A curated catalogue of human genomic structural variation

Variant Details

Variant: esv2758935

Internal ID9634394
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:53022892..53066445hg38UCSC Ensembl
Innerchr1:53488564..53532117hg19UCSC Ensembl
Innerchr1:53261152..53304705hg18UCSC Ensembl
Innerchr1:53200585..53244138hg17UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756843
SamplesNA19128, NA18853
Known GenesPODN, SCP2
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)
Pubmed ID17122850
Accession Number(s)esv2758935
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0

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