A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757204



Internal ID9632663
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr7:3319859..3420723hg38UCSC Ensembl
Innerchr7:3359491..3460355hg19UCSC Ensembl
Innerchr7:3326017..3426881hg18UCSC Ensembl
Innerchr7:3132732..3233596hg17UCSC Ensembl
Cytoband7p22.2
Allele length
AssemblyAllele length
hg38100865
hg19100865
hg18100865
hg17100865
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759500
Supporting Variantsessv3670, essv1554, essv7993, essv14000
SamplesNA19222, NA19221, NA19012, NA18943
Known GenesSDK1
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)esv2757204
Frequency
Sample Size270
Observed Gain2
Observed Loss2
Observed Complex0
Frequencyn/a


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