A curated catalogue of human genomic structural variation




Variant Details

Variant: essv14048



Internal ID9611501
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr17:41510342..41531380hg38UCSC Ensembl
Outerchr17:41510342..41535160hg38UCSC Ensembl
Innerchr17:39666594..39687632hg19UCSC Ensembl
Outerchr17:39666594..39691412hg19UCSC Ensembl
Innerchr17:36920120..36941158hg18UCSC Ensembl
Outerchr17:36920120..36944938hg18UCSC Ensembl
Innerchr17:36920120..36941158hg17UCSC Ensembl
Outerchr17:36920120..36944938hg17UCSC Ensembl
Cytoband17q21.2
Allele length
AssemblyAllele length
hg3824819
hg1924819
hg1824819
hg1724819
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2757658
Supporting Variants
SamplesNA18862
Known GenesKRT15, KRT19, MIR6510
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)essv14048
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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