A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757594



Internal ID9633053
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr15:31683057..32660863hg38UCSC Ensembl
Innerchr15:31975260..32953064hg19UCSC Ensembl
Innerchr15:29762552..30740356hg18UCSC Ensembl
Innerchr15:29762552..30740356hg17UCSC Ensembl
Cytoband15q13.3
Allele length
AssemblyAllele length
hg38977807
hg19977805
hg18977805
hg17977805
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2760023
Supporting Variantsessv19074, essv25119, essv23734
SamplesNA12813, NA10856, NA11830
Known GenesARHGAP11A, CHRNA7, GOLGA8K, GOLGA8O, GOLGA8R, LOC100996255, SCG5, ULK4P1, ULK4P2, ULK4P3, WHAMMP1
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)esv2757594
Frequency
Sample Size270
Observed Gain3
Observed Loss0
Observed Complex0
Frequencyn/a


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