A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757331



Internal ID9979408
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr9:29928568..30009949hg38UCSC Ensembl
Innerchr9:29928566..30009947hg19UCSC Ensembl
Innerchr9:29918566..29999947hg18UCSC Ensembl
Innerchr9:29918566..29999947hg17UCSC Ensembl
Cytoband9p21.1
Allele length
AssemblyAllele length
hg3881382
hg1981382
hg1881382
hg1781382
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759686
Supporting Variantsessv24117, essv23638
SamplesNA07048, NA07055
Known Genes
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)esv2757331
Frequency
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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