A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757484



Internal ID9632943
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:225844..434040hg38UCSC Ensembl
Innerchr12:335010..543206hg19UCSC Ensembl
Innerchr12:205271..413467hg18UCSC Ensembl
Innerchr12:205271..413467hg17UCSC Ensembl
Cytoband12p13.33
Allele length
AssemblyAllele length
hg38208197
hg19208197
hg18208197
hg17208197
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759875
Supporting Variantsessv9499, essv18788, essv18027
SamplesNA18521, NA12891, NA12878
Known GenesCCDC77, KDM5A, SLC6A13
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)esv2757484
Frequency
Sample Size270
Observed Gain1
Observed Loss2
Observed Complex0
Frequencyn/a


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