Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology
Abstract Precision oncology offers new cancer treatment options, yet sequencing methods vary in type and scope. In this study, we compared whole-exome/whole-genome (WES/WGS) and transcriptome sequencing (TS) with broad panel sequencing by resequencing the same tumor DNA and RNA as well as normal tis...
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Nature Portfolio
2025-01-01
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| Series: | npj Precision Oncology |
| Online Access: | https://doi.org/10.1038/s41698-024-00788-3 |
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| author | Irina A. Kerle Thomas Gross Anja Kögler Jonas S. Arnold Maximilian Werner Jan-Niklas Eckardt Elena E. Möhrmann Marie Arlt Barbara Hutter Jennifer Hüllein Daniela Richter Martin M. K. Schneider Mario Hlevnjak Lino Möhrmann Dorothea Hanf Christoph E. Heilig Simon Kreutzfeldt Maria-Veronica Teleanu Evelin Schröck Daniel Hübschmann Peter Horak Christoph Heining Stefan Fröhling Hanno Glimm |
| author_facet | Irina A. Kerle Thomas Gross Anja Kögler Jonas S. Arnold Maximilian Werner Jan-Niklas Eckardt Elena E. Möhrmann Marie Arlt Barbara Hutter Jennifer Hüllein Daniela Richter Martin M. K. Schneider Mario Hlevnjak Lino Möhrmann Dorothea Hanf Christoph E. Heilig Simon Kreutzfeldt Maria-Veronica Teleanu Evelin Schröck Daniel Hübschmann Peter Horak Christoph Heining Stefan Fröhling Hanno Glimm |
| author_sort | Irina A. Kerle |
| collection | DOAJ |
| description | Abstract Precision oncology offers new cancer treatment options, yet sequencing methods vary in type and scope. In this study, we compared whole-exome/whole-genome (WES/WGS) and transcriptome sequencing (TS) with broad panel sequencing by resequencing the same tumor DNA and RNA as well as normal tissue DNA for germline assessment, from 20 patients with rare or advanced tumors, who were originally sequenced by WES/WGS ± TS within the DKFZ/NCT/DKTK MASTER program from 2015 to 2020. Molecular analyses resulted in a median number of 2.5 (gene panel) to 3.5 (WES/WGS ± TS) treatment recommendations per patient. Our results showed that approximately half of the therapy recommendations (TRs) of both sequencing programs were identical, while approximately one-third of the TRs in WES/WGS ± TS relied on biomarkers not covered by the panel. Eight of 10 molecularly informed therapy implementations were supported by the panel, the remaining two were based on biomarkers absent from the panel, highlighting the potential additional clinical benefit of WGS and TS. |
| format | Article |
| id | doaj-art-bd0e91f11f9546919ed87e88b57f10ea |
| institution | Kabale University |
| issn | 2397-768X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Precision Oncology |
| spelling | doaj-art-bd0e91f11f9546919ed87e88b57f10ea2025-01-12T12:06:26ZengNature Portfolionpj Precision Oncology2397-768X2025-01-019111010.1038/s41698-024-00788-3Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncologyIrina A. Kerle0Thomas Gross1Anja Kögler2Jonas S. Arnold3Maximilian Werner4Jan-Niklas Eckardt5Elena E. Möhrmann6Marie Arlt7Barbara Hutter8Jennifer Hüllein9Daniela Richter10Martin M. K. Schneider11Mario Hlevnjak12Lino Möhrmann13Dorothea Hanf14Christoph E. Heilig15Simon Kreutzfeldt16Maria-Veronica Teleanu17Evelin Schröck18Daniel Hübschmann19Peter Horak20Christoph Heining21Stefan Fröhling22Hanno Glimm23Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany; ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Germany; National Center for Tumor Diseases Dresden (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany; German Cancer Consortium (DKTK), Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany, Max Planck Institute of Molecular Cell Biology and GeneticsDepartment for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Department of Internal Medicine I, University Hospital Carl Gustav CarusDepartment for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany; ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Germany; National Center for Tumor Diseases Dresden (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany; German Cancer Consortium (DKTK), Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany, Max Planck Institute of Molecular Cell Biology and GeneticsComputational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZComputational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZDepartment for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Department of Internal Medicine I, University Hospital Carl Gustav CarusComputational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZDepartment for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ)Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ)Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ)Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZDivision of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ)Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ)Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Abstract Precision oncology offers new cancer treatment options, yet sequencing methods vary in type and scope. In this study, we compared whole-exome/whole-genome (WES/WGS) and transcriptome sequencing (TS) with broad panel sequencing by resequencing the same tumor DNA and RNA as well as normal tissue DNA for germline assessment, from 20 patients with rare or advanced tumors, who were originally sequenced by WES/WGS ± TS within the DKFZ/NCT/DKTK MASTER program from 2015 to 2020. Molecular analyses resulted in a median number of 2.5 (gene panel) to 3.5 (WES/WGS ± TS) treatment recommendations per patient. Our results showed that approximately half of the therapy recommendations (TRs) of both sequencing programs were identical, while approximately one-third of the TRs in WES/WGS ± TS relied on biomarkers not covered by the panel. Eight of 10 molecularly informed therapy implementations were supported by the panel, the remaining two were based on biomarkers absent from the panel, highlighting the potential additional clinical benefit of WGS and TS.https://doi.org/10.1038/s41698-024-00788-3 |
| spellingShingle | Irina A. Kerle Thomas Gross Anja Kögler Jonas S. Arnold Maximilian Werner Jan-Niklas Eckardt Elena E. Möhrmann Marie Arlt Barbara Hutter Jennifer Hüllein Daniela Richter Martin M. K. Schneider Mario Hlevnjak Lino Möhrmann Dorothea Hanf Christoph E. Heilig Simon Kreutzfeldt Maria-Veronica Teleanu Evelin Schröck Daniel Hübschmann Peter Horak Christoph Heining Stefan Fröhling Hanno Glimm Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology npj Precision Oncology |
| title | Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology |
| title_full | Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology |
| title_fullStr | Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology |
| title_full_unstemmed | Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology |
| title_short | Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology |
| title_sort | translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology |
| url | https://doi.org/10.1038/s41698-024-00788-3 |
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