A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758660



Internal ID9980805
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:78220032..78383417hg38UCSC Ensembl
Innerchr16:78253929..78417314hg19UCSC Ensembl
Innerchr16:76811430..76974815hg18UCSC Ensembl
Innerchr16:76811430..76974815hg17UCSC Ensembl
Cytoband16q23.1
Allele length
AssemblyAllele length
hg38163386
hg19163386
hg18163386
hg17163386
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757644, esv2758433
SamplesNA19204, NA19127, NA19205
Known GenesWWOX
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)esv2758660
Frequency
Sample Size270
Observed Gain0
Observed Loss3
Observed Complex0
Frequencyn/a


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