| Title: | Implementation of quality controls is essential to prevent batch effects in breathomics data and allow for cross-study comparisons |
| Author(s): | Stavropoulos G; Jonkers D; Mujagic Z; Koek GH; Masclee AAM; Pierik MJ; Dallinga JW; van Schooten FJ; Smolinska A; |
| Address: | "Department of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translational Research, Maastricht University, Maastricht, The Netherlands" |
| ISSN/ISBN: | 1752-7163 (Electronic) 1752-7155 (Linking) |
| Abstract: | "Exhaled breath analysis has become a promising monitoring tool for various ailments by identifying volatile organic compounds (VOCs) as indicative biomarkers excreted in the human body. Throughout the process of sampling, measuring, and data processing, non-biological variations are introduced in the data leading to batch effects. Algorithmic approaches have been developed to cope with within-study batch effects. Batch differences, however, may occur among different studies too, and up-to-date, ways to correct for cross-study batch effects are lacking; ultimately, cross-study comparisons to verify the uniqueness of found VOC profiles for a specific disease may be challenging. This study applies within-study batch-effect-correction approaches to correct for cross-study batch effects; suggestions are made that may help prevent the introduction of cross-study variations. Three batch-effect-correction algorithms were investigated: zero-centering, combat, and the analysis of covariance framework. The breath samples were collected from inflammatory bowel disease ([Formula: see text]), chronic liver disease ([Formula: see text]), and irritable bowel syndrome ([Formula: see text]) patients at different periods, and they were analysed via gas chromatography-mass spectrometry. Multivariate statistics were used to visualise and verify the results. The visualisation of the data before any batch-effect-correction technique was applied showed a clear distinction due to probable batch effects among the datasets of the three cohorts. The visualisation of the three datasets after implementing all three correction techniques showed that the batch effects were still present in the data. Predictions made using partial least squares discriminant analysis and random forest confirmed this observation. The within-study batch-effect-correction approaches fail to correct for cross-study batch effects present in the data. The present study proposes a framework for systematically standardising future breathomics data by using internal standards or quality control samples at regular analysis intervals. Further knowledge regarding the nature of the unsolicited variations among cross-study batches must be obtained to move the field further" |
| Keywords: | Algorithms Biomarkers/analysis Breath Tests/*methods Chronic Disease Discriminant Analysis Exhalation Female Gas Chromatography-Mass Spectrometry Humans Inflammatory Bowel Diseases/diagnosis Irritable Bowel Syndrome/diagnosis Least-Squares Analysis Liver; |
| Notes: | "MedlineStavropoulos, Georgios Jonkers, Daisy M A E Mujagic, Zlatan Koek, Ger H Masclee, Ad A M Pierik, Marieke J Dallinga, Jan W Van Schooten, Frederik-Jan Smolinska, Agnieszka eng Comparative Study Research Support, Non-U.S. Gov't England 2020/03/03 J Breath Res. 2020 Mar 19; 14(2):026012. doi: 10.1088/1752-7163/ab7b8d" |
