A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758634



Internal ID9634093
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:17440243..19147984hg38UCSC Ensembl
Innerchr16:17534100..19159306hg19UCSC Ensembl
Innerchr16:17441601..19066807hg18UCSC Ensembl
Innerchr16:17441601..19066807hg17UCSC Ensembl
Cytoband16p12.3
Allele length
AssemblyAllele length
hg381707742
hg191625207
hg181625207
hg171625207
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2758413, esv2757631
SamplesNA18621, NA18952, NA19209, NA18501, NA18570, NA18545, NA18603, NA07348, NA18994, NA18949, NA19211, NA18508, NA18992, NA07357, NA18547, NA18976, NA19139, NA18562, NA18974, NA18987, NA19138, NA18971, NA18555
Known GenesABCC6P1, ARL6IP1, COQ7, ITPRIPL2, LOC100288162, MIR3179-1, MIR3179-2, MIR3179-3, MIR3180-1, MIR3180-2, MIR3180-3, MIR6511A-2, MIR6770-2, NOMO2, NPIPA7, NPIPA8, RPS15A, SMG1, TMC7, XYLT1
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)esv2758634
Frequency
Sample Size270
Observed Gain13
Observed Loss10
Observed Complex0
Frequencyn/a


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