A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757634



Internal ID9633093
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:25057265..25125931hg38UCSC Ensembl
Innerchr16:25068586..25137252hg19UCSC Ensembl
Innerchr16:24976087..25044753hg18UCSC Ensembl
Innerchr16:24976087..25044753hg17UCSC Ensembl
Cytoband16p12.1
Allele length
AssemblyAllele length
hg3868667
hg1968667
hg1868667
hg1768667
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758638
Supporting Variantsessv10614, essv10712
SamplesNA19211, NA18508
Known GenesLCMT1
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)esv2757634
Frequency
Sample Size270
Observed Gain1
Observed Loss1
Observed Complex0
Frequencyn/a


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