A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757520



Internal ID9632979
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:131238746..131764943hg38UCSC Ensembl
Innerchr12:131723291..132249488hg19UCSC Ensembl
Innerchr12:130289244..130815441hg18UCSC Ensembl
Innerchr12:130248171..130915718hg17UCSC Ensembl
Cytoband12q24.33
Allele length
AssemblyAllele length
hg38526198
hg19526198
hg18526198
hg17667548
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759922
Supporting Variantsessv19310, essv9956, essv19365, essv958, essv4942, essv7484, essv1041, essv7653
SamplesNA19204, NA18561, NA07019, NA18975, NA07022, NA18981, NA18537, NA18632
Known GenesLOC338797, SFSWAP
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)esv2757520
Frequency
Sample Size270
Observed Gain2
Observed Loss6
Observed Complex0
Frequencyn/a


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