A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv13n14



Internal ID20131402
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr16:28630921..28790026hg38UCSC Ensembl
chr16:28642242..28801347hg19UCSC Ensembl
chr16:28549743..28708848hg18UCSC Ensembl
chr16:28549743..28708848hg17UCSC Ensembl
Cytoband16p11.2
Allele length
AssemblyAllele length
hg38159106
hg19159106
hg18159106
hg17159106
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv433442, nsv433441
SamplesNA19240, NA18555
Known GenesEIF3C, EIF3CL, MIR6862-1, MIR6862-2
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)dgv13n14
Frequency
Sample Size9
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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