A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756816



Internal ID9632275
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:80938382..80993537hg38UCSC Ensembl
Innerchr16:80972279..81027142hg19UCSC Ensembl
Innerchr16:79529780..79584643hg18UCSC Ensembl
Innerchr16:79529780..79584643hg17UCSC Ensembl
Cytoband16q23.2
Allele length
AssemblyAllele length
hg3855156
hg1954864
hg1854864
hg1754864
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758663
Supporting Variantsessv7480, essv20517, essv22006, essv187, essv17401, essv18805, essv7241, essv22610, essv7673, essv19344, essv2146, essv1004, essv10187, essv18868, essv21483, essv17687, essv3264, essv21952, essv957, essv3917, essv19723, essv4929, essv6542, essv23718, essv14656, essv6060, essv5004, essv8404, essv25041, essv1073, essv5688, essv15938, essv2557
SamplesNA18855, NA12236, NA18561, NA19145, NA18603, NA07029, NA12801, NA12248, NA12813, NA18967, NA10835, NA18635, NA18960, NA18571, NA18964, NA12815, NA18990, NA18605, NA18515, NA18516, NA18981, NA18537, NA10830, NA06985, NA18974, NA18978, NA12716, NA18994, NA19093, NA18624, NA07000, NA12154, NA18620
Known GenesCMC2
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)esv2756816
Frequency
Sample Size270
Observed Gain1
Observed Loss32
Observed Complex0
Frequencyn/a


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