A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759671



Internal ID9635130
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr9:12235048..12784093hg38UCSC Ensembl
Innerchr9:12235048..12784092hg19UCSC Ensembl
Innerchr9:12225048..12774092hg18UCSC Ensembl
Innerchr9:12225048..12774092hg17UCSC Ensembl
Cytoband9p23
Allele length
AssemblyAllele length
hg38549046
hg19549045
hg18549045
hg17549045
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2758181, esv2758182, esv2757318, esv2757317
SamplesNA19144, NA19130, NA12874
Known GenesLURAP1L, TYRP1
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)esv2759671
Frequency
Sample Size270
Observed Gain0
Observed Loss3
Observed Complex0
Frequencyn/a


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