A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757534



Internal ID9979611
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr13:57128885..57352300hg38UCSC Ensembl
Innerchr13:57703019..57926434hg19UCSC Ensembl
Innerchr13:56601020..56824435hg18UCSC Ensembl
Innerchr13:56601020..56824435hg17UCSC Ensembl
Cytoband13q21.1
Allele length
AssemblyAllele length
hg38223416
hg19223416
hg18223416
hg17223416
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759939
Supporting Variantsessv8699, essv13287, essv13499, essv13242, essv16392, essv13269, essv9957, essv14208, essv14947
SamplesNA19204, NA19201, NA19131, NA19172, NA19202, NA18912, NA19132, NA18914, NA18913
Known GenesPRR20A, PRR20B, PRR20C, PRR20D, PRR20E
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)esv2757534
Frequency
Sample Size270
Observed Gain0
Observed Loss9
Observed Complex0
Frequencyn/a


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