A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757673



Internal ID9633132
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr18:32052786..32095029hg38UCSC Ensembl
Innerchr18:29632749..29674992hg19UCSC Ensembl
Innerchr18:27886747..27928990hg18UCSC Ensembl
Innerchr18:27886747..27928990hg17UCSC Ensembl
Cytoband18q12.1
Allele length
AssemblyAllele length
hg3842244
hg1942244
hg1842244
hg1742244
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758719
Supporting Variantsessv6802
SamplesNA18594
Known GenesRNF125, RNF138
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)esv2757673
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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