A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2759206



Internal ID9634665
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:186619345..186849537hg38UCSC Ensembl
Innerchr3:186337134..186567326hg19UCSC Ensembl
Innerchr3:187819828..188050020hg18UCSC Ensembl
Innerchr3:187819836..188050028hg17UCSC Ensembl
Cytoband3q27.3
Allele length
AssemblyAllele length
hg38230193
hg19230193
hg18230193
hg17230193
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2757908, esv2757025
SamplesNA12801, NA12813
Known GenesADIPOQ, AHSG, EIF4A2, FETUB, HRG, KNG1, MIR1248, RFC4, SNORA4, SNORA63, SNORA81, SNORD2
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)esv2759206
Frequency
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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