A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757013



Internal ID9632472
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:142037699..142375789hg38UCSC Ensembl
Innerchr3:141756541..142094631hg19UCSC Ensembl
Innerchr3:143239231..143577321hg18UCSC Ensembl
Innerchr3:143239239..143577329hg17UCSC Ensembl
Cytoband3q23
Allele length
AssemblyAllele length
hg38338091
hg19338091
hg18338091
hg17338091
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759182
Supporting Variantsessv24627, essv24219
SamplesNA10846, NA12144
Known GenesGK5, TFDP2, XRN1
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)esv2757013
Frequency
Sample Size270
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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