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Stout LA, Hunter C, Schroeder C, Kassem N, Schneider BP. Clinically significant germline pathogenic variants are missed by tumor genomic sequencing. NPJ Genom Med 2023; 8:30. [PMID: 37833309 PMCID: PMC10575977 DOI: 10.1038/s41525-023-00374-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
A germline pathogenic variant may be present even if the results of tumor genomic sequencing do not suggest one. There are key differences in the assay design and reporting of variants between germline and somatic laboratories. When appropriate, both tests should be completed to aid in therapy decisions and determining optimal screening and risk-reduction interventions.
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Affiliation(s)
- Leigh Anne Stout
- Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Health Precision Genomics, Indianapolis, IN, USA
| | - Cynthia Hunter
- Indiana University Health Precision Genomics, Indianapolis, IN, USA
| | | | - Nawal Kassem
- Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Health Precision Genomics, Indianapolis, IN, USA
| | - Bryan P Schneider
- Indiana University School of Medicine, Indianapolis, IN, USA.
- Indiana University Health Precision Genomics, Indianapolis, IN, USA.
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4
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Tung N, Dougherty KC, Gatof ES, DeLeonardis K, Hogan L, Tukachinsky H, Gornstein E, Oxnard GR, McGregor K, Keller RB. Potential pathogenic germline variant reporting from tumor comprehensive genomic profiling complements classic approaches to germline testing. NPJ Precis Oncol 2023; 7:76. [PMID: 37568048 PMCID: PMC10421918 DOI: 10.1038/s41698-023-00429-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Existing guidance regarding clinically informed germline testing for patients with cancer is effective for evaluation of classic hereditary cancer syndromes and established gene/cancer type associations. However, current screening methods may miss patients with rare, reduced penetrance, or otherwise occult hereditary risk. Secondary finding of suspected germline variants that may confer inherited cancer risk via tumor comprehensive genomic profiling (CGP) has the potential to help address these limitations. However, reporting practices for secondary finding of germline variants are inconsistent, necessitating solutions for transparent and coherent communication of these potentially important findings. A workflow for improved confidence detection and clear reporting of potential pathogenic germline variants (PPGV) in select cancer susceptibility genes (CSG) was applied to a research dataset from real-world clinical tumor CGP of > 125,000 patients with advanced cancer. The presence and patterns of PPGVs identified across tumor types was assessed with a focus on scenarios in which traditional clinical germline evaluation may have been insufficient to capture genetic risk. PPGVs were identified in 9.7% of tumor CGP cases using tissue- and liquid-based assays across a broad range of cancer types, including in a number of "off-tumor" contexts. Overall, PPGVs were identified in a similar proportion of cancers with National Comprehensive Cancer Network (NCCN) recommendations for germline testing regardless of family history (11%) as in all other cancer types (9%). These findings suggest that tumor CGP can serve as a tool that is complementary to traditional germline genetic evaluation in helping to ascertain inherited susceptibility in patients with advanced cancer.
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Affiliation(s)
- Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Emily Stern Gatof
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kim DeLeonardis
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Lauren Hogan
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
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5
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Yap TA, Stadler ZK, Stout LA, Schneider BP. Aligning Germline Cancer Predisposition With Tumor-Based Next-Generation Sequencing for Modern Oncology Diagnosis, Interception, and Therapeutic Development. Am Soc Clin Oncol Educ Book 2023; 43:e390738. [PMID: 37390373 DOI: 10.1200/edbk_390738] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
In the era of precision medicine, genomic interrogation for identification of both germline and somatic genetic alterations has become increasingly important. While such germline testing was usually undertaken via a phenotype-driven single-gene approach, with the advent of next-generation sequencing (NGS) technologies, the widespread utilization of multigene panels, often agnostic of cancer phenotype, has become a commonplace in many different cancer types. At the same time, somatic tumor testing in oncology performed for the purpose of guiding therapeutic decisions for targeted therapies has also rapidly expanded, recently starting to incorporate not just patients with recurrent or metastatic cancer but even patients with early-stage disease. An integrated approach may be the best approach for the optimal management of patients with different cancers. The lack of complete congruence between germline and somatic NGS tests does not minimize the power or importance of either, but highlights the need to understand their limitations so as not to overlook an important finding or omission. NGS tests built to more uniformly and comprehensively evaluate both the germline and tumor simultaneously are urgently required and are in development. In this article, we discuss approaches to somatic and germline analyses in patients with cancer and the knowledge gained from integration of tumor-normal sequencing. We also detail strategies for the incorporation of genomic analysis into oncology care delivery models and the important emergence of poly(ADP-ribose) polymerase and other DNA Damage Response inhibitors in the clinic for patients with cancer with germline and somatic BRCA1 and BRCA2 mutations.
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Affiliation(s)
- Timothy A Yap
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Leigh Anne Stout
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN
| | - Bryan P Schneider
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN
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6
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Mehra N, Kloots I, Vlaming M, Aluwini S, Dewulf E, Oprea-Lager DE, van der Poel H, Stoevelaar H, Yakar D, Bangma CH, Bekers E, van den Bergh R, Bergman AM, van den Berkmortel F, Boudewijns S, Dinjens WN, Fütterer J, van der Hulle T, Jenster G, Kroeze LI, van Kruchten M, van Leenders G, van Leeuwen PJ, de Leng WW, van Moorselaar RJA, Noordzij W, Oldenburg RA, van Oort IM, Oving I, Schalken JA, Schoots IG, Schuuring E, Smeenk RJ, Vanneste BG, Vegt E, Vis AN, de Vries K, Willemse PPM, Wondergem M, Ausems M. Genetic Aspects and Molecular Testing in Prostate Cancer: A Report from a Dutch Multidisciplinary Consensus Meeting. EUR UROL SUPPL 2023; 49:23-31. [PMID: 36874601 PMCID: PMC9975012 DOI: 10.1016/j.euros.2022.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2022] [Indexed: 01/27/2023] Open
Abstract
Background Germline and tumour genetic testing in prostate cancer (PCa) is becoming more broadly accepted, but testing indications and clinical consequences for carriers in each disease stage are not yet well defined. Objective To determine the consensus of a Dutch multidisciplinary expert panel on the indication and application of germline and tumour genetic testing in PCa. Design setting and participants The panel consisted of 39 specialists involved in PCa management. We used a modified Delphi method consisting of two voting rounds and a virtual consensus meeting. Outcome measurements and statistical analysis Consensus was reached if ≥75% of the panellists chose the same option. Appropriateness was assessed by the RAND/UCLA appropriateness method. Results and limitations Of the multiple-choice questions, 44% reached consensus. For men without PCa having a relevant family history (familial PCa/BRCA-related hereditary cancer), follow-up by prostate-specific antigen was considered appropriate. For patients with low-risk localised PCa and a family history of PCa, active surveillance was considered appropriate, except in case of the patient being a BRCA2 germline pathogenic variant carrier. Germline and tumour genetic testing should not be done for nonmetastatic hormone-sensitive PCa in the absence of a relevant family history of cancer. Tumour genetic testing was deemed most appropriate for the identification of actionable variants, with uncertainty for germline testing. For tumour genetic testing in metastatic castration-resistant PCa, consensus was not reached for the timing and panel composition. The principal limitations are as follows: (1) a number of topics discussed lack scientific evidence, and therefore the recommendations are partly opinion based, and (2) there was a small number of experts per discipline. Conclusions The outcomes of this Dutch consensus meeting may provide further guidance on genetic counselling and molecular testing related to PCa. Patient summary A group of Dutch specialists discussed the use of germline and tumour genetic testing in prostate cancer (PCa) patients, indication of these tests (which patients and when), and impact of these tests on the management and treatment of PCa.
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Affiliation(s)
- Niven Mehra
- Department of Medical Oncology, Radboud UMC, Nijmegen, The Netherlands
- Corresponding author. Department of Medical Oncology, Radboud University Medical Centre, Postbus 9101, 6500 HB Nijmegen, The Netherlands. Tel. +31 243610354; Fax: +31 243615025.
| | - Iris Kloots
- Department of Medical Oncology, Radboud UMC, Nijmegen, The Netherlands
| | - Michiel Vlaming
- Division Laboratories, Pharmacy and biomedical Genetics, Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Shafak Aluwini
- Department of Radiation Oncology, UMCG, Groningen, The Netherlands
| | - Els Dewulf
- Centre for Decision Analysis & Support, Ismar Healthcare NV, Lier, Belgium
| | - Daniela E. Oprea-Lager
- Department of Radiology & Nuclear Medicine, Amsterdam University Medical Centers, VU University, Amsterdam, The Netherlands
| | - Henk van der Poel
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
- Department of Urology, Amsterdam University Medical Centers, VU University, Amsterdam, The Netherlands
| | - Herman Stoevelaar
- Centre for Decision Analysis & Support, Ismar Healthcare NV, Lier, Belgium
| | - Derya Yakar
- Department of Radiology, UMCG, Groningen, The Netherlands
- Department of Radiology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Chris H. Bangma
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
| | - Elise Bekers
- Department of Pathology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | | | - Andries M. Bergman
- Department of Medical Oncology and Oncogenomics, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | | | - Steve Boudewijns
- Department of Medical Oncology, Bravis Hospital, Roosendaal, The Netherlands
| | | | - Jurgen Fütterer
- Department of Medical Imaging, Radboud UMC, Nijmegen, The Netherlands
| | - Tom van der Hulle
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Michel van Kruchten
- Department of Medical Oncology, University Medical Centre Groningen, Groningen, The Netherlands
| | | | - Pim J. van Leeuwen
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | | | | | - Walter Noordzij
- Department of Nuclear Medicine & Molecular Imaging, University Medical Center Groningen, Groningen, The Netherlands
| | | | | | - Irma Oving
- Department of Internal Medicine, Ziekenhuis Groep Twente, Almelo, The Netherlands
| | | | - Ivo G. Schoots
- Department of Radiology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, Groningen, The Netherlands
| | - Robert J. Smeenk
- Department of Radiation Oncology, Radboud UMC, Nijmegen, The Netherlands
| | - Ben G.L. Vanneste
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
- Department of Human Structure and Repair, Ghent University Hospital, Ghent, Belgium
- Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium
| | - Erik Vegt
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - André N. Vis
- Department of Urology, Amsterdam University Medical Centers, VU University, Amsterdam, The Netherlands
| | - Kim de Vries
- Department of Radiation Oncology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Maurits Wondergem
- Department of Nuclear Medicine, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Margreet Ausems
- Division Laboratories, Pharmacy and biomedical Genetics, Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
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Abstract
PURPOSE OF REVIEW Childhood cancer is rare, but it remains the leading cause of disease-related mortality among children 1-14 years of age. As exposure to environmental factors is lower in children, inherited genetic factors become an important player in the cause of childhood cancer. This review highlights the current knowledge and approach for cancer predisposition syndromes in children. RECENT FINDINGS Current literature suggests that 10-18% of paediatric cancer patients have an underlying genetic susceptibility to their disease. With better knowledge and technology, more genes and syndromes are being discovered, allowing tailored treatment and surveillance for the probands and their families.Studies have demonstrated that focused surveillance can detect early malignancies and increase overall survival in several cancer predisposition syndromes. Various approaches have been proposed to refine early tumour detection strategies while minimizing the burden on patients and families. Newer therapeutic strategies are being investigated to treat, or even prevent, tumours in children with cancer predisposition. SUMMARY This review summarizes the current knowledge about different cancer predisposition syndromes, focusing on the diagnosis, genetic counselling, surveillance and future directions.
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Affiliation(s)
- Yoshiko Nakano
- Division of Haematology/Oncology, The Hospital for Sick Children
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Ron Rabinowicz
- Division of Haematology/Oncology, The Hospital for Sick Children
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
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