A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756781



Internal ID9632240
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
InnerchrX:2785350..3258451hg38UCSC Ensembl
InnerchrX:2703391..3176492hg19UCSC Ensembl
InnerchrX:2713391..3186492hg18UCSC Ensembl
InnerchrX:2696752..3169853hg17UCSC Ensembl
CytobandXp22.33
Allele length
AssemblyAllele length
hg38473102
hg19473102
hg18473102
hg17473102
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758855
Supporting Variantsessv21575, essv3621
SamplesNA12146, NA18966
Known GenesARSD, ARSE, ARSF, ARSH, GYG2, XG
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)esv2756781
Frequency
Sample Size270
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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