A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv433342



Internal ID15031924
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:380792..497538hg38UCSC Ensembl
Innerchr1:321799..438545hg19UCSC Ensembl
Innerchr1:311662..428408hg18UCSC Ensembl
Innerchr1:361662..478408hg17UCSC Ensembl
Cytoband1p36.33
Allele length
AssemblyAllele length
hg38116747
hg19116747
hg18116747
hg17116747
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsdgv1n14
Supporting Variantsnssv463223
SamplesNA18555
Known GenesLOC100132062, LOC100132287, LOC100133331, OR4F16, OR4F29, OR4F3
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)nsv433342
Frequency
Sample Size9
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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