A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757364



Internal ID9632823
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr10:5515061..5678549hg38UCSC Ensembl
Innerchr10:5557024..5720512hg19UCSC Ensembl
Innerchr10:5547024..5760518hg18UCSC Ensembl
Innerchr10:5547024..5760518hg17UCSC Ensembl
Cytoband10p15.1
Allele length
AssemblyAllele length
hg38163489
hg19163489
hg18213495
hg17213495
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759729
Supporting Variantsessv13294, essv8711, essv13227, essv10496, essv14946
SamplesNA19131, NA19200, NA19202, NA19132, NA19143
Known GenesASB13, CALML3
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)esv2757364
Frequency
Sample Size270
Observed Gain5
Observed Loss0
Observed Complex0
Frequencyn/a


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