A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756758



Internal ID9632217
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr22:18148598..19050022hg38UCSC Ensembl
Innerchr22:18631365..19037535hg19UCSC Ensembl
Innerchr22:17011365..17417535hg18UCSC Ensembl
Innerchr22:17005919..17412089hg17UCSC Ensembl
Cytoband22q11.21
Allele length
AssemblyAllele length
hg38901425
hg19406171
hg18406171
hg17406171
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758824
Supporting Variantsessv23300, essv20856, essv25121
SamplesNA11829, NA10856, NA12006
Known GenesDGCR10, DGCR11, DGCR2, DGCR5, DGCR6, DGCR9, GGT3P, PRODH, USP18
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)esv2756758
Frequency
Sample Size270
Observed Gain3
Observed Loss0
Observed Complex0
Frequencyn/a


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