A curated catalogue of human genomic structural variation




Variant Details

Variant: essv22269



Internal ID9620635
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr20:54062616..54065980hg38UCSC Ensembl
Outerchr20:54062598..54068669hg38UCSC Ensembl
Innerchr20:52679155..52682519hg19UCSC Ensembl
Outerchr20:52679137..52685208hg19UCSC Ensembl
Innerchr20:52112562..52115926hg18UCSC Ensembl
Outerchr20:52112544..52118615hg18UCSC Ensembl
Innerchr20:52112562..52115926hg17UCSC Ensembl
Outerchr20:52112544..52118615hg17UCSC Ensembl
Cytoband20q13.2
Allele length
AssemblyAllele length
hg386072
hg196072
hg186072
hg176072
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2756743
Supporting Variants
SamplesNA12762
Known GenesBCAS1, MIR4756
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)essv22269
Frequency
Sample Size270
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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