A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758822



Internal ID9634281
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr21:46566757..46657900hg38UCSC Ensembl
Innerchr21:47986670..48077812hg19UCSC Ensembl
Innerchr21:46811098..46902240hg18UCSC Ensembl
Innerchr21:46811098..46902240hg17UCSC Ensembl
Cytoband21q22.3
Allele length
AssemblyAllele length
hg3891144
hg1991143
hg1891143
hg1791143
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756756
SamplesNA18561
Known GenesDIP2A, PRMT2, S100B
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)esv2758822
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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