Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction
Comprehensive genomic profiling using cancer gene panels has been shown to improve treatment options for a variety of cancer types. However, genomic aberrations detected via such gene panels do not necessarily serve as strong predictors of drug sensitivity. In this study, using pharmacogenomics data...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-11-01
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| Series: | Cancers |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2072-6694/14/22/5604 |
| _version_ | 1797465694506319872 |
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| author | Artem Baranovskii Irem B. Gündüz Vedran Franke Bora Uyar Altuna Akalin |
| author_facet | Artem Baranovskii Irem B. Gündüz Vedran Franke Bora Uyar Altuna Akalin |
| author_sort | Artem Baranovskii |
| collection | DOAJ |
| description | Comprehensive genomic profiling using cancer gene panels has been shown to improve treatment options for a variety of cancer types. However, genomic aberrations detected via such gene panels do not necessarily serve as strong predictors of drug sensitivity. In this study, using pharmacogenomics datasets of cell lines, patient-derived xenografts, and ex vivo treated fresh tumor specimens, we demonstrate that utilizing the transcriptome on top of gene panel features substantially improves drug response prediction performance in cancer. |
| first_indexed | 2024-03-09T18:26:08Z |
| format | Article |
| id | doaj.art-28a7aa21267f4a59bdfc6342d2df3584 |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-09T18:26:08Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-28a7aa21267f4a59bdfc6342d2df35842023-11-24T07:53:49ZengMDPI AGCancers2072-66942022-11-011422560410.3390/cancers14225604Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response PredictionArtem Baranovskii0Irem B. Gündüz1Vedran Franke2Bora Uyar3Altuna Akalin4Non-Coding RNAs and Mechanisms of Cytoplasmic Gene Regulation Lab, Berlin Institute for Medical Systems Biology, Max Delbrück Center (MDC) for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, GermanyIntegrative Cellular Biology & Bioinformatics Lab, Saarland University, 66123 Saarbrücken, GermanyMax Delbrück Center (MDC) for Molecular Medicine, Bioinformatics and Omics Data Science Platform, The Berlin Institute for Medical Systems Biology, Hannoversche Str. 28, 10115 Berlin, GermanyMax Delbrück Center (MDC) for Molecular Medicine, Bioinformatics and Omics Data Science Platform, The Berlin Institute for Medical Systems Biology, Hannoversche Str. 28, 10115 Berlin, GermanyMax Delbrück Center (MDC) for Molecular Medicine, Bioinformatics and Omics Data Science Platform, The Berlin Institute for Medical Systems Biology, Hannoversche Str. 28, 10115 Berlin, GermanyComprehensive genomic profiling using cancer gene panels has been shown to improve treatment options for a variety of cancer types. However, genomic aberrations detected via such gene panels do not necessarily serve as strong predictors of drug sensitivity. In this study, using pharmacogenomics datasets of cell lines, patient-derived xenografts, and ex vivo treated fresh tumor specimens, we demonstrate that utilizing the transcriptome on top of gene panel features substantially improves drug response prediction performance in cancer.https://www.mdpi.com/2072-6694/14/22/5604multi-omicscancerdrug response predictionpharmacogenomicspanel sequencing |
| spellingShingle | Artem Baranovskii Irem B. Gündüz Vedran Franke Bora Uyar Altuna Akalin Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction Cancers multi-omics cancer drug response prediction pharmacogenomics panel sequencing |
| title | Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction |
| title_full | Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction |
| title_fullStr | Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction |
| title_full_unstemmed | Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction |
| title_short | Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction |
| title_sort | multi omics alleviates the limitations of panel sequencing for cancer drug response prediction |
| topic | multi-omics cancer drug response prediction pharmacogenomics panel sequencing |
| url | https://www.mdpi.com/2072-6694/14/22/5604 |
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