A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757598



Internal ID9633057
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr15:43539725..43766436hg38UCSC Ensembl
Innerchr15:43831923..44058634hg19UCSC Ensembl
Innerchr15:41619215..41845926hg18UCSC Ensembl
Innerchr15:41619215..41845926hg17UCSC Ensembl
Cytoband15q15.3
Allele length
AssemblyAllele length
hg38226712
hg19226712
hg18226712
hg17226712
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2760028
Supporting Variantsessv12070, essv7981, essv13953, essv11065, essv20521
SamplesNA19138, NA19238, NA19160, NA12716, NA19240
Known GenesCATSPER2, CATSPER2P1, CKMT1A, CKMT1B, PDIA3, PPIP5K1, RNU6-28P, STRC
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)esv2757598
Frequency
Sample Size270
Observed Gain0
Observed Loss5
Observed Complex0
Frequencyn/a


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