A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759257



Internal ID9634716
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:67911288..68163195hg38UCSC Ensembl
Innerchr4:68777006..69028913hg19UCSC Ensembl
Innerchr4:68459601..68711508hg18UCSC Ensembl
Innerchr4:68605772..68857679hg17UCSC Ensembl
Cytoband4q13.2
Allele length
AssemblyAllele length
hg38251908
hg19251908
hg18251908
hg17251908
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757060, esv2757939
SamplesNA18517
Known GenesLOC550113, SYT14L, TMPRSS11A, TMPRSS11F, TMPRSS11GP
MethodBAC aCGH
SNP array
AnalysisArray images were acquired using an Agilent laser scanner (Agilent Technologies, UK). Fluorescence intensities and log2 ratio values were extracted using Bluefuse software (Bluegnome Ltd).
The 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)
Agilent
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2759257
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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