A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757509



Internal ID9632968
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:71778991..71878199hg38UCSC Ensembl
Innerchr12:72172771..72271979hg19UCSC Ensembl
Innerchr12:70459038..70558246hg18UCSC Ensembl
Innerchr12:70459038..70558246hg17UCSC Ensembl
Cytoband12q21.1
Allele length
AssemblyAllele length
hg3899209
hg1999209
hg1899209
hg1799209
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759907
Supporting Variantsessv4115
SamplesNA18529
Known GenesMRS2P2, RAB21, TBC1D15
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)esv2757509
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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