A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759759



Internal ID9981904
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr10:57062484..57188447hg38UCSC Ensembl
Innerchr10:58822244..58948207hg19UCSC Ensembl
Innerchr10:58492250..58618213hg18UCSC Ensembl
Innerchr10:58492250..58618213hg17UCSC Ensembl
Cytoband10q21.1
Allele length
AssemblyAllele length
hg38125964
hg19125964
hg18125964
hg17125964
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757391
SamplesNA18995, NA18964, NA18975, NA18951, NA18956, NA18948, NA18555, NA18974, NA18542, NA18564, NA18943, NA18971, NA18994, NA18972, NA18623
Known Genes
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)esv2759759
Frequency
Sample Size270
Observed Gain0
Observed Loss15
Observed Complex0
Frequencyn/a


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