Quality control and removal of technical variation of NMR metabolic biomarker data in ~120,000 UK Biobank participants

Scott C. Ritchie; Praveen Surendran; Savita Karthikeyan; Samuel A. Lambert; Thomas Bolton; Lisa Pennells; John Danesh; Emanuele Di Angelantonio; Adam S. Butterworth; Michael Inouye

doi:10.1038/s41597-023-01949-y

Scientific Data (Jan 2023)

Quality control and removal of technical variation of NMR metabolic biomarker data in ~120,000 UK Biobank participants

Scott C. Ritchie,
Praveen Surendran,
Savita Karthikeyan,
Samuel A. Lambert,
Thomas Bolton,
Lisa Pennells,
John Danesh,
Emanuele Di Angelantonio,
Adam S. Butterworth,
Michael Inouye

Affiliations

Scott C. Ritchie: Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge
Praveen Surendran: British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge
Savita Karthikeyan: British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge
Samuel A. Lambert: Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge
Thomas Bolton: British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge
Lisa Pennells: British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge
John Danesh: British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge
Emanuele Di Angelantonio: British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge
Adam S. Butterworth: British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge
Michael Inouye: Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge

DOI: https://doi.org/10.1038/s41597-023-01949-y
Journal volume & issue: Vol. 10, no. 1
pp. 1 – 15

Abstract

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Abstract Metabolic biomarker data quantified by nuclear magnetic resonance (NMR) spectroscopy in approximately 121,000 UK Biobank participants has recently been released as a community resource, comprising absolute concentrations and ratios of 249 circulating metabolites, lipids, and lipoprotein sub-fractions. Here we identify and characterise additional sources of unwanted technical variation influencing individual biomarkers in the data available to download from UK Biobank. These included sample preparation time, shipping plate well, spectrometer batch effects, drift over time within spectrometer, and outlier shipping plates. We developed a procedure for removing this unwanted technical variation, and demonstrate that it increases signal for genetic and epidemiological studies of the NMR metabolic biomarker data in UK Biobank. We subsequently developed an R package, ukbnmr, which we make available to the wider research community to enhance the utility of the UK Biobank NMR metabolic biomarker data and to facilitate rapid analysis.

Published in Scientific Data

ISSN: 2052-4463 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/sdata/

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