title: mQTL.NMR: an integrated suite for genetic mapping of quantitative variations of (1)H NMR-based metabolic profiles.
abstract: High-throughput (1)H nuclear magnetic resonance (NMR) is an increasingly popular robust approach for qualitative and quantitative metabolic profiling, which can be used in conjunction with genomic techniques to discover novel genetic associations through metabotype quantitative trait locus (mQTL) mapping. There is therefore a crucial necessity to develop specialized tools for an accurate detection and unbiased interpretability of the genetically determined metabolic signals. Here we introduce and implement a combined chemoinformatic approach for objective and systematic analysis of untargeted (1)H NMR-based metabolic profiles in quantitative genetic contexts. The R/Bioconductor mQTL.NMR package was designed to (i) perform a series of preprocessing steps restoring spectral dependency in collinear NMR data sets to reduce the multiple testing burden, (ii) carry out robust and accurate mQTL mapping in human cohorts as well as in rodent models, (iii) statistically enhance structural assignment of genetically determined metabolites, and (iv) illustrate results with a series of visualization tools. Built-in flexibility and implementation in the powerful R/Bioconductor framework allow key preprocessing steps such as peak alignment, normalization, or dimensionality reduction to be tailored to specific problems. The mQTL.NMR package is freely available with its source code through the Comprehensive R/Bioconductor repository and its own website ( http://www.ican-institute.org/tools/ ). It represents a significant advance to facilitate untargeted metabolomic data processing and quantitative analysis and their genetic mapping.
authors: Lyamine
authors: L
authors: Hedjazi
authors: Dominique
authors: D
authors: Gauguier
authors: ⊥School of Medicine, Lebanese American University, Beirut 1102 2801, Lebanon.
authors: Pierre A
authors: PA
authors: Zalloua
authors: ‡Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming building, London SW7 2AZ, U.K.
authors: Jeremy K
authors: JK
authors: Nicholson
authors: ‡Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming building, London SW7 2AZ, U.K.
authors: Marc-Emmanuel
authors: ME
authors: Dumas
authors: ∥Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K.|○Centre for Computational Biology, University of Birmingham, Haworth Building, Edgbaston B15 2TT, U.K.
authors: Jean-Baptiste
authors: JB
authors: Cazier
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D019295:Computational Biology; D023281:Genomics; D006801:Humans; D020407:Internet; D009682:Magnetic Resonance Spectroscopy; D055432:Metabolomics; D011522:Protons
chemical_list: D011522:Protons