title: An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors.
abstract: BACKGROUND
  Identification of one or several disease causing variant(s) from the large collection of variants present in an individual is often achieved by the sequential use of heuristic filters. The recent development of whole exome sequencing enrichment designs for several non-model species created the need for a species-independent, fast and versatile analysis tool, capable of tackling a wide variety of standard and more complex inheritance models. With this aim, we developed "Mendelian", an R-package that can be used for heuristic variant filtering.
  
  
  RESULTS
  The R-package Mendelian offers fast and convenient filters to analyze putative variants for both recessive and dominant models of inheritance, with variable degrees of penetrance and detectance. Analysis of trios is supported. Filtering against variant databases and annotation of variants is also included. This package is not species specific and supports parallel computation. We validated this package by reanalyzing data from a whole exome sequencing experiment on intellectual disability in humans. In a second example, we identified the mutations responsible for coat color in the dog. This is the first example of whole exome sequencing without prior mapping in the dog.
  
  
  CONCLUSIONS
  We developed an R-package that enables the identification of disease-causing variants from the long list of variants called in sequencing experiments. The software and a detailed manual are available at https://github.com/BartBroeckx/Mendelian.
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000, Ghent, Belgium. Bart.broeckx@ugent.be.
authors.forename: Bart J G
authors.initials: BJ
authors.lastname: Broeckx
authors.affiliation: Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium. Frank.coopman@ugent.be.
authors.forename: Frank
authors.initials: F
authors.lastname: Coopman
authors.affiliation: Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium. Geertverhoeven@hotmail.com.
authors.forename: Geert
authors.initials: G
authors.lastname: Verhoeven
authors.affiliation: Department of Medicine and Clinical Biology of Small Animals, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium. Tim.Bosmans@ugent.be.
authors.forename: Tim
authors.initials: T
authors.lastname: Bosmans
authors.affiliation: Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium. Ingrid.Gielen@ugent.be.
authors.forename: Ingrid
authors.initials: I
authors.lastname: Gielen
authors.affiliation: Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium. Walter.Dingemanse@ugent.be.
authors.forename: Walter
authors.initials: W
authors.lastname: Dingemanse
authors.affiliation: Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium. Jimmy.Saunders@ugent.be.
authors.forename: Jimmy H
authors.initials: JH
authors.lastname: Saunders
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000, Ghent, Belgium. Dieter.Deforce@ugent.be.
authors.forename: Dieter
authors.initials: D
authors.lastname: Deforce
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000, Ghent, Belgium. Filip.VanNieuwerburgh@UGent.be.
authors.forename: Filip
authors.initials: F
authors.lastname: Van Nieuwerburgh
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D004285:Dogs; D059472:Exome / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D006200:Hair Color / Q000235:genetics*; D000066506:Heuristics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008607:Intellectual Disability / Q000235:genetics*; D010641:Phenotype; D017422:Sequence Analysis, DNA; D012984:Software