A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756867



Internal ID9632326
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:162094678..162390218hg38UCSC Ensembl
Innerchr1:162064468..162360008hg19UCSC Ensembl
Innerchr1:160331092..160626632hg18UCSC Ensembl
Innerchr1:158796126..159091666hg17UCSC Ensembl
Cytoband1q23.3
Allele length
AssemblyAllele length
hg38295541
hg19295541
hg18295541
hg17295541
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758973
Supporting Variantsessv19155, essv25027, essv5883
SamplesNA12801, NA12812, NA18576
Known GenesC1orf111, C1orf226, MIR4654, MIR556, NOS1AP
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)esv2756867
Frequency
Sample Size270
Observed Gain3
Observed Loss0
Observed Complex0
Frequencyn/a


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