A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757248



Internal ID9632707
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr8:237639..465401hg38UCSC Ensembl
Innerchr8:187639..415401hg19UCSC Ensembl
Innerchr8:177639..405401hg18UCSC Ensembl
Innerchr8:177639..405401hg17UCSC Ensembl
Cytoband8p23.3
Allele length
AssemblyAllele length
hg38227763
hg19227763
hg18227763
hg17227763
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759581
Supporting Variantsessv10608, essv7923, essv9303
SamplesNA19209, NA19211, NA18852
Known GenesFAM87A, FBXO25, ZNF596
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)esv2757248
Frequency
Sample Size270
Observed Gain2
Observed Loss1
Observed Complex0
Frequencyn/a


Hosted by The Centre for Applied Genomics
Grant support for DGV
Please read the usage disclaimer