A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758772



Internal ID9634231
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:55026094..55139319hg38UCSC Ensembl
Innerchr19:55537462..55650687hg19UCSC Ensembl
Innerchr19:60229274..60342499hg18UCSC Ensembl
Innerchr19:60229274..60342499hg17UCSC Ensembl
Cytoband19q13.42
Allele length
AssemblyAllele length
hg38113226
hg19113226
hg18113226
hg17113226
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757704
SamplesNA18620
Known GenesEPS8L1, GP6, PPP1R12C, RDH13, TNNT1
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)esv2758772
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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