A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756810



Internal ID9632269
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr8:16401632..17048016hg38UCSC Ensembl
Innerchr8:16259141..16905525hg19UCSC Ensembl
Innerchr8:16303512..16949896hg18UCSC Ensembl
Innerchr8:16303512..16949896hg17UCSC Ensembl
Cytoband8p22
Allele length
AssemblyAllele length
hg38646385
hg19646385
hg18646385
hg17646385
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759599
Supporting Variantsessv25091, essv20693, essv14679
SamplesNA12814, NA19145, NA12802
Known GenesFGF20, MICU3
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)esv2756810
Frequency
Sample Size270
Observed Gain3
Observed Loss0
Observed Complex0
Frequencyn/a


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