Introduction

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.GeneCOST software is freely available at www.igbam.bilgem.tubitak.gov.tr/en/softwares/genecost-en/index.html.buozer@gmail.comSupplementary data are available at Bioinformatics online.

Publications

  1. GeneCOST: a novel scoring-based prioritization framework for identifying disease causing genes.
    Cite this
    Ozer B, Sağıroğlu M, Demirci H, 2015-11-01 - Bioinformatics (Oxford, England)

Credits

  1. Bugra Ozer
    Developer

    Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK), Turkey

  2. Mahmut Sağıroğlu
    Developer

    Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK), Turkey

  3. Hüseyin Demirci
    Investigator

    Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK), Turkey

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Summary
AccessionBT006378
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionTurkey
Submitted ByHüseyin Demirci