A curated catalogue of human genomic structural variation

Variant Details

Variant: esv2758866

Internal ID9634325
Location Information
TypeCoordinatesAssemblyOther Links
InnerchrX:47907511..48287275hg38UCSC Ensembl
InnerchrX:47766910..48146710hg19UCSC Ensembl
InnerchrX:47651854..48031654hg18UCSC Ensembl
InnerchrX:47523164..47902964hg17UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2758568, esv2756771
SamplesNA19137, NA10831, NA19127, NA18951, NA18563, NA18856, NA19129, NA19238, NA19139, NA19159, NA12156, NA19240, NA18913
Known GenesSPACA5, SPACA5B, SSX1, SSX5, SSX6, ZNF182, ZNF630, ZNF81
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)
Pubmed ID17122850
Accession Number(s)esv2758866
Sample Size270
Observed Gain10
Observed Loss3
Observed Complex0

Hosted by The Centre for Applied Genomics
Grant support for DGV
Please read the usage disclaimer