A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758652



Internal ID9634111
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:69821219..70279319hg38UCSC Ensembl
Innerchr16:69855122..70313222hg19UCSC Ensembl
Innerchr16:68412623..68870723hg18UCSC Ensembl
Innerchr16:68412623..68870723hg17UCSC Ensembl
Cytoband16q22.1
Allele length
AssemblyAllele length
hg38458101
hg19458101
hg18458101
hg17458101
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2758428, esv2757640
SamplesNA18966, NA18603, NA18608, NA19210, NA18949, NA11839, NA18854, NA12762, NA18547, NA18973, NA19000, NA19102, NA19154, NA12057, NA18552, NA19138, NA19205, NA18852, NA18981, NA10854
Known GenesAARS, CLEC18A, CLEC18C, EXOSC6, LOC100506060, MIR140, MIR1972-1, MIR1972-2, PDPR, PDXDC2P, WWP2
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)esv2758652
Frequency
Sample Size270
Observed Gain8
Observed Loss12
Observed Complex0
Frequencyn/a


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