A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759899



Internal ID9635358
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:52169480..52391735hg38UCSC Ensembl
Innerchr12:52563264..52785519hg19UCSC Ensembl
Innerchr12:50849531..51071786hg18UCSC Ensembl
Innerchr12:50849531..51071786hg17UCSC Ensembl
Cytoband12q13.13
Allele length
AssemblyAllele length
hg38222256
hg19222256
hg18222256
hg17222256
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757503, esv2758308
SamplesNA12239
Known GenesC12orf80, KRT7, KRT80, KRT81, KRT83, KRT84, KRT85, KRT86, LINC00592
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)esv2759899
Frequency
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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