Machine learning techniques for personalized breast cancer risk prediction: comparison with the BCRAT and BOADICEA models
Abstract Background Comprehensive breast cancer risk prediction models enable identifying and targeting women at high-risk, while reducing interventions in those at low-risk. Breast cancer risk prediction models used in clinical practice have low discriminatory accuracy (0.53–0.64). Machine learning...
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| Format: | Article |
| Language: | English |
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BMC
2019-06-01
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| Series: | Breast Cancer Research |
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| Online Access: | http://link.springer.com/article/10.1186/s13058-019-1158-4 |
| _version_ | 1818724178266685440 |
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| author | Chang Ming Valeria Viassolo Nicole Probst-Hensch Pierre O. Chappuis Ivo D. Dinov Maria C. Katapodi |
| author_facet | Chang Ming Valeria Viassolo Nicole Probst-Hensch Pierre O. Chappuis Ivo D. Dinov Maria C. Katapodi |
| author_sort | Chang Ming |
| collection | DOAJ |
| description | Abstract Background Comprehensive breast cancer risk prediction models enable identifying and targeting women at high-risk, while reducing interventions in those at low-risk. Breast cancer risk prediction models used in clinical practice have low discriminatory accuracy (0.53–0.64). Machine learning (ML) offers an alternative approach to standard prediction modeling that may address current limitations and improve accuracy of those tools. The purpose of this study was to compare the discriminatory accuracy of ML-based estimates against a pair of established methods—the Breast Cancer Risk Assessment Tool (BCRAT) and Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) models. Methods We quantified and compared the performance of eight different ML methods to the performance of BCRAT and BOADICEA using eight simulated datasets and two retrospective samples: a random population-based sample of U.S. breast cancer patients and their cancer-free female relatives (N = 1143), and a clinical sample of Swiss breast cancer patients and cancer-free women seeking genetic evaluation and/or testing (N = 2481). Results Predictive accuracy (AU-ROC curve) reached 88.28% using ML-Adaptive Boosting and 88.89% using ML-random forest versus 62.40% with BCRAT for the U.S. population-based sample. Predictive accuracy reached 90.17% using ML-adaptive boosting and 89.32% using ML-Markov chain Monte Carlo generalized linear mixed model versus 59.31% with BOADICEA for the Swiss clinic-based sample. Conclusions There was a striking improvement in the accuracy of classification of women with and without breast cancer achieved with ML algorithms compared to the state-of-the-art model-based approaches. High-accuracy prediction techniques are important in personalized medicine because they facilitate stratification of prevention strategies and individualized clinical management. |
| first_indexed | 2024-12-17T21:22:17Z |
| format | Article |
| id | doaj.art-162e5e5d61ff466e8c93e24ceaca8699 |
| institution | Directory Open Access Journal |
| issn | 1465-542X |
| language | English |
| last_indexed | 2024-12-17T21:22:17Z |
| publishDate | 2019-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Breast Cancer Research |
| spelling | doaj.art-162e5e5d61ff466e8c93e24ceaca86992022-12-21T21:32:08ZengBMCBreast Cancer Research1465-542X2019-06-0121111110.1186/s13058-019-1158-4Machine learning techniques for personalized breast cancer risk prediction: comparison with the BCRAT and BOADICEA modelsChang Ming0Valeria Viassolo1Nicole Probst-Hensch2Pierre O. Chappuis3Ivo D. Dinov4Maria C. Katapodi5Nursing Science, Faculty of Medicine, University of BaselOncogenetics and Cancer Prevention, Geneva University HospitalsSwiss Tropical and Public Health Institute, University of BaselOncogenetics and Cancer Prevention, Geneva University HospitalsDepartment of Computational Medicine and Bioinformatics, University of MichiganNursing Science, Faculty of Medicine, University of BaselAbstract Background Comprehensive breast cancer risk prediction models enable identifying and targeting women at high-risk, while reducing interventions in those at low-risk. Breast cancer risk prediction models used in clinical practice have low discriminatory accuracy (0.53–0.64). Machine learning (ML) offers an alternative approach to standard prediction modeling that may address current limitations and improve accuracy of those tools. The purpose of this study was to compare the discriminatory accuracy of ML-based estimates against a pair of established methods—the Breast Cancer Risk Assessment Tool (BCRAT) and Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) models. Methods We quantified and compared the performance of eight different ML methods to the performance of BCRAT and BOADICEA using eight simulated datasets and two retrospective samples: a random population-based sample of U.S. breast cancer patients and their cancer-free female relatives (N = 1143), and a clinical sample of Swiss breast cancer patients and cancer-free women seeking genetic evaluation and/or testing (N = 2481). Results Predictive accuracy (AU-ROC curve) reached 88.28% using ML-Adaptive Boosting and 88.89% using ML-random forest versus 62.40% with BCRAT for the U.S. population-based sample. Predictive accuracy reached 90.17% using ML-adaptive boosting and 89.32% using ML-Markov chain Monte Carlo generalized linear mixed model versus 59.31% with BOADICEA for the Swiss clinic-based sample. Conclusions There was a striking improvement in the accuracy of classification of women with and without breast cancer achieved with ML algorithms compared to the state-of-the-art model-based approaches. High-accuracy prediction techniques are important in personalized medicine because they facilitate stratification of prevention strategies and individualized clinical management.http://link.springer.com/article/10.1186/s13058-019-1158-4Breast cancerRisk predictionMachine learningBig dataPersonalized medicineCancer screening |
| spellingShingle | Chang Ming Valeria Viassolo Nicole Probst-Hensch Pierre O. Chappuis Ivo D. Dinov Maria C. Katapodi Machine learning techniques for personalized breast cancer risk prediction: comparison with the BCRAT and BOADICEA models Breast Cancer Research Breast cancer Risk prediction Machine learning Big data Personalized medicine Cancer screening |
| title | Machine learning techniques for personalized breast cancer risk prediction: comparison with the BCRAT and BOADICEA models |
| title_full | Machine learning techniques for personalized breast cancer risk prediction: comparison with the BCRAT and BOADICEA models |
| title_fullStr | Machine learning techniques for personalized breast cancer risk prediction: comparison with the BCRAT and BOADICEA models |
| title_full_unstemmed | Machine learning techniques for personalized breast cancer risk prediction: comparison with the BCRAT and BOADICEA models |
| title_short | Machine learning techniques for personalized breast cancer risk prediction: comparison with the BCRAT and BOADICEA models |
| title_sort | machine learning techniques for personalized breast cancer risk prediction comparison with the bcrat and boadicea models |
| topic | Breast cancer Risk prediction Machine learning Big data Personalized medicine Cancer screening |
| url | http://link.springer.com/article/10.1186/s13058-019-1158-4 |
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