A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756951



Internal ID9979028
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:152798685..152942318hg38UCSC Ensembl
Innerchr2:153655199..153798832hg19UCSC Ensembl
Innerchr2:153363445..153507078hg18UCSC Ensembl
Innerchr2:153480707..153624340hg17UCSC Ensembl
Cytoband2q23.3
Allele length
AssemblyAllele length
hg38143634
hg19143634
hg18143634
hg17143634
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759097
Supporting Variantsessv6939, essv3430
SamplesNA18956, NA18608
Known Genes
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)esv2756951
Frequency
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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