A curated catalogue of human genomic structural variation

Variant Details

Variant: esv2756771

Internal ID9632230
Location Information
TypeCoordinatesAssemblyOther Links
InnerchrX:47959425..48209787hg38UCSC Ensembl
InnerchrX:47818824..48069222hg19UCSC Ensembl
InnerchrX:47703768..47954166hg18UCSC Ensembl
InnerchrX:47575078..47825476hg17UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758866
Supporting Variantsessv13379, essv9283, essv2422, essv11486, essv8979, essv7968, essv23168, essv11377, essv12060, essv14899, essv6213, essv14228, essv18493
SamplesNA19137, NA10831, NA19127, NA18951, NA18563, NA18856, NA19129, NA19238, NA19139, NA19159, NA12156, NA19240, NA18913
Known GenesSPACA5, SPACA5B, SSX5, SSX6, ZNF182, ZNF630
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)
Pubmed ID17122850
Accession Number(s)esv2756771
Sample Size270
Observed Gain10
Observed Loss3
Observed Complex0

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