A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758722



Internal ID9634181
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr18:36470072..36901904hg38UCSC Ensembl
Innerchr18:34050035..34481867hg19UCSC Ensembl
Innerchr18:32304033..32735865hg18UCSC Ensembl
Innerchr18:32304033..32735865hg17UCSC Ensembl
Cytoband18q12.2
Allele length
AssemblyAllele length
hg38431833
hg19431833
hg18431833
hg17431833
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756822, esv2758475
SamplesNA18971
Known GenesFHOD3, KIAA1328, TPGS2
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)esv2758722
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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