A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv3n14



Internal ID20131392
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr1:103589135..103760817hg38UCSC Ensembl
chr1:104131757..104303439hg19UCSC Ensembl
chr1:103933280..104104962hg18UCSC Ensembl
chr1:103843778..104015460hg17UCSC Ensembl
Cytoband1p21.1
Allele length
AssemblyAllele length
hg38171683
hg19171683
hg18171683
hg17171683
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv433187, nsv433186
SamplesNA15510, NA12156
Known GenesAMY1A, AMY1B, AMY1C, AMY2A
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)dgv3n14
Frequency
Sample Size9
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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