A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2760023



Internal ID9635482
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr15:31474097..32694378hg38UCSC Ensembl
Innerchr15:31766300..32986579hg19UCSC Ensembl
Innerchr15:29553592..30773871hg18UCSC Ensembl
Innerchr15:29553592..30773871hg17UCSC Ensembl
Cytoband15q13.3
Allele length
AssemblyAllele length
hg381220282
hg191220280
hg181220280
hg171220280
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757594, esv2758375
SamplesNA19142, NA10831, NA11881, NA19207, NA18870, NA12154, NA19127, NA19152, NA18871, NA12801, NA18523, NA12875, NA12264, NA19223, NA12815, NA18603, NA18516, NA12813, NA18542, NA19208, NA12865, NA19140, NA19161, NA12763, NA19211, NA11994, NA12155, NA18576, NA18960, NA18623, NA18990, NA18959, NA18973, NA18593, NA19153, NA18515, NA19102, NA19119, NA19154, NA10856, NA19221, NA19131, NA18582, NA07055, NA19138, NA10860, NA19101, NA19201, NA18872, NA12156, NA19116, NA19132, NA10830, NA18577, NA19099, NA12878, NA11830, NA11992, NA18852, NA18611, NA18981, NA19007, NA19202, NA10861
Known GenesARHGAP11A, CHRNA7, GOLGA8K, GOLGA8O, GOLGA8R, LOC100996255, OTUD7A, SCG5, ULK4P1, ULK4P2, ULK4P3, WHAMMP1
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)esv2760023
Frequency
Sample Size270
Observed Gain6
Observed Loss61
Observed Complex0
Frequencyn/a


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