A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2760069



Internal ID9635528
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:4922849..5374828hg38UCSC Ensembl
Innerchr16:4972850..5424829hg19UCSC Ensembl
Innerchr16:4912851..5364830hg18UCSC Ensembl
Innerchr16:4912851..5364830hg17UCSC Ensembl
Cytoband16p13.3
Allele length
AssemblyAllele length
hg38451980
hg19451980
hg18451980
hg17451980
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757620, esv2758408
SamplesNA18855, NA12864, NA18981
Known GenesALG1, C16orf89, FAM86A, NAGPA, NAGPA-AS1, PPL, SEC14L5
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)esv2760069
Frequency
Sample Size270
Observed Gain2
Observed Loss1
Observed Complex0
Frequencyn/a


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