A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759380



Internal ID9634839
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:135829912..136139310hg38UCSC Ensembl
Innerchr5:135165601..135474999hg19UCSC Ensembl
Innerchr5:135193500..135502898hg18UCSC Ensembl
Innerchr5:135193500..135502898hg17UCSC Ensembl
Cytoband5q31.1
Allele length
AssemblyAllele length
hg38309399
hg19309399
hg18309399
hg17309399
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757139, esv2758018
SamplesNA18529, NA18547
Known GenesFBXL21, IL9, LECT2, SLC25A48, SMAD5, SMAD5-AS1, TGFBI, VTRNA2-1
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)esv2759380
Frequency
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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