A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759355



Internal ID9634814
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:95896002..96204729hg38UCSC Ensembl
Innerchr5:95231706..95540433hg19UCSC Ensembl
Innerchr5:95257462..95566189hg18UCSC Ensembl
Innerchr5:95257462..95566189hg17UCSC Ensembl
Cytoband5q15
Allele length
AssemblyAllele length
hg38308728
hg19308728
hg18308728
hg17308728
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757121, esv2758003
SamplesNA18582
Known GenesELL2, MIR583
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)esv2759355
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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