A curated catalogue of human genomic structural variation

Variant Details

Variant: esv2422005

Internal ID3031558
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:234648708..234658623hg19UCSC Ensembl
Innerchr2:234313447..234323362hg18UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV Deletion
Copy Number
Allele State
Allele Origin
Probe Count
Merged StatusM
Merged Variants
Supporting Variantsessv5030576, essv5099013, essv5053975, essv5124226, essv5115808, essv5058999, essv5145405, essv5058038, essv5033905, essv5112393, essv5064386, essv5070586, essv5082545, essv5079847, essv5128553, essv5133026, essv5114054, essv5070886, essv5027450, essv5055564, essv5024938, essv5030755, essv5059577, essv5119072, essv5116620, essv5051949, essv5030236, essv5092527, essv5097097, essv5034555, essv5022915, essv5007124, essv5132696, essv5096087, essv5109650
SamplesNA18863, NA18861, NA21438, NA21524, NA21478, NA21487, NA18517, NA19109, NA21825, NA21415, NA19383, NA18934, NA19107, NA19444, NA19096, NA21363, NA19908, NA18515, NA21525, NA19373, NA21717, NA19027, NA21379, NA21739, NA19708, NA21485, NA21418, NA19328, NA21336, NA21486, NA21439, NA19097, NA19446, NA21576, NA19448
Known GenesDNAJB3, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9
AnalysisThese sample-specific calls were then collapsed into discrete CNP segments. For our subsequent analysis, we focused on variation that was observed in at least 1% of the samples. In order to refine the CNP breakpoint definitions using many samples simultaneously, we developed an approach utilizing the correlation structure of the probe-intensity data across samples. First, we agglomeratively clustered overlapping CNP calls to identify a series of discrete regions for more-detailed follow-up. We then analyzed each such region (together with 100 kb of flanking sequence on each side) individually. Each region involved a set of samples with putative CNPs
PlatformAffymetrix Genome-Wide Human SNP 6.0 Array + Illumina Human1Mv1 DNA Analysis BeadChip
Pubmed ID20811451
Accession Number(s)esv2422005
Sample Size1184
Observed Gain0
Observed Loss35
Observed Complex0

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