Robust identification of temporal biomarkers in longitudinal omics studies.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
02 08 2022
02 08 2022
Historique:
received:
29
11
2021
revised:
28
04
2022
accepted:
26
06
2022
pubmed:
29
6
2022
medline:
15
11
2022
entrez:
28
6
2022
Statut:
ppublish
Résumé
Longitudinal studies increasingly collect rich 'omics' data sampled frequently over time and across large cohorts to capture dynamic health fluctuations and disease transitions. However, the generation of longitudinal omics data has preceded the development of analysis tools that can efficiently extract insights from such data. In particular, there is a need for statistical frameworks that can identify not only which omics features are differentially regulated between groups but also over what time intervals. Additionally, longitudinal omics data may have inconsistencies, including non-uniform sampling intervals, missing data points, subject dropout and differing numbers of samples per subject. In this work, we developed OmicsLonDA, a statistical method that provides robust identification of time intervals of temporal omics biomarkers. OmicsLonDA is based on a semi-parametric approach, in which we use smoothing splines to model longitudinal data and infer significant time intervals of omics features based on an empirical distribution constructed through a permutation procedure. We benchmarked OmicsLonDA on five simulated datasets with diverse temporal patterns, and the method showed specificity greater than 0.99 and sensitivity greater than 0.87. Applying OmicsLonDA to the iPOP cohort revealed temporal patterns of genes, proteins, metabolites and microbes that are differentially regulated in male versus female subjects following a respiratory infection. In addition, we applied OmicsLonDA to a longitudinal multi-omics dataset of pregnant women with and without preeclampsia, and OmicsLonDA identified potential lipid markers that are temporally significantly different between the two groups. We provide an open-source R package (https://bioconductor.org/packages/OmicsLonDA), to enable widespread use. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 35762936
pii: 6619161
doi: 10.1093/bioinformatics/btac403
pmc: PMC9344853
doi:
Substances chimiques
Biomarkers
0
Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
3802-3811Subventions
Organisme : NIDDK NIH HHS
ID : P30 DK020579
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK116074
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR003142
Pays : United States
Organisme : NIH Common Fund Human Microbiome Project (HMP)
ID : 1U54DE02378901
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press.
Références
Cureus. 2020 Jun 30;12(6):e8925
pubmed: 32642389
Stat Med. 2006 Apr 30;25(8):1307-22
pubmed: 16217846
Syst Biol Reprod Med. 2018 Oct;64(5):324-339
pubmed: 29965778
J Clin Virol. 2017 Jan;86:14-19
pubmed: 27893998
Nat Rev Immunol. 2016 Oct;16(10):626-38
pubmed: 27546235
Mol Biosyst. 2013 Jul;9(7):1576-83
pubmed: 23525368
Equine Vet J. 1984 May;16(3):163-75
pubmed: 6428879
Stat Med. 2004 Oct 30;23(20):3093-104
pubmed: 15449333
Microbiome. 2018 Feb 13;6(1):32
pubmed: 29439731
Nat Commun. 2020 Oct 1;11(1):4933
pubmed: 33004787
Stat Methods Med Res. 2014 Feb;23(1):42-59
pubmed: 22523185
Nature. 2019 May;569(7758):663-671
pubmed: 31142858
Mol Cell. 2015 May 21;58(4):586-97
pubmed: 26000844
Fetal Diagn Ther. 2012;31(3):147-53
pubmed: 22472943
J Immunol. 2017 May 15;198(10):4046-4053
pubmed: 28373583
Sci Signal. 2010 Oct 12;3(143):pe36
pubmed: 20940425
Prostaglandins Other Lipid Mediat. 2004 Apr;73(3-4):173-80
pubmed: 15287150
Semin Perinatol. 2012 Feb;36(1):56-9
pubmed: 22280867
Circ Res. 2018 Apr 27;122(9):1169-1171
pubmed: 29700064
Mol Syst Biol. 2013;9:649
pubmed: 23511207
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12837-42
pubmed: 16141318
Educ Psychol Meas. 2017 Apr;77(2):305-329
pubmed: 29795915
Front Microbiol. 2018 Apr 23;9:785
pubmed: 29740416
Virol J. 2016 Mar 08;13:39
pubmed: 26952107
Prostaglandins Other Lipid Mediat. 2018 Nov;139:19-23
pubmed: 30248406
J Med Virol. 2017 Oct;89(10):1726-1733
pubmed: 28504416
J Lipid Res. 2016 Apr;57(4):687-96
pubmed: 26891737
Bioinformatics. 2004 Nov 1;20(16):2493-503
pubmed: 15130923
BMC Syst Biol. 2011 Oct 31;5:180
pubmed: 22041191
Biom J. 2007 Dec;49(6):863-75
pubmed: 17638292
J Proteome Res. 2019 Jan 4;18(1):1-6
pubmed: 30296097
Free Radic Biol Med. 2002 Jun 1;32(11):1050-60
pubmed: 12031889
PLoS One. 2016 Sep 28;11(9):e0163527
pubmed: 27683082
Biol Sex Differ. 2013 Sep 01;4:16
pubmed: 24128344