A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757593



Internal ID9633052
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr15:30313633..30885273hg38UCSC Ensembl
Innerchr15:30605836..31177476hg19UCSC Ensembl
Innerchr15:28393128..28964768hg18UCSC Ensembl
Innerchr15:28393128..28964768hg17UCSC Ensembl
Cytoband15q13.2
Allele length
AssemblyAllele length
hg38571641
hg19571641
hg18571641
hg17571641
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2760022
Supporting Variantsessv1321, essv963, essv3493, essv8660, essv3914, essv2950, essv993
SamplesNA18999, NA18960, NA18964, NA18973, NA18981, NA19101, NA18972
Known GenesARHGAP11B, CHRFAM7A, GOLGA8H, HERC2P10, LOC100288637, LOC101059918, ULK4P1, ULK4P2
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)esv2757593
Frequency
Sample Size270
Observed Gain0
Observed Loss7
Observed Complex0
Frequencyn/a


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