A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756745



Internal ID9632204
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr21:10428610..10592439hg38UCSC Ensembl
Innerchr21:10920018..11083847hg19UCSC Ensembl
Innerchr21:9941889..10105718hg18UCSC Ensembl
Innerchr21:9941889..10105718hg17UCSC Ensembl
Cytoband21p11.1
Allele length
AssemblyAllele length
hg38163830
hg19163830
hg18163830
hg17163830
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758808
Supporting Variantsessv17681, essv21623, essv4309, essv7881, essv10189, essv2706, essv18016, essv1328, essv17364, essv18782
SamplesNA18944, NA10835, NA12891, NA18973, NA12878, NA18516, NA18517, NA18564, NA19140, NA07348
Known GenesBAGE, BAGE2, BAGE3, BAGE4, BAGE5, TPTE
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)esv2756745
Frequency
Sample Size270
Observed Gain4
Observed Loss6
Observed Complex0
Frequencyn/a


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