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Integrated epigenomic exposure signature discovery.

Publication ,  Journal Article
Schuetter, J; Minard-Smith, A; Hill, B; Beare, JL; Vornholt, A; Burke, TW; Murugan, V; Smith, AK; Chandrasekaran, T; Shamma, HJ; Kahaian, SC ...
Published in: Epigenomics
2024
Published version (DOI) Link to item

Aim: The epigenome influences gene regulation and phenotypes in response to exposures. Epigenome assessment can determine exposure history aiding in diagnosis.Materials & methods: Here we developed and implemented a machine learning algorithm, the exposure signature discovery algorithm (ESDA), to identify the most important features present in multiple epigenomic and transcriptomic datasets to produce an integrated exposure signature (ES).Results: Signatures were developed for seven exposures including Staphylococcus aureus, human immunodeficiency virus, SARS-CoV-2, influenza A (H3N2) virus and Bacillus anthracis vaccinations. ESs differed in the assays and features selected and predictive value.Conclusion: Integrated ESs can potentially be utilized for diagnosis or forensic attribution. The ESDA identifies the most distinguishing features enabling diagnostic panel development for future precision health deployment.

Duke Scholars

Micah Thomas McClain
Author Micah Thomas McClain Medicine, Infectious Diseases
Vance Garrison Fowler Jr.
Author Vance Garrison Fowler Jr. Medicine, Infectious Diseases
Christopher Wildrick Woods
Author Christopher Wildrick Woods Medicine, Infectious Diseases

Published In

Epigenomics

DOI

10.1080/17501911.2024.2375187

EISSN

1750-192X

Publication Date

2024

Volume

16

Issue

14

Start / End Page

1013 / 1029

Location

England

Related Subject Headings

  • Transcriptome
  • Staphylococcus aureus
  • SARS-CoV-2
  • Machine Learning
  • Influenza, Human
  • Influenza A Virus, H3N2 Subtype
  • Humans
  • HIV Infections
  • Epigenomics
  • Epigenome
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Schuetter, J., Minard-Smith, A., Hill, B., Beare, J. L., Vornholt, A., Burke, T. W., … Spurbeck, R. R. (2024). Integrated epigenomic exposure signature discovery. Epigenomics, 16(14), 1013–1029. https://doi.org/10.1080/17501911.2024.2375187
Schuetter, Jared, Angela Minard-Smith, Brandon Hill, Jennifer L. Beare, Alexandria Vornholt, Thomas W. Burke, Vel Murugan, et al. “Integrated epigenomic exposure signature discovery.” Epigenomics 16, no. 14 (2024): 1013–29. https://doi.org/10.1080/17501911.2024.2375187.
Schuetter J, Minard-Smith A, Hill B, Beare JL, Vornholt A, Burke TW, et al. Integrated epigenomic exposure signature discovery. Epigenomics. 2024;16(14):1013–29.
Schuetter, Jared, et al. “Integrated epigenomic exposure signature discovery.” Epigenomics, vol. 16, no. 14, 2024, pp. 1013–29. Pubmed, doi:10.1080/17501911.2024.2375187.
Schuetter J, Minard-Smith A, Hill B, Beare JL, Vornholt A, Burke TW, Murugan V, Smith AK, Chandrasekaran T, Shamma HJ, Kahaian SC, Fillinger KL, Amper MAS, Cheng W-S, Ge Y, George MC, Guevara K, Lovette-Okwara N, Mahajan A, Marjanovic N, Mendelev N, Fowler VG, McClain MT, Miller CM, Mofsowitz S, Nair VD, Nudelman G, Evans TG, Castellino F, Ramos I, Rirak S, Ruf-Zamojski F, Seenarine N, Soares-Shanoski A, Vangeti S, Vasoya M, Yu X, Zaslavsky E, Ndhlovu LC, Corley MJ, Bowler S, Deeks SG, Letizia AG, Sealfon SC, Woods CW, Spurbeck RR. Integrated epigenomic exposure signature discovery. Epigenomics. 2024;16(14):1013–1029.
Journal cover image

Published In

Epigenomics

DOI

10.1080/17501911.2024.2375187

EISSN

1750-192X

Publication Date

2024

Volume

16

Issue

14

Start / End Page

1013 / 1029

Location

England

Related Subject Headings

  • Transcriptome
  • Staphylococcus aureus
  • SARS-CoV-2
  • Machine Learning
  • Influenza, Human
  • Influenza A Virus, H3N2 Subtype
  • Humans
  • HIV Infections
  • Epigenomics
  • Epigenome