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Quantifying the Predictive Accuracy of a Polygenic Risk Score for Predicting Incident Cancer Cases : Application to the CARTaGENE Cohort
With the increasing use of polygenic risk scores (PRS) there is a need for adapted methods to evaluate the predictivity of these tools. In this work, we propose a new pseudo-R(2) criterion to evaluate PRS predictive accuracy for time-to-event data. This new criterion is related to the score statisti...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193029/ https://www.ncbi.nlm.nih.gov/pubmed/32391062 http://dx.doi.org/10.3389/fgene.2020.00408 |
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author | Duhazé, Julianne Jantzen, Rodolphe Payette, Yves De Malliard, Thibault Labbé, Catherine Noisel, Nolwenn Broët, Philippe |
author_facet | Duhazé, Julianne Jantzen, Rodolphe Payette, Yves De Malliard, Thibault Labbé, Catherine Noisel, Nolwenn Broët, Philippe |
author_sort | Duhazé, Julianne |
collection | PubMed |
description | With the increasing use of polygenic risk scores (PRS) there is a need for adapted methods to evaluate the predictivity of these tools. In this work, we propose a new pseudo-R(2) criterion to evaluate PRS predictive accuracy for time-to-event data. This new criterion is related to the score statistic derived under a two-component mixture model. It evaluates the effect of the PRS on both the propensity to experience the event and on the dynamic of the event among the susceptible subjects. Simulation results show that our index has good properties. We compared our index to other implemented pseudo-R(2) for survival data. Along with our index, two other indices have comparable good behavior when the PRS has a non-null propensity effect, and our index is the only one to detect when the PRS has only a dynamic effect. We evaluated the 5-year predictivity of an 18-single-nucleotide-polymorphism PRS for incident breast cancer cases on the CARTaGENE cohort using several pseudo-R(2) indices. We report that our index, which summarizes both a propensity and a dynamic effect, had the highest predictive accuracy. In conclusion, our proposed pseudo-R(2) is easy to implement and well suited to evaluate PRS for predicting incident events in cohort studies. |
format | Online Article Text |
id | pubmed-7193029 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-71930292020-05-08 Quantifying the Predictive Accuracy of a Polygenic Risk Score for Predicting Incident Cancer Cases : Application to the CARTaGENE Cohort Duhazé, Julianne Jantzen, Rodolphe Payette, Yves De Malliard, Thibault Labbé, Catherine Noisel, Nolwenn Broët, Philippe Front Genet Genetics With the increasing use of polygenic risk scores (PRS) there is a need for adapted methods to evaluate the predictivity of these tools. In this work, we propose a new pseudo-R(2) criterion to evaluate PRS predictive accuracy for time-to-event data. This new criterion is related to the score statistic derived under a two-component mixture model. It evaluates the effect of the PRS on both the propensity to experience the event and on the dynamic of the event among the susceptible subjects. Simulation results show that our index has good properties. We compared our index to other implemented pseudo-R(2) for survival data. Along with our index, two other indices have comparable good behavior when the PRS has a non-null propensity effect, and our index is the only one to detect when the PRS has only a dynamic effect. We evaluated the 5-year predictivity of an 18-single-nucleotide-polymorphism PRS for incident breast cancer cases on the CARTaGENE cohort using several pseudo-R(2) indices. We report that our index, which summarizes both a propensity and a dynamic effect, had the highest predictive accuracy. In conclusion, our proposed pseudo-R(2) is easy to implement and well suited to evaluate PRS for predicting incident events in cohort studies. Frontiers Media S.A. 2020-04-24 /pmc/articles/PMC7193029/ /pubmed/32391062 http://dx.doi.org/10.3389/fgene.2020.00408 Text en Copyright © 2020 Duhazé, Jantzen, Payette, De Malliard, Labbé, Noisel and Broët. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Duhazé, Julianne Jantzen, Rodolphe Payette, Yves De Malliard, Thibault Labbé, Catherine Noisel, Nolwenn Broët, Philippe Quantifying the Predictive Accuracy of a Polygenic Risk Score for Predicting Incident Cancer Cases : Application to the CARTaGENE Cohort |
title | Quantifying the Predictive Accuracy of a Polygenic Risk Score for Predicting Incident Cancer Cases : Application to the CARTaGENE Cohort |
title_full | Quantifying the Predictive Accuracy of a Polygenic Risk Score for Predicting Incident Cancer Cases : Application to the CARTaGENE Cohort |
title_fullStr | Quantifying the Predictive Accuracy of a Polygenic Risk Score for Predicting Incident Cancer Cases : Application to the CARTaGENE Cohort |
title_full_unstemmed | Quantifying the Predictive Accuracy of a Polygenic Risk Score for Predicting Incident Cancer Cases : Application to the CARTaGENE Cohort |
title_short | Quantifying the Predictive Accuracy of a Polygenic Risk Score for Predicting Incident Cancer Cases : Application to the CARTaGENE Cohort |
title_sort | quantifying the predictive accuracy of a polygenic risk score for predicting incident cancer cases : application to the cartagene cohort |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193029/ https://www.ncbi.nlm.nih.gov/pubmed/32391062 http://dx.doi.org/10.3389/fgene.2020.00408 |
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