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Fast and efficient QTL mapper for thousands of molecular phenotypes

Motivation: In order to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing. Re...

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Autores principales: Ongen, Halit, Buil, Alfonso, Brown, Andrew Anand, Dermitzakis, Emmanouil T., Delaneau, Olivier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866519/
https://www.ncbi.nlm.nih.gov/pubmed/26708335
http://dx.doi.org/10.1093/bioinformatics/btv722
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author Ongen, Halit
Buil, Alfonso
Brown, Andrew Anand
Dermitzakis, Emmanouil T.
Delaneau, Olivier
author_facet Ongen, Halit
Buil, Alfonso
Brown, Andrew Anand
Dermitzakis, Emmanouil T.
Delaneau, Olivier
author_sort Ongen, Halit
collection PubMed
description Motivation: In order to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing. Results: We have developed FastQTL, a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing. The outcome of permutations is modeled using beta distributions trained from a few permutations and from which adjusted P-values can be estimated at any level of significance with little computational cost. The Geuvadis & GTEx pilot datasets can be now easily analyzed an order of magnitude faster than previous approaches. Availability and implementation: Source code, binaries and comprehensive documentation of FastQTL are freely available to download at http://fastqtl.sourceforge.net/ Contact: emmanouil.dermitzakis@unige.ch or olivier.delaneau@unige.ch Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-48665192016-05-16 Fast and efficient QTL mapper for thousands of molecular phenotypes Ongen, Halit Buil, Alfonso Brown, Andrew Anand Dermitzakis, Emmanouil T. Delaneau, Olivier Bioinformatics Original Papers Motivation: In order to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing. Results: We have developed FastQTL, a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing. The outcome of permutations is modeled using beta distributions trained from a few permutations and from which adjusted P-values can be estimated at any level of significance with little computational cost. The Geuvadis & GTEx pilot datasets can be now easily analyzed an order of magnitude faster than previous approaches. Availability and implementation: Source code, binaries and comprehensive documentation of FastQTL are freely available to download at http://fastqtl.sourceforge.net/ Contact: emmanouil.dermitzakis@unige.ch or olivier.delaneau@unige.ch Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2016-05-15 2015-12-26 /pmc/articles/PMC4866519/ /pubmed/26708335 http://dx.doi.org/10.1093/bioinformatics/btv722 Text en © The Author 2015. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Papers
Ongen, Halit
Buil, Alfonso
Brown, Andrew Anand
Dermitzakis, Emmanouil T.
Delaneau, Olivier
Fast and efficient QTL mapper for thousands of molecular phenotypes
title Fast and efficient QTL mapper for thousands of molecular phenotypes
title_full Fast and efficient QTL mapper for thousands of molecular phenotypes
title_fullStr Fast and efficient QTL mapper for thousands of molecular phenotypes
title_full_unstemmed Fast and efficient QTL mapper for thousands of molecular phenotypes
title_short Fast and efficient QTL mapper for thousands of molecular phenotypes
title_sort fast and efficient qtl mapper for thousands of molecular phenotypes
topic Original Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866519/
https://www.ncbi.nlm.nih.gov/pubmed/26708335
http://dx.doi.org/10.1093/bioinformatics/btv722
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