A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759068



Internal ID9981213
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:77899263..78483906hg38UCSC Ensembl
Innerchr2:78126389..78711032hg19UCSC Ensembl
Innerchr2:77979897..78564540hg18UCSC Ensembl
Innerchr2:78038044..78622687hg17UCSC Ensembl
Cytoband2p12
Allele length
AssemblyAllele length
hg38584644
hg19584644
hg18584644
hg17584644
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756933, esv2757811
SamplesNA18558, NA18859
Known GenesSNAR-H
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)esv2759068
Frequency
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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