A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756763



Internal ID9632222
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr22:42439721..42644428hg38UCSC Ensembl
Innerchr22:42835727..43040434hg19UCSC Ensembl
Innerchr22:41165671..41370378hg18UCSC Ensembl
Innerchr22:41160225..41364932hg17UCSC Ensembl
Cytoband22q13.2
Allele length
AssemblyAllele length
hg38204708
hg19204708
hg18204708
hg17204708
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758839
Supporting Variantsessv4940
SamplesNA18537
Known GenesATP5L2, CYB5R3, POLDIP3, RNU12, RRP7A, RRP7B, SERHL, SERHL2
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)esv2756763
Frequency
Sample Size270
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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