A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756922



Internal ID9978999
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:57155304..57214676hg38UCSC Ensembl
Innerchr2:57382439..57441811hg19UCSC Ensembl
Innerchr2:57235943..57295315hg18UCSC Ensembl
Innerchr2:57294090..57353462hg17UCSC Ensembl
Cytoband2p16.1
Allele length
AssemblyAllele length
hg3859373
hg1959373
hg1859373
hg1759373
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759053
Supporting Variantsessv21594, essv23155
SamplesNA12155, NA10831
Known Genes
MethodSNP array
AnalysisThe algorithm used to call CNVs using the 500K EA platform was developed to accurately define CNV regions using a large set of reference samples and is described in detail in a separate publication (Komura 2006). The algorithm contains three major parts: 1) Intensity pre-processing using an improved version of Genomic Imbalance Map (GIM) (Ishikawa et al. 2005), including probe selection, noise reduction, normalization, and intensity ratio adjustment based on affinity differences between alleles of a SNP, 2) CNV extraction, which identifies CNVs from all pair-wise comparisons using a modified SW-ARRAY, and 3) A copy number inference step which utilizes signal ratios and SNP information to more precisely define CNV boundaries and the copy number within each region.
PlatformAffymetrix GeneChip Early Access Mapping 500K Set Array (250K_Nsp_SNP)
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2756922
Frequency
Sample Size270
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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