A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757197



Internal ID9632656
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:160011299..160649838hg38UCSC Ensembl
Innerchr6:160432331..161070870hg19UCSC Ensembl
Innerchr6:160352321..160990860hg18UCSC Ensembl
Innerchr6:160402742..161041281hg17UCSC Ensembl
Cytoband6q25.3
Allele length
AssemblyAllele length
hg38638540
hg19638540
hg18638540
hg17638540
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759484
Supporting Variantsessv3847, essv24539
SamplesNA11831, NA18953
Known GenesIGF2R, LOC729603, LPA, LPAL2, SLC22A1, SLC22A2, SLC22A3
MethodSNP array
AnalysisThe 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)
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2757197
Frequency
Sample Size270
Observed Gain1
Observed Loss1
Observed Complex0
Frequencyn/a


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