A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757264



Internal ID9632723
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr8:17481592..17746348hg38UCSC Ensembl
Innerchr8:17339101..17603857hg19UCSC Ensembl
Innerchr8:17383467..17648137hg18UCSC Ensembl
Innerchr8:17383467..17648137hg17UCSC Ensembl
Cytoband8p22
Allele length
AssemblyAllele length
hg38264757
hg19264757
hg18264671
hg17264671
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759600
Supporting Variantsessv13812, essv1536, essv15915, essv7945
SamplesNA19203, NA19205, NA18853, NA19012
Known GenesMTUS1, PDGFRL, SLC7A2
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)esv2757264
Frequency
Sample Size270
Observed Gain0
Observed Loss4
Observed Complex0
Frequencyn/a


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