A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758715



Internal ID9634174
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr18:13998749..15377894hg38UCSC Ensembl
Innerchr18:13998748..15377893hg19UCSC Ensembl
Innerchr18:13988748..15367893hg18UCSC Ensembl
Innerchr18:13988748..15367893hg17UCSC Ensembl
Cytoband18p11.21
Allele length
AssemblyAllele length
hg381379146
hg191379146
hg181379146
hg171379146
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756821, esv2758472, esv2757670
SamplesNA12248, NA10857, NA12155, NA18563, NA07048, NA18529, NA18976, NA10838, NA19000, NA18570, NA18945, NA06991, NA18540, NA18612
Known GenesANKRD20A5P, ANKRD30B, CXADRP3, CYP4F35P, LOC400644, LOC644669, MIR3156-2, POTEC, ZNF519
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)esv2758715
Frequency
Sample Size270
Observed Gain14
Observed Loss0
Observed Complex0
Frequencyn/a


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