A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759898



Internal ID9635357
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:48035919..48431716hg38UCSC Ensembl
Innerchr12:48429702..48825499hg19UCSC Ensembl
Innerchr12:46715969..47111766hg18UCSC Ensembl
Innerchr12:46715969..47111766hg17UCSC Ensembl
Cytoband12q13.11
Allele length
AssemblyAllele length
hg38395798
hg19395798
hg18395798
hg17395798
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2758307, esv2757502
SamplesNA18635, NA18563
Known GenesASB8, C12orf68, H1FNT, MIR6505, OR10AD1, PFKM, SENP1, ZNF641
MethodBAC aCGH
SNP array
AnalysisArray images were acquired using an Agilent laser scanner (Agilent Technologies, UK). Fluorescence intensities and log2 ratio values were extracted using Bluefuse software (Bluegnome Ltd).
The 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)
Agilent
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2759898
Frequency
Sample Size270
Observed Gain1
Observed Loss1
Observed Complex0
Frequencyn/a


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