A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759003



Internal ID9634462
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:225477992..225515783hg38UCSC Ensembl
Innerchr1:225665694..225703485hg19UCSC Ensembl
Innerchr1:223732317..223770108hg18UCSC Ensembl
Innerchr1:221972429..222010220hg17UCSC Ensembl
Cytoband1q42.12
Allele length
AssemblyAllele length
hg3837792
hg1937792
hg1837792
hg1737792
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756886
SamplesNA18621, NA18635, NA18555, NA18564
Known GenesENAH
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)esv2759003
Frequency
Sample Size270
Observed Gain4
Observed Loss0
Observed Complex0
Frequencyn/a


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