A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757190



Internal ID9632649
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:117142885..117288366hg38UCSC Ensembl
Innerchr6:117464048..117609529hg19UCSC Ensembl
Innerchr6:117570741..117716222hg18UCSC Ensembl
Innerchr6:117570741..117716222hg17UCSC Ensembl
Cytoband6q22.1
Allele length
AssemblyAllele length
hg38145482
hg19145482
hg18145482
hg17145482
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759465
Supporting Variantsessv9540, essv11297
SamplesNA18861, NA18863
Known GenesVGLL2
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)esv2757190
Frequency
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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