A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv433242



Internal ID15031824
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr8:7422928..7536511hg38UCSC Ensembl
Innerchr8:7280450..7394033hg19UCSC Ensembl
Innerchr8:7267860..7381443hg18UCSC Ensembl
Innerchr8:7267860..7381443hg17UCSC Ensembl
Cytoband8p23.1
Allele length
AssemblyAllele length
hg38113584
hg19113584
hg18113584
hg17113584
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsdgv31n14
Supporting Variantsnssv463123
SamplesNA19240
Known GenesDEFB103A, DEFB103B, DEFB104A, DEFB104B, DEFB105A, DEFB105B, DEFB106A, DEFB106B, DEFB107A, DEFB107B, SPAG11B
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)nsv433242
Frequency
Sample Size9
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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