DNA methylation-based epigenetic signatures predict somatic genomic alterations in gliomas.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
29 07 2022
29 07 2022
Historique:
received:
03
09
2020
accepted:
05
07
2022
entrez:
29
7
2022
pubmed:
30
7
2022
medline:
3
8
2022
Statut:
epublish
Résumé
Molecular classification has improved diagnosis and treatment for patients with malignant gliomas. However, classification has relied on individual assays that are both costly and slow, leading to frequent delays in treatment. Here, we propose the use of DNA methylation, as an emerging clinical diagnostic platform, to classify gliomas based on major genomic alterations and provide insight into subtype characteristics. We show that using machine learning models, DNA methylation signatures can accurately predict somatic alterations and show improvement over existing classifiers. The established Unified Diagnostic Pipeline (UniD) we develop is rapid and cost-effective for genomic alterations and gene expression subtypes diagnostic at early clinical phase and improves over individual assays currently in clinical use. The significant relationship between genetic alteration and epigenetic signature indicates broad applicability of our approach to other malignancies.
Identifiants
pubmed: 35906213
doi: 10.1038/s41467-022-31827-x
pii: 10.1038/s41467-022-31827-x
pmc: PMC9338285
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
4410Subventions
Organisme : NCI NIH HHS
ID : R01 CA190121
Pays : United States
Informations de copyright
© 2022. The Author(s).
Références
J Stat Softw. 2010;33(1):1-22
pubmed: 20808728
BMC Genomics. 2011 Jun 06;12:293
pubmed: 21645359
Cell. 2013 Oct 10;155(2):462-77
pubmed: 24120142
Cell. 2016 Jan 28;164(3):550-63
pubmed: 26824661
BMC Bioinformatics. 2010 Nov 30;11:587
pubmed: 21118553
Nat Commun. 2022 Jul 29;13(1):4410
pubmed: 35906213
Genome Biol. 2012 Jun 15;13(6):R44
pubmed: 22703947
Bioinformatics. 2012 Feb 1;28(3):311-7
pubmed: 22155872
Bioinformatics. 2013 Jan 15;29(2):189-96
pubmed: 23175756
N Engl J Med. 2016 Sep 22;375(12):1109-12
pubmed: 27653561
Acta Neuropathol. 2012 Oct;124(4):547-60
pubmed: 22810491
Proc Natl Acad Sci U S A. 2004 Mar 23;101(12):4164-9
pubmed: 15016911
Nat Biotechnol. 2012 May;30(5):413-21
pubmed: 22544022
Nat Protoc. 2009;4(1):44-57
pubmed: 19131956
Brief Bioinform. 2014 Nov;15(6):929-41
pubmed: 23990268
Nat Biotechnol. 2013 Mar;31(3):213-9
pubmed: 23396013
Cancer Cell. 2010 May 18;17(5):510-22
pubmed: 20399149
Proc Natl Acad Sci U S A. 1999 Jul 20;96(15):8681-6
pubmed: 10411935
Brain. 2019 Apr 1;142(4):847-866
pubmed: 30946477
J Mol Diagn. 2008 Jul;10(4):332-7
pubmed: 18556773
Mol Oncol. 2015 Mar;9(3):555-68
pubmed: 25468711
Cancer Cell. 2017 Jul 10;32(1):42-56.e6
pubmed: 28697342
N Engl J Med. 2005 Mar 10;352(10):997-1003
pubmed: 15758010
Genome Biol. 2016 Aug 24;17(1):178
pubmed: 27557938
Carcinogenesis. 2010 Jan;31(1):27-36
pubmed: 19752007
N Engl J Med. 2015 Jun 25;372(26):2499-508
pubmed: 26061753
Genes Dis. 2018 Feb 21;5(1):43-45
pubmed: 30258934
Genet Mol Res. 2015 Aug 07;14(3):9200-14
pubmed: 26345853
J Clin Oncol. 2009 Dec 10;27(35):5874-80
pubmed: 19901110
Genome Biol. 2014 Feb 03;15(2):R30
pubmed: 24490765
Nature. 2018 Mar 22;555(7697):469-474
pubmed: 29539639
Acta Neuropathol. 2018 Nov;136(5):805-810
pubmed: 30259105
Epigenomics. 2011 Dec;3(6):771-84
pubmed: 22126295
Genes Dev. 2011 Dec 15;25(24):2594-609
pubmed: 22190458
Nature. 2012 Jul 18;487(7407):330-7
pubmed: 22810696
Bioinformatics. 2009 Sep 1;25(17):2283-5
pubmed: 19542151
Int J Mol Sci. 2019 Jan 08;20(1):
pubmed: 30625996
Neuro Oncol. 2021 Aug 2;23(8):1231-1251
pubmed: 34185076
Expert Opin Ther Targets. 2018 Jul;22(7):599-613
pubmed: 29889582
Cancer Cell. 2006 Mar;9(3):157-73
pubmed: 16530701
N Engl J Med. 2015 Jun 25;372(26):2481-98
pubmed: 26061751
Genome Biol. 2013 Sep 24;14(9):r105
pubmed: 24063430