A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758896



Internal ID9634355
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
InnerchrX:140904098..141745811hg38UCSC Ensembl
InnerchrX:139986263..140834012hg19UCSC Ensembl
InnerchrX:139813929..140661678hg18UCSC Ensembl
InnerchrX:139711783..140559532hg17UCSC Ensembl
CytobandXq27.1
Allele length
AssemblyAllele length
hg38841714
hg19847750
hg18847750
hg17847750
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2756778, esv2756791, esv2758594
SamplesNA19141, NA11829, NA12814, NA18603, NA12248, NA19171, NA18940, NA12812, NA10846, NA18860, NA12762, NA19130, NA18949, NA12005, NA19207, NA19128, NA18966, NA19200, NA19210, NA19120, NA19194, NA12003, NA12872, NA19161, NA18871, NA19103, NA11839, NA19208, NA19142, NA18856, NA19154, NA18857, NA18853, NA19101, NA18555, NA19160, NA12043, NA12716, NA12864, NA18863, NA18913, NA19144, NA12874, NA18501, NA19173, NA19211, NA19102, NA18854, NA18872
Known GenesLDOC1, MIR320D2, SPANXA1, SPANXA2, SPANXA2-OT1, SPANXB1, SPANXB2, SPANXC, SPANXD, SPANXE, SPANXF1
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)esv2758896
Frequency
Sample Size270
Observed Gain49
Observed Loss1
Observed Complex0
Frequencyn/a


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