A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757620



Internal ID9633079
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:5005940..5320409hg38UCSC Ensembl
Innerchr16:5055941..5370410hg19UCSC Ensembl
Innerchr16:4995942..5310411hg18UCSC Ensembl
Innerchr16:4995942..5310411hg17UCSC Ensembl
Cytoband16p13.3
Allele length
AssemblyAllele length
hg38314470
hg19314470
hg18314470
hg17314470
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2760069
Supporting Variantsessv17400
SamplesNA18855
Known GenesALG1, C16orf89, FAM86A, NAGPA, NAGPA-AS1, SEC14L5
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)esv2757620
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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