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An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors

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 creat...

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Autores principales: Broeckx, Bart J. G., Coopman, Frank, Verhoeven, Geert, Bosmans, Tim, Gielen, Ingrid, Dingemanse, Walter, Saunders, Jimmy H., Deforce, Dieter, Van Nieuwerburgh, Filip
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4656174/
https://www.ncbi.nlm.nih.gov/pubmed/26597515
http://dx.doi.org/10.1186/s12859-015-0822-7
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author Broeckx, Bart J. G.
Coopman, Frank
Verhoeven, Geert
Bosmans, Tim
Gielen, Ingrid
Dingemanse, Walter
Saunders, Jimmy H.
Deforce, Dieter
Van Nieuwerburgh, Filip
author_facet Broeckx, Bart J. G.
Coopman, Frank
Verhoeven, Geert
Bosmans, Tim
Gielen, Ingrid
Dingemanse, Walter
Saunders, Jimmy H.
Deforce, Dieter
Van Nieuwerburgh, Filip
author_sort Broeckx, Bart J. G.
collection PubMed
description 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. CONCLUSION: 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0822-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-46561742015-11-24 An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors Broeckx, Bart J. G. Coopman, Frank Verhoeven, Geert Bosmans, Tim Gielen, Ingrid Dingemanse, Walter Saunders, Jimmy H. Deforce, Dieter Van Nieuwerburgh, Filip BMC Bioinformatics Software 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. CONCLUSION: 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0822-7) contains supplementary material, which is available to authorized users. BioMed Central 2015-11-19 /pmc/articles/PMC4656174/ /pubmed/26597515 http://dx.doi.org/10.1186/s12859-015-0822-7 Text en © Broeckx et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Broeckx, Bart J. G.
Coopman, Frank
Verhoeven, Geert
Bosmans, Tim
Gielen, Ingrid
Dingemanse, Walter
Saunders, Jimmy H.
Deforce, Dieter
Van Nieuwerburgh, Filip
An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors
title An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors
title_full An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors
title_fullStr An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors
title_full_unstemmed An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors
title_short An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors
title_sort heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4656174/
https://www.ncbi.nlm.nih.gov/pubmed/26597515
http://dx.doi.org/10.1186/s12859-015-0822-7
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