A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758694



Internal ID9634153
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr17:48525311..48759475hg38UCSC Ensembl
Innerchr17:46602673..46836837hg19UCSC Ensembl
Innerchr17:43957672..44191836hg18UCSC Ensembl
Innerchr17:43957672..44191836hg17UCSC Ensembl
Cytoband17q21.32
Allele length
AssemblyAllele length
hg38234165
hg19234165
hg18234165
hg17234165
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757661, esv2758459
SamplesNA12004, NA10838
Known GenesHOXB1, HOXB13, HOXB2, HOXB3, HOXB4, HOXB5, HOXB6, HOXB7, HOXB8, HOXB9, HOXB-AS1, HOXB-AS3, MIR10A, MIR196A1, MIR3185, PRAC1, PRAC2
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)esv2758694
Frequency
Sample Size270
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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