A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757668



Internal ID9633127
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr18:3794119..4122410hg38UCSC Ensembl
Innerchr18:3794119..4122410hg19UCSC Ensembl
Innerchr18:3784119..4112410hg18UCSC Ensembl
Innerchr18:3784119..4112410hg17UCSC Ensembl
Cytoband18p11.31
Allele length
AssemblyAllele length
hg38328292
hg19328292
hg18328292
hg17328292
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758710
Supporting Variantsessv20859, essv24635
SamplesNA10846, NA12145
Known GenesDLGAP1, DLGAP1-AS3, DLGAP1-AS4, MIR6718
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)esv2757668
Frequency
Sample Size270
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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