title: KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels.
abstract: BACKGROUND
  Non-synonymous single nucleotide polymorphisms (nsSNPs) in voltage-gated potassium (Kv) channels cause diseases with potentially fatal consequences in seemingly healthy individuals. Identifying disease-causing genetic variation will aid presymptomatic diagnosis and treatment of such disorders. NsSNP-effect predictors are hypothesized to perform best when developed for specific gene families. We, thus, created KvSNP: a method that assigns a disease-causing probability to Kv-channel nsSNPs.
  
  
  RESULTS
  KvSNP outperforms popular non gene-family-specific methods (SNPs&GO, SIFT and Polyphen) in predicting the disease potential of Kv-channel variants, according to all tested metrics (accuracy, Matthews correlation coefficient and area under receiver operator characteristic curve). Most significantly, it increases the separation of the median predicted disease probabilities between benign and disease-causing SNPs by 26% on the next-best competitor. KvSNP has ranked 172 uncharacterized Kv-channel nsSNPs by disease-causing probability.
  
  
  METHODS
  KvSNP, a WEKA implementation is available at www.bioinformatics.leeds.ac.uk/KvDB/KvSNP.html.
  
  
  BACKGROUND
  d.r.westhead@leeds.ac.uk
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Molecular and Cellular Biology, Faculty of Biological Sciences and Institute of Membrane and Systems Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
authors.forename: L F
authors.initials: LF
authors.lastname: Stead
authors.forename: I C
authors.initials: IC
authors.lastname: Wood
authors.forename: D R
authors.initials: DR
authors.lastname: Westhead
mesh_terms: D000328:Adult; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D024642:Potassium Channels, Voltage-Gated / Q000235:genetics*; D011336:Probability; D012984:Software
chemical_list: D024642:Potassium Channels, Voltage-Gated