A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759837



Internal ID9635296
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr11:74131564..74846552hg38UCSC Ensembl
Innerchr11:73842609..74557597hg19UCSC Ensembl
Innerchr11:73520257..74235245hg18UCSC Ensembl
Innerchr11:73520257..74235245hg17UCSC Ensembl
Cytoband11q13.4
Allele length
AssemblyAllele length
hg38714989
hg19714989
hg18714989
hg17714989
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2758277, esv2757451
SamplesNA18582
Known GenesC2CD3, CHRDL2, KCNE3, LIPT2, MIR4696, P4HA3, PGM2L1, POLD3, PPME1, RNF169, XRRA1
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)esv2759837
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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