A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757025



Internal ID9632484
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:186652561..186709551hg38UCSC Ensembl
Innerchr3:186370350..186427340hg19UCSC Ensembl
Innerchr3:187853044..187910034hg18UCSC Ensembl
Innerchr3:187853052..187910042hg17UCSC Ensembl
Cytoband3q27.3
Allele length
AssemblyAllele length
hg3856991
hg1956991
hg1856991
hg1756991
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759206
Supporting Variantsessv25049, essv23735
SamplesNA12801, NA12813
Known GenesFETUB, HRG
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)esv2757025
Frequency
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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