A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757242



Internal ID9632701
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr7:149849614..150208958hg38UCSC Ensembl
Innerchr7:149546703..149906047hg19UCSC Ensembl
Innerchr7:149177636..149536980hg18UCSC Ensembl
Innerchr7:148984351..149343695hg17UCSC Ensembl
Cytoband7q36.1
Allele length
AssemblyAllele length
hg38359345
hg19359345
hg18359345
hg17359345
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759571
Supporting Variantsessv4520, essv2380, essv6486, essv3648
SamplesNA18991, NA18976, NA18636, NA18623
Known GenesATP6V0E2, ATP6V0E2-AS1, ZNF862
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)esv2757242
Frequency
Sample Size270
Observed Gain4
Observed Loss0
Observed Complex0
Frequencyn/a


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