A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757145



Internal ID9632604
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:172607097..172788409hg38UCSC Ensembl
Innerchr5:172034100..172215412hg19UCSC Ensembl
Innerchr5:171966705..172148018hg18UCSC Ensembl
Innerchr5:171966705..172148018hg17UCSC Ensembl
Cytoband5q35.1
Allele length
AssemblyAllele length
hg38181313
hg19181313
hg18181314
hg17181314
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759393
Supporting Variantsessv9266, essv14666, essv14258, essv10497, essv13987
SamplesNA19145, NA19098, NA19137, NA19100, NA19143
Known GenesDUSP1, NEURL1B
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)esv2757145
Frequency
Sample Size270
Observed Gain5
Observed Loss0
Observed Complex0
Frequencyn/a


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