A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv433211



Internal ID5948965
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:234648708..234658250hg19UCSC Ensembl
Innerchr2:234313447..234322989hg18UCSC Ensembl
Innerchr2:234430708..234440250hg17UCSC Ensembl
Cytoband2q37.1
Allele length
AssemblyAllele length
hg19n/a
hg18n/a
hg17n/a
Variant TypeCNV Loss
Copy Number
Allele StateHemizygous
Allele OriginNot tested
Probe Count
Merged StatusS
Merged Variants
Supporting Variantsnssv463092
SamplesNA18517
Known GenesDNAJB3, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9
MethodSNP_array
AnalysisLarge CNV discovery was accomplished by using HMMSeg, considering both the ‘LogR ratio’ and ‘B-allele frequency’ data for each sample simultaneously. We used a four-state model, one each for null (homozygous deletion), hemizygous deletion, diploid and amplification. Initial segmentation results were merged and filtered, requiring all variants to be larger than 1 kb in length and to span at least 10 probes for amplifications or hemizygous deletions, or 3 probes for homozygous deletions. We then used a combination of paired-end sequence maps, oligo array-CGH, and variant resequencing (described in Kidd et al. 2008) to support the calls.
PlatformIllumina Human1Mv1 DNA Analysis BeadChip (Human1Mv1_C)
Comments
ReferenceCooper et al 2008
Pubmed ID18776910
Accession Number(s)nsv433211
Frequency
Sample Size9
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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