A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759116



Internal ID9634575
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:228046174..228056037hg38UCSC Ensembl
Innerchr2:228910890..228920753hg19UCSC Ensembl
Innerchr2:228619134..228628997hg18UCSC Ensembl
Innerchr2:228736395..228746258hg17UCSC Ensembl
Cytoband2q36.3
Allele length
AssemblyAllele length
hg389864
hg199864
hg189864
hg179864
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756963
SamplesNA11830
Known GenesSPHKAP
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)esv2759116
Frequency
Sample Size270
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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