A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv12n14



Internal ID20131401
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr16:28592322..28607988hg38UCSC Ensembl
chr16:28603643..28619309hg19UCSC Ensembl
chr16:28511144..28526810hg18UCSC Ensembl
chr16:28511144..28526810hg17UCSC Ensembl
Cytoband16p11.2
Allele length
AssemblyAllele length
hg3815667
hg1915667
hg1815667
hg1715667
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv433300, nsv433298
SamplesNA12878, NA19240
Known GenesSULT1A1, SULT1A2
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)dgv12n14
Frequency
Sample Size9
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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