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Prediction of homologous recombination deficiency from cancer gene expression data
OBJECTIVE: Homologous recombination deficiency (HRD) is the main mechanism of tumorigenesis in some cancers. HRD causes abnormal double-strand break repair, resulting in genomic scars. Some scoring HRD tests have been approved as companion diagnostics of polyadenosine diphosphate-ribose polymerase (...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
SAGE Publications
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9676333/ https://www.ncbi.nlm.nih.gov/pubmed/36380518 http://dx.doi.org/10.1177/03000605221133655 |
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author | Kang, Jun Lee, Jieun Lee, Ahwon Lee, Youn Soo |
author_facet | Kang, Jun Lee, Jieun Lee, Ahwon Lee, Youn Soo |
author_sort | Kang, Jun |
collection | PubMed |
description | OBJECTIVE: Homologous recombination deficiency (HRD) is the main mechanism of tumorigenesis in some cancers. HRD causes abnormal double-strand break repair, resulting in genomic scars. Some scoring HRD tests have been approved as companion diagnostics of polyadenosine diphosphate-ribose polymerase (PARP) inhibitor treatment. This study aimed to build an HRD prediction model using gene expression data from various cancer types. METHODS: The cancer genome atlas data were used for HRD prediction modeling. A total of 10,567 cases of 33 cancer types were included, and expression data from 5128 out of 20,502 genes were included as predictors. A penalized logistic regression model was chosen as a modeling technique. RESULTS: The area under the curve of the receiver operating characteristic curve of HRD status prediction was 0.98 for the training set and 0.93 for the test set. The accuracy of HRD status prediction was 0.93 for the training set and 0.88 for the test set. CONCLUSIONS: Our study suggests that the HRD prediction model based on penalized logistic regression using gene expression data can be used to select patients for treatment with PARP inhibitors. |
format | Online Article Text |
id | pubmed-9676333 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | SAGE Publications |
record_format | MEDLINE/PubMed |
spelling | pubmed-96763332022-11-22 Prediction of homologous recombination deficiency from cancer gene expression data Kang, Jun Lee, Jieun Lee, Ahwon Lee, Youn Soo J Int Med Res Pre-Clinical Research Report OBJECTIVE: Homologous recombination deficiency (HRD) is the main mechanism of tumorigenesis in some cancers. HRD causes abnormal double-strand break repair, resulting in genomic scars. Some scoring HRD tests have been approved as companion diagnostics of polyadenosine diphosphate-ribose polymerase (PARP) inhibitor treatment. This study aimed to build an HRD prediction model using gene expression data from various cancer types. METHODS: The cancer genome atlas data were used for HRD prediction modeling. A total of 10,567 cases of 33 cancer types were included, and expression data from 5128 out of 20,502 genes were included as predictors. A penalized logistic regression model was chosen as a modeling technique. RESULTS: The area under the curve of the receiver operating characteristic curve of HRD status prediction was 0.98 for the training set and 0.93 for the test set. The accuracy of HRD status prediction was 0.93 for the training set and 0.88 for the test set. CONCLUSIONS: Our study suggests that the HRD prediction model based on penalized logistic regression using gene expression data can be used to select patients for treatment with PARP inhibitors. SAGE Publications 2022-11-15 /pmc/articles/PMC9676333/ /pubmed/36380518 http://dx.doi.org/10.1177/03000605221133655 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by-nc/4.0/Creative Commons Non Commercial CC BY-NC: This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). |
spellingShingle | Pre-Clinical Research Report Kang, Jun Lee, Jieun Lee, Ahwon Lee, Youn Soo Prediction of homologous recombination deficiency from cancer gene expression data |
title | Prediction of homologous recombination deficiency from cancer gene expression data |
title_full | Prediction of homologous recombination deficiency from cancer gene expression data |
title_fullStr | Prediction of homologous recombination deficiency from cancer gene expression data |
title_full_unstemmed | Prediction of homologous recombination deficiency from cancer gene expression data |
title_short | Prediction of homologous recombination deficiency from cancer gene expression data |
title_sort | prediction of homologous recombination deficiency from cancer gene expression data |
topic | Pre-Clinical Research Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9676333/ https://www.ncbi.nlm.nih.gov/pubmed/36380518 http://dx.doi.org/10.1177/03000605221133655 |
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