title: GeneCOST: a novel scoring-based prioritization framework for identifying disease causing genes.
abstract: Due to the big data produced by next-generation sequencing studies, there is an evident need for methods to extract the valuable information gathered from these experiments. In this work, we propose GeneCOST, a novel scoring-based method to evaluate every gene for their disease association. Without any prior filtering and any prior knowledge, we assign a disease likelihood score to each gene in correspondence with their variations. Then, we rank all genes based on frequency, conservation, pedigree and detailed variation information to find out the causative reason of the disease state. We demonstrate the usage of GeneCOST with public and real life Mendelian disease cases including recessive, dominant, compound heterozygous and sporadic models. As a result, we were able to identify causative reason behind the disease state in top rankings of our list, proving that this novel prioritization framework provides a powerful environment for the analysis in genetic disease studies alternative to filtering-based approaches.
  
  
  METHODS
  GeneCOST software is freely available at www.igbam.bilgem.tubitak.gov.tr/en/softwares/genecost-en/index.html.
  
  
  BACKGROUND
  buozer@gmail.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK), Gebze, Kocaeli, Turkey and Department of Biological Sciences and Bioengineering, Sabanci University, 34956, Istanbul, Turkey.
authors.forename: Bugra
authors.initials: B
authors.lastname: Ozer
authors.affiliation: Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK), Gebze, Kocaeli, Turkey and.
authors.forename: Mahmut
authors.initials: M
authors.lastname: Sağıroğlu
authors.affiliation: Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK), Gebze, Kocaeli, Turkey and.
authors.forename: Hüseyin
authors.initials: H
authors.lastname: Demirci
mesh_terms: D004194:Disease / Q000235:genetics*; D005190:Family; D056726:Genetic Association Studies / Q000379:methods*; D006801:Humans; D009154:Mutation / Q000235:genetics; D012984:Software