Diagnosis and prognosis of COVID-19 employing analysis of patients' plasma and serum via LC-MS and machine learning.
Biomarker
COVID 19
Diagnosis
Fatality
Machine learning
Severity
Journal
Computers in biology and medicine
ISSN: 1879-0534
Titre abrégé: Comput Biol Med
Pays: United States
ID NLM: 1250250
Informations de publication
Date de publication:
07 2022
07 2022
Historique:
received:
20
02
2022
revised:
11
05
2022
accepted:
18
05
2022
entrez:
25
6
2022
pubmed:
26
6
2022
medline:
29
6
2022
Statut:
ppublish
Résumé
To implement and evaluate machine learning (ML) algorithms for the prediction of COVID-19 diagnosis, severity, and fatality and to assess biomarkers potentially associated with these outcomes. Serum (n = 96) and plasma (n = 96) samples from patients with COVID-19 (acute, severe and fatal illness) from two independent hospitals in China were analyzed by LC-MS. Samples from healthy volunteers and from patients with pneumonia caused by other viruses (i.e. negative RT-PCR for COVID-19) were used as controls. Seven different ML-based models were built: PLS-DA, ANNDA, XGBoostDA, SIMCA, SVM, LREG and KNN. The PLS-DA model presented the best performance for both datasets, with accuracy rates to predict the diagnosis, severity and fatality of COVID-19 of 93%, 94% and 97%, respectively. Low levels of the metabolites ribothymidine, 4-hydroxyphenylacetoylcarnitine and uridine were associated with COVID-19 positivity, whereas high levels of N-acetyl-glucosamine-1-phosphate, cysteinylglycine, methyl isobutyrate, l-ornithine and 5,6-dihydro-5-methyluracil were significantly related to greater severity and fatality from COVID-19. The PLS-DA model can help to predict SARS-CoV-2 diagnosis, severity and fatality in daily practice. Some biomarkers typically increased in COVID-19 patients' serum or plasma (i.e. ribothymidine, N-acetyl-glucosamine-1-phosphate, l-ornithine, 5,6-dihydro-5-methyluracil) should be further evaluated as prognostic indicators of the disease.
Identifiants
pubmed: 35751188
pii: S0010-4825(22)00451-6
doi: 10.1016/j.compbiomed.2022.105659
pmc: PMC9123826
pii:
doi:
Substances chimiques
Biomarkers
0
Phosphates
0
Ornithine
E524N2IXA3
Glucosamine
N08U5BOQ1K
Thymine
QR26YLT7LT
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
105659Informations de copyright
Copyright © 2022 Elsevier Ltd. All rights reserved.
Références
Front Immunol. 2019 Jul 04;10:1551
pubmed: 31333675
Ann Lab Med. 2021 Mar 1;41(2):129-138
pubmed: 33063674
Int J Mol Sci. 2021 Mar 09;22(5):
pubmed: 33803217
Viruses. 2021 Oct 13;13(10):
pubmed: 34696485
PLoS One. 2021 Mar 23;16(3):e0248957
pubmed: 33755708
Metabolomics. 2019 Oct 18;15(11):142
pubmed: 31628551
Mol Cell Proteomics. 2019 Aug;18(8):1683-1699
pubmed: 31097671
BMC Bioinformatics. 2020 Dec 9;21(Suppl 1):2
pubmed: 33297937
Rev Med Virol. 2022 May;32(3):e2292
pubmed: 34590761
Science. 2019 Oct 18;366(6463):
pubmed: 31624181
Front Immunol. 2021 Jun 28;12:700782
pubmed: 34262570
J Pers Med. 2021 Sep 30;11(10):
pubmed: 34683133
Sci Rep. 2021 May 24;11(1):10738
pubmed: 34031483
Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2021 Jul;38(7):1105-1117
pubmed: 33989115
N Engl J Med. 2021 Jul 8;385(2):187-189
pubmed: 33951357
Sci Adv. 2020 Apr 15;6(16):eaaz7086
pubmed: 32494619
AAPS J. 2021 Jan 5;23(1):14
pubmed: 33400058
Sci Rep. 2021 Aug 18;11(1):16740
pubmed: 34408169
Comput Struct Biotechnol J. 2019 Dec 26;18:241-252
pubmed: 33489002
Metabolomics. 2018 Mar 20;14(5):54
pubmed: 30830328
Clin Nutr. 2022 Dec;41(12):3077-3084
pubmed: 33933299
Intern Emerg Med. 2020 Nov;15(8):1435-1443
pubmed: 32812204
Nat Commun. 2021 May 21;12(1):3008
pubmed: 34021151
Nat Protoc. 2022 Jan;17(1):129-151
pubmed: 34952956
Biomed Res Int. 2020 Apr 14;2020:7091718
pubmed: 32382566
Talanta. 2013 Jan 15;103:276-84
pubmed: 23200388
Genomics. 2020 Nov;112(6):5204-5213
pubmed: 32966857
Cureus. 2020 Aug 3;12(8):e9540
pubmed: 32905500
PLoS One. 2021 Jun 23;16(6):e0253293
pubmed: 34161373
Heliyon. 2020 Aug;6(8):e04696
pubmed: 32844126
Clin Nutr. 2021 Apr;40(4):2420-2426
pubmed: 33160700
Nutrients. 2021 Apr 26;13(5):
pubmed: 33925783
Front Cell Dev Biol. 2020 Jul 31;8:683
pubmed: 32850809
Anal Bioanal Chem. 2004 Oct;380(3):419-29
pubmed: 15448969
Life (Basel). 2021 Nov 22;11(11):
pubmed: 34833156
Brief Bioinform. 2021 May 20;22(3):
pubmed: 32510556
Front Bioeng Biotechnol. 2020 Apr 15;8:260
pubmed: 32351945
Sci Rep. 2021 Aug 19;11(1):16897
pubmed: 34413397
Clin Nutr Open Sci. 2021 Dec;40:102-110
pubmed: 34806074
Nucleic Acids Res. 2021 Jul 2;49(W1):W388-W396
pubmed: 34019663
Metabolomics. 2019 Nov 15;15(12):150
pubmed: 31728648
Nat Metab. 2020 Jul;2(7):572-585
pubmed: 32694793
Epidemiol Infect. 2020 Aug 04;148:e168
pubmed: 32746957
Brief Bioinform. 2021 Sep 2;22(5):
pubmed: 33866355
Nat Commun. 2019 Oct 3;10(1):4505
pubmed: 31582752
J Proteomics. 2021 Feb 10;232:104023
pubmed: 33130111
Brief Bioinform. 2022 Mar 10;23(2):
pubmed: 35183059
J Virol. 2021 Mar 1;:
pubmed: 33649194
Front Med (Lausanne). 2021 Sep 30;8:704256
pubmed: 34660623
Expert Rev Respir Med. 2021 Feb;15(2):197-212
pubmed: 32924671
Brief Bioinform. 2020 Mar 23;21(2):621-636
pubmed: 30649171
Chem Soc Rev. 2011 Jan;40(1):387-426
pubmed: 20717559
Emerg Infect Dis. 2021 May;27(5):1522-1524
pubmed: 33605869
Emerg Microbes Infect. 2022 Dec;11(1):567-572
pubmed: 35060426
Clin Microbiol Infect. 2020 Dec;26(12):1622-1629
pubmed: 32711058
Comput Biol Med. 2021 Jul;134:104531
pubmed: 34091385
J Appl Spectrosc. 2021;88(4):765-771
pubmed: 34538886
Front Microbiol. 2018 Mar 20;9:491
pubmed: 29662472
Future Microbiol. 2021 May;16:577-588
pubmed: 33973485
Lancet. 2021 Feb 27;397(10276):777-778
pubmed: 33607000
Nucleic Acids Res. 2020 Jul 2;48(W1):W436-W448
pubmed: 32324219
Clin Microbiol Infect. 2021 Jan;27(1):83-88
pubmed: 32745596
Front Immunol. 2021 Jun 15;12:693074
pubmed: 34211479
Metabolites. 2021 Jan 09;11(1):
pubmed: 33435351
Neurobiol Dis. 2020 Feb;135:104704
pubmed: 31837420
Nicotine Tob Res. 2021 Jun 8;23(7):1133-1142
pubmed: 33165576
Anal Chim Acta. 2015 Jun 16;879:10-23
pubmed: 26002472
NPJ Digit Med. 2019 Jul 26;2:69
pubmed: 31372505
Oxid Med Cell Longev. 2021 Sep 18;2021:9221693
pubmed: 34557267
Arch Toxikol. 1974 Feb 28;31(3):243-63
pubmed: 4826870
Proc Natl Acad Sci U S A. 2021 Jun 22;118(25):
pubmed: 34088793
Lancet Microbe. 2020 Jul;1(3):e105
pubmed: 32835339
Aging (Albany NY). 2020 Jun 24;12(13):12517-12533
pubmed: 32580166
Brief Bioinform. 2020 May 21;21(3):1058-1068
pubmed: 31157371
Front Endocrinol (Lausanne). 2020 Jul 07;11:514
pubmed: 32733388
Nature. 2018 Jul;559(7715):547-555
pubmed: 30046072