A curated catalogue of human genomic structural variation




Variant Details

Variant: essv3653



Internal ID9625144
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr11:59043768..59079703hg38UCSC Ensembl
Outerchr11:59009027..59123819hg38UCSC Ensembl
Innerchr11:58811241..58847176hg19UCSC Ensembl
Outerchr11:58776500..58891292hg19UCSC Ensembl
Innerchr11:58567817..58603752hg18UCSC Ensembl
Outerchr11:58533076..58647868hg18UCSC Ensembl
Innerchr11:58567817..58603752hg17UCSC Ensembl
Outerchr11:58533076..58647868hg17UCSC Ensembl
Cytoband11q12.1
Allele length
AssemblyAllele length
hg38114793
hg19114793
hg18114793
hg17114793
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2757447
Supporting Variants
SamplesNA18991
Known GenesFAM111B, LOC283194
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)essv3653
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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