A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757609



Internal ID9633068
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr15:84159214..84559840hg38UCSC Ensembl
Innerchr15:84827966..85103071hg19UCSC Ensembl
Innerchr15:82618970..82904075hg18UCSC Ensembl
Innerchr15:82618970..82904075hg17UCSC Ensembl
Cytoband15q25.2
Allele length
AssemblyAllele length
hg38400627
hg19275106
hg18285106
hg17285106
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2760048
Supporting Variantsessv3, essv205, essv2554, essv18057, essv1973, essv9505
SamplesNA18942, NA06993, NA18945, NA18974, NA18994, NA18521
Known GenesDNM1P41, GOLGA6L4, GOLGA6L5P, LOC100505679, LOC388152, LOC440300, LOC642423, UBE2Q2P1
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)esv2757609
Frequency
Sample Size270
Observed Gain5
Observed Loss1
Observed Complex0
Frequencyn/a


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