A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv31n14



Internal ID20131420
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr8:7385193..7536511hg38UCSC Ensembl
chr8:7242715..7394033hg19UCSC Ensembl
chr8:7230125..7381443hg18UCSC Ensembl
chr8:7230125..7381443hg17UCSC Ensembl
Cytoband8p23.1
Allele length
AssemblyAllele length
hg38151319
hg19151319
hg18151319
hg17151319
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv433241, nsv433240, nsv433242
SamplesNA18517, NA18507, NA19240
Known GenesDEFB103A, DEFB103B, DEFB104A, DEFB104B, DEFB105A, DEFB105B, DEFB106A, DEFB106B, DEFB107A, DEFB107B, DEFB4B, 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)dgv31n14
Frequency
Sample Size9
Observed Gain0
Observed Loss3
Observed Complex0
Frequencyn/a


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