A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756777



Internal ID9632236
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
InnerchrX:135606603..135831108hg38UCSC Ensembl
InnerchrX:134740528..134948034hg19UCSC Ensembl
InnerchrX:134568194..134775700hg18UCSC Ensembl
InnerchrX:134466048..134673554hg17UCSC Ensembl
CytobandXq26.3
Allele length
AssemblyAllele length
hg38224506
hg19207507
hg18207507
hg17207507
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758895
Supporting Variantsessv8044, essv12947, essv20730, essv21642, essv8684
SamplesNA12761, NA12752, NA19103, NA18912, NA19102
Known GenesCT45A1, CT45A2, CT45A3, CT45A4, CT45A5
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)esv2756777
Frequency
Sample Size270
Observed Gain5
Observed Loss0
Observed Complex0
Frequencyn/a


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