Stone, Timothy C;
Ward, Vanessa;
Hogan, Aine;
Ho, Kai Ma;
Wilson, Ash;
McBain, Hazel;
Duku, Margaret;
... SPIT Study Group Collaborators:; + view all
(2024)
Using saliva epigenetic data to develop and validate a multivariable predictor of esophageal cancer status.
Epigenomics
10.2217/epi-2023-0248.
(In press).
Preview |
PDF
stone-et-al-2024-using-saliva-epigenetic-data-to-develop-and-validate-a-multivariable-predictor-of-esophageal-cancer.pdf - Published Version Download (2MB) | Preview |
Abstract
Background: Salivary epigenetic biomarkers may detect esophageal cancer. Methods: A total of 256 saliva samples from esophageal adenocarcinoma patients and matched volunteers were analyzed with Illumina EPIC methylation arrays. Three datasets were created, using 64% for discovery, 16% for testing and 20% for validation. Modules of gene-based methylation probes were created using weighted gene coexpression network analysis. Module significance to disease and gene importance to module were determined and a random forest classifier generated using best-scoring gene-related epigenetic probes. A cost-sensitive wrapper algorithm maximized cancer diagnosis. Results: Using age, sex and seven probes, esophageal adenocarcinoma was detected with area under the curve of 0.72 in discovery, 0.73 in testing and 0.75 in validation datasets. Cancer sensitivity was 88% with specificity of 31%. Conclusion: We have demonstrated a potentially clinically viable classifier of esophageal cancer based on saliva methylation.
| Type: | Article |
|---|---|
| Title: | Using saliva epigenetic data to develop and validate a multivariable predictor of esophageal cancer status |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.2217/epi-2023-0248 |
| Publisher version: | http://dx.doi.org/10.2217/epi-2023-0248 |
| Language: | English |
| Additional information: | This work is licensed under the Creative Commons Attribution 4.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
| Keywords: | biomarker panel, diagnosis, epigenetics, esophageal adenocarcinoma, saliva |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Surgery and Interventional Sci UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Surgery and Interventional Sci > Department of Targeted Intervention |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10185815 |
Archive Staff Only
 |
View Item |
