A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757656



Internal ID9633115
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr17:36588163..36674124hg38UCSC Ensembl
Innerchr17:34944593..35030559hg19UCSC Ensembl
Innerchr17:32018706..32104672hg18UCSC Ensembl
Innerchr17:32018706..32104672hg17UCSC Ensembl
Cytoband17q12
Allele length
AssemblyAllele length
hg3885962
hg1985967
hg1885967
hg1785967
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758686
Supporting Variantsessv9000, essv14253, essv12443
SamplesNA19194, NA19152, NA19100
Known GenesDHRS11, GGNBP2, MRM1
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)esv2757656
Frequency
Sample Size270
Observed Gain3
Observed Loss0
Observed Complex0
Frequencyn/a


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