A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757432



Internal ID9979509
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr11:25673063..25706614hg38UCSC Ensembl
Innerchr11:25694609..25728161hg19UCSC Ensembl
Innerchr11:25651185..25684737hg18UCSC Ensembl
Innerchr11:25651185..25684737hg17UCSC Ensembl
Cytoband11p14.3
Allele length
AssemblyAllele length
hg3833552
hg1933553
hg1833553
hg1733553
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759811
Supporting Variantsessv7949, essv13241, essv14940, essv8066, essv11071, essv16619, essv13104, essv13361, essv9955, essv16601
SamplesNA19203, NA19204, NA18860, NA19131, NA19138, NA19159, NA19161, NA18859, NA19208, NA19132
Known Genes
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)esv2757432
Frequency
Sample Size270
Observed Gain0
Observed Loss10
Observed Complex0
Frequencyn/a


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