A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv20n14



Internal ID20131409
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr2:75596036..75687909hg38UCSC Ensembl
chr2:75823162..75915035hg19UCSC Ensembl
chr2:75676670..75768543hg18UCSC Ensembl
chr2:75734817..75826690hg17UCSC Ensembl
Cytoband2p12
Allele length
AssemblyAllele length
hg3891874
hg1991874
hg1891874
hg1791874
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv433353, nsv433355
SamplesNA18956, NA18555
Known GenesGCFC2, MRPL19
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)dgv20n14
Frequency
Sample Size9
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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