five such families are studied, which consists of four trios and one singleton. Various array platforms are used to interogate these families to identify de novo CNVs.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL15746

9 Samples

Download data: GFF, PAIR

(Submitter supplied) We describe a multiple de novo CNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional de novo CNVs. Five such families are studied, which consists of four trios and one singleton. Various array platforms are used to interogate these families to identify de novo CNVs.

Organism:

Homo sapiens

Type:

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

Platform:

GPL16131

5 Samples

Download data: CEL, CYCHP

(Submitter supplied) Purpose: To determine the genetic variation underlying phenotypic trait manifestation in a Multiple de novo copy number variant (MdnCNV) case. Method: Clinical microarray identified a previously unreported MdnCNV proband. Short and long-read genomic sequencing, SV analyses, and visualization tools for merged datasets were implemented to characterize MdnCNV mutagenesis. Human phenotype ontology based quantitative analyses identified gene(s) driving proband phenotype.Results: Eight dnCNVs of average length ~1 Mb were mapped in the MdnCNV proband. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8736

6 Samples

Download data: TXT

(Submitter supplied) We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array and breakpoint junction sequence analysis. Analysis of these data enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL27580

50 Samples

Download data: TXT

(Submitter supplied) Bru-seq nascent RNA sequencing (PubMed ID 23973811) was performed on two primary human fibroblast cell lines, mouse embryonic stem cells, and GM12878 human lymphoblastoid cells. Read data, which include both exon and intron signals, were used to identify transcription unit spans genome-wide, where a transcription unit is roughly correspondent to the longest expressed isoform of a gene. However, because algorithms were not constrained by annotated genes, transcription units need not and often do not correspond precisely to gene boundaries and include extragenic transcription. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

8 Samples

Download data: BED

(Submitter supplied) Interpreting the genomic and phenotypic consequences of copy number variation (CNV) is essential to understand the etiology of genetic disorders. Whereas deletion CNVs obviously lead to haploinsufficiency, duplications may cause disease through triplosensitivity, gene disruption, or gene fusion at breakpoints. The mutational spectrum of duplications has been studied at certain loci and in some cases these copy number gains are complex chromosome rearrangements involving triplications and/or inversions. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

19 related Platforms

161 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:

GPL26059 GPL26057 GPL26058

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 genome tiling array

Platforms:

GPL17522 GPL17521

31 Samples

Download data: TXT

(Submitter supplied) The goal of this experiment was to determine the size, genomic extent and gene content of each Xq28 rearrangement.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL17522

9 Samples

Download data: TXT

(Submitter supplied) The goal of this experiment was to determine the size, genomic extent and gene content of each Xq28 rearrangement.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL17521

22 Samples

Download data: TXT

(Submitter supplied) We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics Laboratories using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH). Custom high-density aCGH was performed on individuals with available DNA, and breakpoint junctions were fine-mapped at nucleotide resolution by long-range PCR and DNA sequencing to glean insights into potential mechanisms of formation.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

4 related Platforms

8 Samples

Download data: TXT

(Submitter supplied) We examined the effects of hydroxyurea (HU) treatment on germline copy number variants (CNVs) in vivo in male mice. Several trials of HU administration were performed by oral gavage and subcutaneous pump, with CNVs characterized in C57BL/6 x C3H/HeJ hybrid mouse offspring by microarray and mate-pair sequencing. This accession contains the Nimblegen aCGH microarray data from mice treated by oral gavage or by subcutaneous pump.

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL25017

110 Samples

Download data: PAIR, TXT

(Submitter supplied) We describe an 18-month-old male (BAB7221)with split-hand malformation. Custom high-density array and digital droplet PCR revealed the copy-number gains were actually quadruplications in the mother (BAB7219), the fetus (BAB7218) and her later born son (BAB7221). This quadruplication-normal-quadruplication pattern was shown to be expanded from the triplication-normal-triplication CNV at the same loci in the maternal grandmother (BAB8247).

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL21159

6 Samples

Download data: TXT

(Submitter supplied) Following previous work, we extend the use of a reliable detection method to a wide progeny in white spruce in order to genetically map a maximum of inherited gene CNVs and linked those to phenotypic traits related to adaptation. We selected probes targeting 3911 genes likely in CNV in this progeny and performed genetic mapping for those harboring a 1:1 segregation. In addition, the link between gene CNVs and phenotypic variation was tested using budburst, budset and growth data for the same samples. more...

Organism:

Picea glauca

Type:

Genome variation profiling by array

Platform:

GPL23818

115 Samples

Download data: TXT