A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757630



Internal ID9633089
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:16259309..16651787hg38UCSC Ensembl
Innerchr16:16353166..16745644hg19UCSC Ensembl
Innerchr16:16260667..16653145hg18UCSC Ensembl
Innerchr16:16260667..16653145hg17UCSC Ensembl
Cytoband16p13.11
Allele length
AssemblyAllele length
hg38392479
hg19392479
hg18392479
hg17392479
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758633
Supporting Variantsessv7468, essv499, essv6062, essv6426, essv197
SamplesNA18603, NA18545, NA18633, NA18952, NA18994
Known GenesLOC100288162, MIR3179-1, MIR3179-2, MIR3179-3, MIR3180-1, MIR3180-2, MIR3180-3, MIR6511A-2, MIR6770-2, NOMO3, NPIPA7, NPIPA8, PKD1P1
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)esv2757630
Frequency
Sample Size270
Observed Gain1
Observed Loss4
Observed Complex0
Frequencyn/a


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