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CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma
BACKGROUND: There are currently no screening tests in routine use for oral and pharyngeal cancer beyond visual inspection and palpation, which are provided on an opportunistic basis, indicating a need for development of novel methods for early detection, particularly in high-risk populations. We sou...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4668652/ https://www.ncbi.nlm.nih.gov/pubmed/26635906 http://dx.doi.org/10.1186/s13148-015-0160-7 |
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author | Langevin, Scott M. Eliot, Melissa Butler, Rondi A. Cheong, Agnes Zhang, Xiang McClean, Michael D. Koestler, Devin C. Kelsey, Karl T. |
author_facet | Langevin, Scott M. Eliot, Melissa Butler, Rondi A. Cheong, Agnes Zhang, Xiang McClean, Michael D. Koestler, Devin C. Kelsey, Karl T. |
author_sort | Langevin, Scott M. |
collection | PubMed |
description | BACKGROUND: There are currently no screening tests in routine use for oral and pharyngeal cancer beyond visual inspection and palpation, which are provided on an opportunistic basis, indicating a need for development of novel methods for early detection, particularly in high-risk populations. We sought to address this need through comprehensive interrogation of CpG island methylation in oral rinse samples. METHODS: We used the Infinium HumanMethylation450 BeadArray to interrogate DNA methylation in oral rinse samples collected from 154 patients with incident oral or pharyngeal carcinoma prior to treatment and 72 cancer-free control subjects. Subjects were randomly allocated to either a training or a testing set. For each subject, average methylation was calculated for each CpG island represented on the array. We applied a semi-supervised recursively partitioned mixture model to the CpG island methylation data to identify a classifier for prediction of case status in the training set. We then applied the resultant classifier to the testing set for validation and to assess the predictive accuracy. RESULTS: We identified a methylation classifier comprised of 22 CpG islands, which predicted oral and pharyngeal carcinoma with a high degree of accuracy (AUC = 0.92, 95 % CI 0.86, 0.98). CONCLUSIONS: This novel methylation panel is a strong predictor of oral and pharyngeal carcinoma case status in oral rinse samples and may have utility in early detection and post-treatment follow-up. |
format | Online Article Text |
id | pubmed-4668652 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-46686522015-12-04 CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma Langevin, Scott M. Eliot, Melissa Butler, Rondi A. Cheong, Agnes Zhang, Xiang McClean, Michael D. Koestler, Devin C. Kelsey, Karl T. Clin Epigenetics Research BACKGROUND: There are currently no screening tests in routine use for oral and pharyngeal cancer beyond visual inspection and palpation, which are provided on an opportunistic basis, indicating a need for development of novel methods for early detection, particularly in high-risk populations. We sought to address this need through comprehensive interrogation of CpG island methylation in oral rinse samples. METHODS: We used the Infinium HumanMethylation450 BeadArray to interrogate DNA methylation in oral rinse samples collected from 154 patients with incident oral or pharyngeal carcinoma prior to treatment and 72 cancer-free control subjects. Subjects were randomly allocated to either a training or a testing set. For each subject, average methylation was calculated for each CpG island represented on the array. We applied a semi-supervised recursively partitioned mixture model to the CpG island methylation data to identify a classifier for prediction of case status in the training set. We then applied the resultant classifier to the testing set for validation and to assess the predictive accuracy. RESULTS: We identified a methylation classifier comprised of 22 CpG islands, which predicted oral and pharyngeal carcinoma with a high degree of accuracy (AUC = 0.92, 95 % CI 0.86, 0.98). CONCLUSIONS: This novel methylation panel is a strong predictor of oral and pharyngeal carcinoma case status in oral rinse samples and may have utility in early detection and post-treatment follow-up. BioMed Central 2015-12-03 /pmc/articles/PMC4668652/ /pubmed/26635906 http://dx.doi.org/10.1186/s13148-015-0160-7 Text en © Langevin et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Langevin, Scott M. Eliot, Melissa Butler, Rondi A. Cheong, Agnes Zhang, Xiang McClean, Michael D. Koestler, Devin C. Kelsey, Karl T. CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma |
title | CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma |
title_full | CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma |
title_fullStr | CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma |
title_full_unstemmed | CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma |
title_short | CpG island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma |
title_sort | cpg island methylation profile in non-invasive oral rinse samples is predictive of oral and pharyngeal carcinoma |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4668652/ https://www.ncbi.nlm.nih.gov/pubmed/26635906 http://dx.doi.org/10.1186/s13148-015-0160-7 |
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