A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758690



Internal ID9634149
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr17:41145123..41740591hg38UCSC Ensembl
Innerchr17:39301375..39896843hg19UCSC Ensembl
Innerchr17:36554901..37150369hg18UCSC Ensembl
Innerchr17:36554901..37150369hg17UCSC Ensembl
Cytoband17q21.2
Allele length
AssemblyAllele length
hg38595469
hg19595469
hg18595469
hg17595469
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757658, esv2758455
SamplesNA18863, NA18862, NA19129, NA18564, NA19101
Known GenesEIF1, GAST, HAP1, KRT13, KRT14, KRT15, KRT16, KRT17, KRT19, KRT31, KRT32, KRT33A, KRT33B, KRT34, KRT35, KRT36, KRT37, KRT38, KRT42P, KRT9, KRTAP16-1, KRTAP17-1, KRTAP29-1, KRTAP4-1, KRTAP4-2, KRTAP4-3, KRTAP4-4, KRTAP4-5, KRTAP9-1, KRTAP9-2, KRTAP9-3, KRTAP9-4, KRTAP9-6, KRTAP9-7, KRTAP9-8, KRTAP9-9, LINC00974, LOC100505782, MIR6510
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)esv2758690
Frequency
Sample Size270
Observed Gain3
Observed Loss2
Observed Complex0
Frequencyn/a


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