A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758797



Internal ID9634256
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr20:46619371..46660550hg38UCSC Ensembl
Innerchr20:45248010..45289189hg19UCSC Ensembl
Innerchr20:44681417..44722596hg18UCSC Ensembl
Innerchr20:44681417..44722596hg17UCSC Ensembl
Cytoband20q13.12
Allele length
AssemblyAllele length
hg3841180
hg1941180
hg1841180
hg1741180
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756740
SamplesNA18547
Known GenesSLC13A3
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)esv2758797
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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