A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757699



Internal ID9633158
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:51756318..52101372hg38UCSC Ensembl
Innerchr19:52259571..52604625hg19UCSC Ensembl
Innerchr19:56951383..57296437hg18UCSC Ensembl
Innerchr19:56951383..57296437hg17UCSC Ensembl
Cytoband19q13.33
Allele length
AssemblyAllele length
hg38345055
hg19345055
hg18345055
hg17345055
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758767
Supporting Variantsessv18468, essv20826
SamplesNA10855, NA11832
Known GenesFPR2, FPR3, HCCAT3, ZNF350, ZNF432, ZNF577, ZNF613, ZNF614, ZNF615, ZNF649, ZNF841
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)esv2757699
Frequency
Sample Size270
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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