A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759817



Internal ID9635276
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr11:34891768..34942181hg38UCSC Ensembl
Innerchr11:34913315..34963728hg19UCSC Ensembl
Innerchr11:34869891..34920304hg18UCSC Ensembl
Innerchr11:34869891..34920304hg17UCSC Ensembl
Cytoband11p13
Allele length
AssemblyAllele length
hg3850414
hg1950414
hg1850414
hg1750414
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757436
SamplesNA10860, NA11992
Known GenesAPIP, MIR1343, PDHX
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)esv2759817
Frequency
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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