A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757387



Internal ID9979464
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr10:54676748..54713994hg38UCSC Ensembl
Innerchr10:56436508..56473754hg19UCSC Ensembl
Innerchr10:56106514..56143760hg18UCSC Ensembl
Innerchr10:56106514..56143760hg17UCSC Ensembl
Cytoband10q21.1
Allele length
AssemblyAllele length
hg3837247
hg1937247
hg1837247
hg1737247
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759754
Supporting Variantsessv21939, essv22255, essv20844, essv25130, essv25193, essv25141, essv18893, essv21101, essv24160, essv23696, essv18562, essv24952
SamplesNA12717, NA11829, NA10851, NA12751, NA10854, NA11992, NA11839, NA11840, NA12707, NA10856, NA12057, NA12740
Known GenesPCDH15
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)esv2757387
Frequency
Sample Size270
Observed Gain12
Observed Loss0
Observed Complex0
Frequencyn/a


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