A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757475



Internal ID9979552
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr11:105025149..105108990hg38UCSC Ensembl
Innerchr11:104895876..104979717hg19UCSC Ensembl
Innerchr11:104401086..104484927hg18UCSC Ensembl
Innerchr11:104401086..104484927hg17UCSC Ensembl
Cytoband11q22.3
Allele length
AssemblyAllele length
hg3883842
hg1983842
hg1883842
hg1783842
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759863
Supporting Variantsessv15910, essv8579, essv11069, essv9484, essv14948, essv12898, essv9958, essv15443, essv9519, essv8986, essv8252, essv11410, essv14683, essv13947, essv8713, essv13347, essv9862, essv15959, essv16617, essv12885, essv12133
SamplesNA18502, NA19204, NA19145, NA19192, NA19138, NA19130, NA19200, NA19194, NA19205, NA19208, NA19142, NA19154, NA19160, NA19132, NA19206, NA19144, NA19173, NA18521, NA18500, NA18522, NA19153
Known GenesCARD16, CARD17, CASP1
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)esv2757475
Frequency
Sample Size270
Observed Gain2
Observed Loss19
Observed Complex0
Frequencyn/a


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