title: Workflow for Integrated Processing of Multicohort Untargeted1H NMR Metabolomics Data in Large-Scale Metabolic Epidemiology.
abstract: Large-scale metabolomics studies involving thousands of samples present multiple challenges in data analysis, particularly when an untargeted platform is used. Studies with multiple cohorts and analysis platforms exacerbate existing problems such as peak alignment and normalization. Therefore, there is a need for robust processing pipelines that can ensure reliable data for statistical analysis. The COMBI-BIO project incorporates serum from ∼8000 individuals, in three cohorts, profiled by six assays in two phases using both1H NMR and UPLC-MS. Here we present the COMBI-BIO NMR analysis pipeline and demonstrate its fitness for purpose using representative quality control (QC) samples. NMR spectra were first aligned and normalized. After eliminating interfering signals, outliers identified using Hotelling's T2were removed and a cohort/phase adjustment was applied, resulting in two NMR data sets (CPMG and NOESY). Alignment of the NMR data was shown to increase the correlation-based alignment quality measure from 0.319 to 0.391 for CPMG and from 0.536 to 0.586 for NOESY, showing that the improvement was present across both large and small peaks. End-to-end quality assessment of the pipeline was achieved using Hotelling's T2distributions. For CPMG spectra, the interquartile range decreased from 1.425 in raw QC data to 0.679 in processed spectra, while the corresponding change for NOESY spectra was from 0.795 to 0.636, indicating an improvement in precision following processing. PCA indicated that gross phase and cohort differences were no longer present. These results illustrate that the pipeline produces robust and reproducible data, successfully addressing the methodological challenges of this large multifaceted study.
authors.affiliation: Medical Research Council - Public Health England (MRC-PHE) Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London , St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom.
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Karaman
authors.affiliation: Medical Research Council - Public Health England (MRC-PHE) Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London , St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom.
authors.forename: Diana L S
authors.initials: DL
authors.lastname: Ferreira
authors.affiliation: Metabometrix, Ltd. , Bioincubator Unit, Bessemer Building, Prince Consort Road, SW7 2BP South Kensington, London, United Kingdom.
authors.forename: Claire L
authors.initials: CL
authors.lastname: Boulangé
authors.affiliation: Metabometrix, Ltd. , Bioincubator Unit, Bessemer Building, Prince Consort Road, SW7 2BP South Kensington, London, United Kingdom.
authors.forename: Manuja R
authors.initials: MR
authors.lastname: Kaluarachchi
authors.affiliation: Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Boulevard , Winston-Salem, North Carolina 27157, United States.
authors.forename: David
authors.initials: D
authors.lastname: Herrington
authors.affiliation: Metabometrix, Ltd. , Bioincubator Unit, Bessemer Building, Prince Consort Road, SW7 2BP South Kensington, London, United Kingdom.|Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London , Sir Alexander Fleming Building, South Kensington, SW7 2AZ London, United Kingdom.
authors.forename: Anthony C
authors.initials: AC
authors.lastname: Dona
authors.affiliation: Medical Research Council - Public Health England (MRC-PHE) Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London , St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom.
authors.forename: Raphaële
authors.initials: R
authors.lastname: Castagné
authors.affiliation: Medical Research Council - Public Health England (MRC-PHE) Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London , St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom.
authors.forename: Alireza
authors.initials: A
authors.lastname: Moayyeri
authors.affiliation: Medical Research Council - Public Health England (MRC-PHE) Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London , St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Lehne
authors.affiliation: Medical Research Council - Public Health England (MRC-PHE) Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London , St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom.
authors.forename: Marie
authors.initials: M
authors.lastname: Loh
authors.affiliation: Department of Epidemiology, Erasmus University, Erasmus Medical Center , Dr Molewaterplein 50, 3015 GE Rotterdam, Netherlands.
authors.forename: Paul S
authors.initials: PS
authors.lastname: de Vries
authors.affiliation: Department of Epidemiology, Erasmus University, Erasmus Medical Center , Dr Molewaterplein 50, 3015 GE Rotterdam, Netherlands.
authors.forename: Abbas
authors.initials: A
authors.lastname: Dehghan
authors.affiliation: Department of Epidemiology, Erasmus University, Erasmus Medical Center , Dr Molewaterplein 50, 3015 GE Rotterdam, Netherlands.
authors.forename: Oscar H
authors.initials: OH
authors.lastname: Franco
authors.affiliation: Department of Epidemiology, Erasmus University, Erasmus Medical Center , Dr Molewaterplein 50, 3015 GE Rotterdam, Netherlands.
authors.forename: Albert
authors.initials: A
authors.lastname: Hofman
authors.affiliation: Medical Research Council - Public Health England (MRC-PHE) Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London , St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom.|Department of Hygiene and Epidemiology, University of Ioannina School of Medicine , University Campus, P.O. Box 1186, 45110 Ioannina, Greece.
authors.forename: Evangelos
authors.initials: E
authors.lastname: Evangelou
authors.affiliation: Medical Research Council - Public Health England (MRC-PHE) Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London , St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom.|Department of Hygiene and Epidemiology, University of Ioannina School of Medicine , University Campus, P.O. Box 1186, 45110 Ioannina, Greece.
authors.forename: Ioanna
authors.initials: I
authors.lastname: Tzoulaki
authors.affiliation: Medical Research Council - Public Health England (MRC-PHE) Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London , St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom.
authors.forename: Paul
authors.initials: P
authors.lastname: Elliott
authors.affiliation: Metabometrix, Ltd. , Bioincubator Unit, Bessemer Building, Prince Consort Road, SW7 2BP South Kensington, London, United Kingdom.|Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London , Sir Alexander Fleming Building, South Kensington, SW7 2AZ London, United Kingdom.
authors.forename: John C
authors.initials: JC
authors.lastname: Lindon
authors.affiliation: Metabometrix, Ltd. , Bioincubator Unit, Bessemer Building, Prince Consort Road, SW7 2BP South Kensington, London, United Kingdom.|Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London , Sir Alexander Fleming Building, South Kensington, SW7 2AZ London, United Kingdom.
authors.forename: Timothy M D
authors.initials: TM
authors.lastname: Ebbels
mesh_terms: D003627:Data Interpretation, Statistical; D006801:Humans; D055432:Metabolomics / Q000295:instrumentation / Q000379:methods* / Q000706:statistics & numerical data; D017720:Molecular Epidemiology; D066244:Proton Magnetic Resonance Spectroscopy / Q000379:methods* / Q000592:standards / Q000706:statistics & numerical data; D011786:Quality Control; D015203:Reproducibility of Results; D057188:Workflow
keywords: NMR; alignment; epidemiology; large scale; metabolomics; multicohort; normalization; preprocessing; quality control