A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759081



Internal ID9634540
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:107833421..108606881hg38UCSC Ensembl
Innerchr2:108449877..109223337hg19UCSC Ensembl
Innerchr2:107816309..108589769hg18UCSC Ensembl
Innerchr2:107908395..108681855hg17UCSC Ensembl
Cytoband2q12.3
Allele length
AssemblyAllele length
hg38773461
hg19773461
hg18773461
hg17773461
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757823, esv2756940
SamplesNA18870, NA18872
Known GenesGCC2, LIMS1, RGPD4, SLC5A7, SULT1C2, SULT1C2P1, SULT1C3, SULT1C4
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)esv2759081
Frequency
Sample Size270
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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