A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757631



Internal ID9633090
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:17440243..19071713hg38UCSC Ensembl
Innerchr16:17534100..19083035hg19UCSC Ensembl
Innerchr16:17441601..18990536hg18UCSC Ensembl
Innerchr16:17441601..18990536hg17UCSC Ensembl
Cytoband16p12.3
Allele length
AssemblyAllele length
hg381631471
hg191548936
hg181548936
hg171548936
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758634
Supporting Variantsessv1681, essv7626, essv202
SamplesNA18994, NA18992, NA18547
Known GenesABCC6P1, ARL6IP1, COQ7, LOC100288162, MIR3179-1, MIR3179-2, MIR3179-3, MIR3180-1, MIR3180-2, MIR3180-3, MIR6511A-2, MIR6770-2, NOMO2, NPIPA7, NPIPA8, RPS15A, SMG1, TMC7, XYLT1
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)esv2757631
Frequency
Sample Size270
Observed Gain3
Observed Loss0
Observed Complex0
Frequencyn/a


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