A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759430



Internal ID9634889
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:52928056..52996406hg38UCSC Ensembl
Innerchr6:52792854..52861204hg19UCSC Ensembl
Innerchr6:52900813..52969163hg18UCSC Ensembl
Innerchr6:52900813..52969163hg17UCSC Ensembl
Cytoband6p12.1
Allele length
AssemblyAllele length
hg3868351
hg1968351
hg1868351
hg1768351
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757168
SamplesNA19127, NA19144, NA19129, NA19145
Known GenesGSTA4
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)esv2759430
Frequency
Sample Size270
Observed Gain0
Observed Loss4
Observed Complex0
Frequencyn/a


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