A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757519



Internal ID9632978
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:129527431..130608908hg38UCSC Ensembl
Innerchr12:130011976..131093453hg19UCSC Ensembl
Innerchr12:128577929..129659406hg18UCSC Ensembl
Innerchr12:128536856..129618333hg17UCSC Ensembl
Cytoband12q24.32
Allele length
AssemblyAllele length
hg381081478
hg191081478
hg181081478
hg171081478
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759921
Supporting Variantsessv5614
SamplesNA18593
Known GenesFZD10, FZD10-AS1, LOC100190940, PIWIL1, RIMBP2, TMEM132D
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)esv2757519
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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