A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757430



Internal ID9979507
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr11:25067166..25301052hg38UCSC Ensembl
Innerchr11:25088712..25322598hg19UCSC Ensembl
Innerchr11:25045288..25279174hg18UCSC Ensembl
Innerchr11:25045288..25279174hg17UCSC Ensembl
Cytoband11p14.3
Allele length
AssemblyAllele length
hg38233887
hg19233887
hg18233887
hg17233887
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759810
Supporting Variantsessv12085, essv14238, essv12946, essv13974
SamplesNA19098, NA19099, NA19100, NA19102
Known GenesLUZP2
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)esv2757430
Frequency
Sample Size270
Observed Gain1
Observed Loss3
Observed Complex0
Frequencyn/a


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