A curated catalogue of human genomic structural variation




Variant Details

Variant: essv93



Internal ID9631417
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:322696..375377hg38UCSC Ensembl
Outerchr6:257461..378970hg38UCSC Ensembl
Innerchr6:322696..375377hg19UCSC Ensembl
Outerchr6:257461..378970hg19UCSC Ensembl
Innerchr6:267696..320377hg18UCSC Ensembl
Outerchr6:202461..323970hg18UCSC Ensembl
Innerchr6:267696..320377hg17UCSC Ensembl
Outerchr6:202461..323970hg17UCSC Ensembl
Cytoband6p25.3
Allele length
AssemblyAllele length
hg38121510
hg19121510
hg18121510
hg17121510
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2757151
Supporting Variants
SamplesNA19005
Known GenesDUSP22
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)essv93
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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