A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759262



Internal ID9634721
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:76343443..76534252hg38UCSC Ensembl
Innerchr4:77264596..77455405hg19UCSC Ensembl
Innerchr4:77483620..77674429hg18UCSC Ensembl
Innerchr4:77621775..77812584hg17UCSC Ensembl
Cytoband4q21.1
Allele length
AssemblyAllele length
hg38190810
hg19190810
hg18190810
hg17190810
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757941, esv2757069
SamplesNA12145, NA19103, NA19102
Known GenesCCDC158, SHROOM3
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)esv2759262
Frequency
Sample Size270
Observed Gain0
Observed Loss3
Observed Complex0
Frequencyn/a


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