1
|
Ball M, Ourailidis I, Kluck K, Menzel M, Kirchner M, Allgäuer M, Tay TKY, Schnecko F, Volckmar AL, Goldschmid H, Neuman O, Fröhling S, Schirmacher P, Budczies J, Stenzinger A, Kazdal D. Leveraging Off-Target Reads in Panel Sequencing for Homologous Recombination Repair Deficiency Screening in Tumor. J Mol Diagn 2024; 26:479-486. [PMID: 38522840 DOI: 10.1016/j.jmoldx.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/24/2024] [Accepted: 02/14/2024] [Indexed: 03/26/2024] Open
Abstract
Targeted tumor only sequencing has become a standard practice in cancer diagnostics. This study aims to develop an approach for robust copy number variant calling in tumor samples using only off-target region (OTR) reads. We also established a clinical use case for homologous recombination deficiency (HRD) score estimation (HRDest) using the sum of telomeric-allelic imbalance and large-scale state transition scores without the need for loss of heterozygosity information. A strong correlation was found between HRD score and the sum of telomeric-allelic imbalance + large-scale state transition in The Cancer Genome Atlas cohort (ρ = 0.99, P < 2.2 × 10-16) and in a clinical in-house cohort of 34 tumors (ρ = 0.9, P = 5.1 × 10-13) comparing whole-exome sequencing and targeted sequencing data. HRDest scores from 1086 clinical cases were compared with The Cancer Genome Atlas data set. There were no significant differences in HRD score distribution within the analyzed tumor types. As a control, commercially available HRD standards were also sequenced, and the HRDest scores obtained from the OTR reads were well within the HRD reference range provided by the manufacturer. In conclusion, OTR reads of tumor-only panel sequencing can be used to determine genome-wide copy number variant profiles and to approximate HRD scores.
Collapse
Affiliation(s)
- Markus Ball
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Klaus Kluck
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Menzel
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martina Kirchner
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Allgäuer
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Timothy Kwang Yong Tay
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Department of Anatomical Pathology, Singapore General Hospital, Singapore; Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Fabian Schnecko
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hannah Goldschmid
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olaf Neuman
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Fröhling
- Department of Translational Medical Oncology, National Center for Tumor Diseases, Heidelberg, Germany; German Cancer Consortium, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Center for Personalized Medicine Heidelberg, Heidelberg, Germany
| | - Jan Budczies
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; German Cancer Consortium, Heidelberg, Germany; Center for Personalized Medicine Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg, German Center for Lung Research, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; German Cancer Consortium, Heidelberg, Germany; Center for Personalized Medicine Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg, German Center for Lung Research, Heidelberg, Germany.
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; German Cancer Consortium, Heidelberg, Germany; Translational Lung Research Center Heidelberg, German Center for Lung Research, Heidelberg, Germany.
| |
Collapse
|
3
|
Scaglione GL, Pignata S, Pettinato A, Paolillo C, Califano D, Scandurra G, Lombardo V, Di Gaudio F, Pecorino B, Mereu L, Scollo P, Capoluongo ED. Homologous Recombination Deficiency (HRD) Scoring, by Means of Two Different Shallow Whole-Genome Sequencing Pipelines (sWGS), in Ovarian Cancer Patients: A Comparison with Myriad MyChoice Assay. Int J Mol Sci 2023; 24:17095. [PMID: 38069422 PMCID: PMC10707691 DOI: 10.3390/ijms242317095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
High-grade serous ovarian cancer (HGSOC) patients carrying the BRCA1/2 mutation or deficient in the homologous recombination repair system (HRD) generally benefit from treatment with PARP inhibitors. Some international recommendations suggest that BRCA1/2 genetic testing should be offered for all newly diagnosed epithelial ovarian cancer, along with HRD assessment. Academic tests (ATs) are continuously under development, in order to break down the barriers patients encounter in accessing HRD testing. Two different methods for shallow whole-genome sequencing (sWGS) were compared to the reference assay, Myriad. All these three assays were performed on 20 retrospective HGSOC samples. Moreover, HRD results were correlated with the progression-free survival rate (PFS). Both sWGS chemistries showed good correlation with each other and a complete agreement, even when compared to the Myriad score. Our academic HRD assay categorized patients as HRD-Deficient, HRM-Mild and HRN-Negative. These three groups were matched with PFS, providing interesting findings in terms of HRD scoring and months of survival. Both our sWGS assays and the Myriad test correlated with the patient's response to treatments. Finally, our AT confirms its capability of determining HRD status, with the advantage of being faster, cheaper, and easier to carry out. Our results showed a prognostic value for the HRD score.
Collapse
Affiliation(s)
- Giovanni L. Scaglione
- Laboratory of Molecular Oncology, IDI-IRCCS, Via dei Monti di Creta, 104, 00167 Rome, Italy;
| | - Sandro Pignata
- Department of Urology and Gynecology, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Via Mariano Semmola, 53, 80131 Naples, Italy;
| | - Angela Pettinato
- Department of Pathological Anatomy, A.O.E. Cannizzaro, Via Messina, 829, 95126 Catania, Italy;
| | - Carmela Paolillo
- Department of Clinical and Experimental Medicine, University of Foggia, Viale Luigi Pinto, 71122 Foggia, Italy;
| | - Daniela Califano
- Functional Genomic Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Via Mariano Semmola, 53, 80131 Naples, Italy;
| | - Giuseppa Scandurra
- Department of Medical Oncology, A.O.E. Cannizzaro, Via Messina, 829, 95126 Catania, Italy; (G.S.); (V.L.)
| | - Valentina Lombardo
- Department of Medical Oncology, A.O.E. Cannizzaro, Via Messina, 829, 95126 Catania, Italy; (G.S.); (V.L.)
| | | | - Basilio Pecorino
- Department of Obstetrics and Gynecology, A.O.E. Cannizzaro, Via Messina, 829, 95126 Catania, Italy; (B.P.); (P.S.)
| | - Liliana Mereu
- Division of Obstetrics and Gynecology, Department of General Surgery and Medical-Surgical Specialism, University of Catania, P.O. “G Rodolico”, Via Santa Sofia, 78, 95123 Catania, Italy;
| | - Paolo Scollo
- Department of Obstetrics and Gynecology, A.O.E. Cannizzaro, Via Messina, 829, 95126 Catania, Italy; (B.P.); (P.S.)
- Faculty of Medicine, “Kore” University, Cittadella Universitaria, 94100 Enna, Italy
| | - Ettore D. Capoluongo
- Department of Clinical Pathology and Genomics, A.O.E. Cannizzaro, Via Messina 829, 95126 Catania, Italy
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Via Pansini, 5, 80131 Naples, Italy
| |
Collapse
|
4
|
Menzel M, Ossowski S, Kral S, Metzger P, Horak P, Marienfeld R, Boerries M, Wolter S, Ball M, Neumann O, Armeanu-Ebinger S, Schroeder C, Matysiak U, Goldschmid H, Schipperges V, Fürstberger A, Allgäuer M, Eberhardt T, Niewöhner J, Blaumeiser A, Ploeger C, Haack TB, Tay TKY, Kelemen O, Pauli T, Kirchner M, Kluck K, Ott A, Renner M, Admard J, Gschwind A, Lassmann S, Kestler H, Fend F, Illert AL, Werner M, Möller P, Seufferlein TTW, Malek N, Schirmacher P, Fröhling S, Kazdal D, Budczies J, Stenzinger A. Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients. NPJ Precis Oncol 2023; 7:106. [PMID: 37864096 PMCID: PMC10589320 DOI: 10.1038/s41698-023-00457-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/26/2023] [Indexed: 10/22/2023] Open
Abstract
A growing number of druggable targets and national initiatives for precision oncology necessitate broad genomic profiling for many cancer patients. Whole exome sequencing (WES) offers unbiased analysis of the entire coding sequence, segmentation-based detection of copy number alterations (CNAs), and accurate determination of complex biomarkers including tumor mutational burden (TMB), homologous recombination repair deficiency (HRD), and microsatellite instability (MSI). To assess the inter-institution variability of clinical WES, we performed a comparative pilot study between German Centers of Personalized Medicine (ZPMs) from five participating institutions. Tumor and matched normal DNA from 30 patients were analyzed using custom sequencing protocols and bioinformatic pipelines. Calling of somatic variants was highly concordant with a positive percentage agreement (PPA) between 91 and 95% and a positive predictive value (PPV) between 82 and 95% compared with a three-institution consensus and full agreement for 16 of 17 druggable targets. Explanations for deviations included low VAF or coverage, differing annotations, and different filter protocols. CNAs showed overall agreement in 76% for the genomic sequence with high wet-lab variability. Complex biomarkers correlated strongly between institutions (HRD: 0.79-1, TMB: 0.97-0.99) and all institutions agreed on microsatellite instability. This study will contribute to the development of quality control frameworks for comprehensive genomic profiling and sheds light onto parameters that require stringent standardization.
Collapse
Affiliation(s)
- Michael Menzel
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Sebastian Kral
- Institute for Surgical Pathology, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Personalized Medicine (ZPM), Freiburg, Germany
| | - Patrick Metzger
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Horak
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ralf Marienfeld
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
- Center for Personalized Medicine (ZPM), Ulm, Germany
| | - Melanie Boerries
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Wolter
- Institute for Surgical Pathology, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Personalized Medicine (ZPM), Freiburg, Germany
| | - Markus Ball
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Sorin Armeanu-Ebinger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Uta Matysiak
- Institute for Surgical Pathology, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Personalized Medicine (ZPM), Freiburg, Germany
| | - Hannah Goldschmid
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Vincent Schipperges
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Axel Fürstberger
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
- Center for Personalized Medicine (ZPM), Ulm, Germany
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Michael Allgäuer
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Timo Eberhardt
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
- Center for Personalized Medicine (ZPM), Ulm, Germany
| | - Jakob Niewöhner
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Andreas Blaumeiser
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolin Ploeger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Tobias Bernd Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Timothy Kwang Yong Tay
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Olga Kelemen
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Thomas Pauli
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martina Kirchner
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Klaus Kluck
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Alexander Ott
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Marcus Renner
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Axel Gschwind
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Personalized Medicine (ZPM), Tübingen, Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Personalized Medicine (ZPM), Freiburg, Germany
| | - Hans Kestler
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
- Center for Personalized Medicine (ZPM), Ulm, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Anna Lena Illert
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79085, Freiburg, Germany
- Medical Department for Hematology and Oncology, Klinikum Rechts der Isar, Technische Universität München, 80333, Munich, Germany
- German Cancer Consortium (DKTK) Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Personalized Medicine (ZPM), Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Möller
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | | | - Nisar Malek
- Center for Personalized Medicine (ZPM), Tübingen, Germany
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan Fröhling
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Jan Budczies
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Center for Personalized Medicine (ZPM), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Center for Personalized Medicine (ZPM), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
| |
Collapse
|