A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757422



Internal ID9632881
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr11:5846825..5986383hg38UCSC Ensembl
Innerchr11:5868055..6007613hg19UCSC Ensembl
Innerchr11:5824631..5964189hg18UCSC Ensembl
Innerchr11:5824631..5964189hg17UCSC Ensembl
Cytoband11p15.4
Allele length
AssemblyAllele length
hg38139559
hg19139559
hg18139559
hg17139559
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759801
Supporting Variantsessv5678, essv4107, essv4941, essv1292, essv189, essv5015, essv6536, essv7509
SamplesNA18980, NA18571, NA18611, NA18605, NA18529, NA18537, NA18532, NA18994
Known GenesOR52E4, OR52E8, OR52L1, OR56A3, OR56A5
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)esv2757422
Frequency
Sample Size270
Observed Gain8
Observed Loss0
Observed Complex0
Frequencyn/a


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