A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759216



Internal ID9634675
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:29099..66439hg38UCSC Ensembl
Innerchr4:29099..66331hg19UCSC Ensembl
Innerchr4:19099..56331hg18UCSC Ensembl
Innerchr4:19099..56331hg17UCSC Ensembl
Cytoband4p16.3
Allele length
AssemblyAllele length
hg3837341
hg1937233
hg1837233
hg1737233
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757030
SamplesNA18603, NA12813, NA18593
Known GenesZNF595, ZNF718
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)esv2759216
Frequency
Sample Size270
Observed Gain1
Observed Loss2
Observed Complex0
Frequencyn/a


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