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Forster VJ, Aronson M, Zhang C, Chung J, Sudhaman S, Galati MA, Kelly J, Negm L, Ercan AB, Stengs L, Durno C, Edwards M, Komosa M, Oldfield LE, Nunes NM, Pedersen S, Wellum J, Siddiqui I, Bianchi V, Weil BR, Fox VL, Pugh TJ, Kamihara J, Tabori U. Biallelic EPCAM deletions induce tissue-specific DNA repair deficiency and cancer predisposition. NPJ Precis Oncol 2024; 8:69. [PMID: 38467830 PMCID: PMC10928233 DOI: 10.1038/s41698-024-00537-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/08/2024] [Indexed: 03/13/2024] Open
Abstract
We report a case of Mismatch Repair Deficiency (MMRD) caused by germline homozygous EPCAM deletion leading to tissue-specific loss of MSH2. Through the use of patient-derived cells and organoid technologies, we performed stepwise in vitro differentiation of colonic and brain organoids from reprogrammed EPCAMdel iPSC derived from patient fibroblasts. Differentiation of iPSC to epithelial-colonic organoids exhibited continuous increased EPCAM expression and hypermethylation of the MSH2 promoter. This was associated with loss of MSH2 expression, increased mutational burden, MMRD signatures and MS-indel accumulation, the hallmarks of MMRD. In contrast, maturation into brain organoids and examination of blood and fibroblasts failed to show similar processes, preserving MMR proficiency. The combined use of iPSC, organoid technologies and functional genomics analyses highlights the potential of cutting-edge cellular and molecular analysis techniques to define processes controlling tumorigenesis and uncovers a new paradigm of tissue-specific MMRD, which affects the clinical management of these patients.
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Affiliation(s)
- V J Forster
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - M Aronson
- Zane Cohen Centre, Sinai Health System and Faculty of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - C Zhang
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - J Chung
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - S Sudhaman
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - M A Galati
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - J Kelly
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - L Negm
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - A B Ercan
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - L Stengs
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - C Durno
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON, Canada
| | - M Edwards
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - M Komosa
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - N M Nunes
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - S Pedersen
- University Health Network, Toronto, ON, Canada
| | - J Wellum
- University Health Network, Toronto, ON, Canada
| | - I Siddiqui
- Department of Paediatric Laboratory Medicine and Pathobiology, Division of Pathology, The Hospital for Sick Children, Toronto, ON, Canada
| | - V Bianchi
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - B R Weil
- Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - V L Fox
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - T J Pugh
- University Health Network, Toronto, ON, Canada
| | - J Kamihara
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - U Tabori
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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2
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Adi-Wauran E, Clausen M, Shickh S, Gagliardi AR, Denburg A, Oldfield LE, Sam J, Reble E, Krishnapillai S, Regier DA, Baxter NN, Dawson L, Penney LS, Foulkes W, Basik M, Sun S, Schrader KA, Karsan A, Pollett A, Pugh TJ, Kim RH, Bombard Y. "I just wanted more": Hereditary cancer syndromes patients' perspectives on the utility of circulating tumour DNA testing for cancer screening. Eur J Hum Genet 2024; 32:176-181. [PMID: 37821757 PMCID: PMC10853540 DOI: 10.1038/s41431-023-01473-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023] Open
Abstract
Hereditary cancer syndromes (HCS) predispose individuals to a higher risk of developing multiple cancers. However, current screening strategies have limited ability to screen for all cancer risks. Circulating tumour DNA (ctDNA) detects DNA fragments shed by tumour cells in the bloodstream and can potentially detect cancers early. This study aimed to explore patients' perspectives on ctDNA's utility to help inform its clinical adoption and implementation. We conducted a qualitative interpretive description study using semi-structured phone interviews. Participants were purposively sampled adult HCS patients recruited from a Canadian HCS research consortium. Thirty HCS patients were interviewed (n = 19 women, age range 20s-70s, n = 25 were white). Participants were highly concerned about developing cancers, particularly those without reliable screening options for early detection. They "just wanted more" than their current screening strategies. Participants were enthusiastic about ctDNA's potential to be comprehensive (detect multiple cancers), predictive (detect cancers early) and tailored (lead to personalized clinical management). Participants also acknowledged ctDNA's potential limitations, including false positives/negatives risks and experiencing additional anxiety. However, they saw ctDNA's potential benefits outweighing its limitations. In conclusion, participants' belief in ctDNA's potential to improve their care overshadowed its limitations, indicating patients' support for using ctDNA in HCS care.
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Affiliation(s)
- Ella Adi-Wauran
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Canada
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, Canada
| | - Marc Clausen
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Canada
| | - Salma Shickh
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Canada
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, Canada
| | - Anna R Gagliardi
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Avram Denburg
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, Canada
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada
| | - Leslie E Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Jordan Sam
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Canada
| | - Emma Reble
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Canada
| | - Suvetha Krishnapillai
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Canada
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, Canada
| | - Dean A Regier
- BC Cancer, Vancouver, Canada
- University of British Columbia, Vancouver, Canada
| | - Nancy N Baxter
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, Canada
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
- University of Toronto, Toronto, Canada
| | - Lesa Dawson
- Memorial University, St. John's, Canada
- Eastern Health Authority, St. John's, Canada
| | | | - William Foulkes
- McGill University, Montréal, Canada
- Jewish General Hospital, Montréal, Canada
| | - Mark Basik
- McGill University, Montréal, Canada
- Jewish General Hospital, Montréal, Canada
| | - Sophie Sun
- BC Cancer, Vancouver, Canada
- University of British Columbia, Vancouver, Canada
| | | | - Aly Karsan
- BC Cancer, Vancouver, Canada
- University of British Columbia, Vancouver, Canada
| | | | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Raymond H Kim
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.
- University of Toronto, Toronto, Canada.
- Mount Sinai Hospital, Toronto, Canada.
- Ontario Institute for Cancer Research, Toronto, Canada.
| | - Yvonne Bombard
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Canada.
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, Canada.
- Ontario Institute for Cancer Research, Toronto, Canada.
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3
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Wong D, Luo P, Oldfield LE, Gong H, Brunga L, Rabinowicz R, Subasri V, Chan C, Downs T, Farncombe KM, Luu B, Norman M, Sobotka JA, Uju P, Eagles J, Pedersen S, Wellum J, Danesh A, Prokopec SD, Stutheit-Zhao EY, Znassi N, Heisler LE, Jovelin R, Lam B, Lujan Toro BE, Marsh K, Sundaravadanam Y, Torti D, Man C, Goldenberg A, Xu W, Veit-Haibach P, Doria AS, Malkin D, Kim RH, Pugh TJ. Early Cancer Detection in Li-Fraumeni Syndrome with Cell-Free DNA. Cancer Discov 2024; 14:104-119. [PMID: 37874259 PMCID: PMC10784744 DOI: 10.1158/2159-8290.cd-23-0456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/07/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
People with Li-Fraumeni syndrome (LFS) harbor a germline pathogenic variant in the TP53 tumor suppressor gene, face a near 100% lifetime risk of cancer, and routinely undergo intensive surveillance protocols. Liquid biopsy has become an attractive tool for a range of clinical applications, including early cancer detection. Here, we provide a proof-of-principle for a multimodal liquid biopsy assay that integrates a targeted gene panel, shallow whole-genome, and cell-free methylated DNA immunoprecipitation sequencing for the early detection of cancer in a longitudinal cohort of 89 LFS patients. Multimodal analysis increased our detection rate in patients with an active cancer diagnosis over uni-modal analysis and was able to detect cancer-associated signal(s) in carriers prior to diagnosis with conventional screening (positive predictive value = 67.6%, negative predictive value = 96.5%). Although adoption of liquid biopsy into current surveillance will require further clinical validation, this study provides a framework for individuals with LFS. SIGNIFICANCE By utilizing an integrated cell-free DNA approach, liquid biopsy shows earlier detection of cancer in patients with LFS compared with current clinical surveillance methods such as imaging. Liquid biopsy provides improved accessibility and sensitivity, complementing current clinical surveillance methods to provide better care for these patients. See related commentary by Latham et al., p. 23. This article is featured in Selected Articles from This Issue, p. 5.
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Affiliation(s)
- Derek Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ping Luo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Leslie E. Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Haifan Gong
- The Hospital for Sick Children, Toronto, Canada
| | | | | | - Vallijah Subasri
- The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Vector Institute, Toronto, Canada
| | - Clarissa Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Tiana Downs
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | - Beatrice Luu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Maia Norman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Julia A. Sobotka
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Precious Uju
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Jenna Eagles
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Stephanie Pedersen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Johanna Wellum
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | | | - Nadia Znassi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | | | - Bernard Lam
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Kayla Marsh
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Dax Torti
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Carina Man
- The Hospital for Sick Children, Toronto, Canada
| | - Anna Goldenberg
- The Hospital for Sick Children, Toronto, Canada
- Vector Institute, Toronto, Canada
| | - Wei Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Patrick Veit-Haibach
- Joint Department of Medical Imaging, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada
| | | | - David Malkin
- The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Raymond H. Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- The Hospital for Sick Children, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
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4
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Farncombe KM, Wong D, Norman ML, Oldfield LE, Sobotka JA, Basik M, Bombard Y, Carile V, Dawson L, Foulkes WD, Malkin D, Karsan A, Parkin P, Penney LS, Pollett A, Schrader KA, Pugh TJ, Kim RH. Current and new frontiers in hereditary cancer surveillance: Opportunities for liquid biopsy. Am J Hum Genet 2023; 110:1616-1627. [PMID: 37802042 PMCID: PMC10577078 DOI: 10.1016/j.ajhg.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 10/08/2023] Open
Abstract
At least 5% of cancer diagnoses are attributed to a causal pathogenic or likely pathogenic germline genetic variant (hereditary cancer syndrome-HCS). These individuals are burdened with lifelong surveillance monitoring organs for a wide spectrum of cancers. This is associated with substantial uncertainty and anxiety in the time between screening tests and while the individuals are awaiting results. Cell-free DNA (cfDNA) sequencing has recently shown potential as a non-invasive strategy for monitoring cancer. There is an opportunity for high-yield cancer early detection in HCS. To assess clinical validity of cfDNA in individuals with HCS, representatives from eight genetics centers from across Canada founded the CHARM (cfDNA in Hereditary and High-Risk Malignancies) Consortium in 2017. In this perspective, we discuss operationalization of this consortium and early data emerging from the most common and well-characterized HCSs: hereditary breast and ovarian cancer, Lynch syndrome, Li-Fraumeni syndrome, and Neurofibromatosis type 1. We identify opportunities for the incorporation of cfDNA sequencing into surveillance protocols; these opportunities are backed by examples of earlier cancer detection efficacy in HCSs from the CHARM Consortium. We seek to establish a paradigm shift in early cancer surveillance in individuals with HCSs, away from highly centralized, regimented medical screening visits and toward more accessible, frequent, and proactive care for these high-risk individuals.
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Affiliation(s)
- Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Derek Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maia L Norman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Leslie E Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Julia A Sobotka
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mark Basik
- Department of Surgery, McGill University Medical School, Montreal, QC, Canada; Department of Oncology, McGill University Medical School, Montreal, QC, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada; Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Victoria Carile
- Jewish General Hospital Stroll Cancer Prevention Centre, Montreal, QC, Canada
| | - Lesa Dawson
- Memorial University, St. John's, NL, Canada; Eastern Health Authority, St. John's, NL, Canada
| | - William D Foulkes
- Jewish General Hospital Stroll Cancer Prevention Centre, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - David Malkin
- Division of Hematology-Oncology, Hospital for Sick Children, Toronto, ON, Canada; Department of Pediatrics, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | | | - Patricia Parkin
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada; Division of Pediatric Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | | | | | - Kasmintan A Schrader
- BC Cancer, Vancouver, BC, Canada; University of British Columbia, Vancouver, BC, Canada
| | - Trevor J Pugh
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| | - Raymond H Kim
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Sinai Health System, Toronto, ON, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medicine, University of Toronto, Toronto, ON, Canada.
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5
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Lheureux S, Prokopec SD, Oldfield LE, Gonzalez-Ochoa E, Bruce JP, Wong D, Danesh A, Torti D, Torchia J, Fortuna A, Singh S, Irving M, Marsh K, Lam B, Speers V, Yosifova A, Oaknin A, Madariaga A, Dhani NC, Bowering V, Oza AM, Pugh TJ. Identifying Mechanisms of Resistance by Circulating Tumor DNA in EVOLVE, a Phase II Trial of Cediranib Plus Olaparib for Ovarian Cancer at Time of PARP Inhibitor Progression. Clin Cancer Res 2023; 29:3706-3716. [PMID: 37327320 PMCID: PMC10502468 DOI: 10.1158/1078-0432.ccr-23-0797] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/04/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023]
Abstract
PURPOSE To evaluate the use of blood cell-free DNA (cfDNA) to identify emerging mechanisms of resistance to PARP inhibitors (PARPi) in high-grade serous ovarian cancer (HGSOC). EXPERIMENTAL DESIGN We used targeted sequencing (TS) to analyze 78 longitudinal cfDNA samples collected from 30 patients with HGSOC enrolled in a phase II clinical trial evaluating cediranib (VEGF inhibitor) plus olaparib (PARPi) after progression on PARPi alone. cfDNA was collected at baseline, before treatment cycle 2, and at end of treatment. These were compared with whole-exome sequencing (WES) of baseline tumor tissues. RESULTS At baseline (time of initial PARPi progression), cfDNA tumor fractions were 0.2% to 67% (median, 3.25%), and patients with high ctDNA levels (>15%) had a higher tumor burden (sum of target lesions; P = 0.043). Across all timepoints, cfDNA detected 74.4% of mutations known from prior tumor WES, including three of five expected BRCA1/2 reversion mutations. In addition, cfDNA identified 10 novel mutations not detected by WES, including seven TP53 mutations annotated as pathogenic by ClinVar. cfDNA fragmentation analysis attributed five of these novel TP53 mutations to clonal hematopoiesis of indeterminate potential (CHIP). At baseline, samples with significant differences in mutant fragment size distribution had shorter time to progression (P = 0.001). CONCLUSIONS Longitudinal testing of cfDNA by TS provides a noninvasive tool for detection of tumor-derived mutations and mechanisms of PARPi resistance that may aid in directing patients to appropriate therapeutic strategies. With cfDNA fragmentation analyses, CHIP was identified in several patients and warrants further investigation.
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Affiliation(s)
- Stephanie Lheureux
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stephenie D. Prokopec
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Leslie E. Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Jeffrey P. Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Derek Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dax Torti
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | - Sharanjit Singh
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Matthew Irving
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Kayla Marsh
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Bernard Lam
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vanessa Speers
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aleksandra Yosifova
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ana Oaknin
- Gynaecologic Cancer Programme, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Ainhoa Madariaga
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Neesha C. Dhani
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Valerie Bowering
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Amit M. Oza
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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6
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Oldfield LE, Jones V, Gill B, Kodous N, Fazelzad R, Rodin D, Sandhu H, Umakanthan B, Papadakos J, Giuliani ME. Synthesis of Existent Oncology Curricula for Primary Care Providers: A Scoping Review With a Global Equity Lens. JCO Glob Oncol 2023; 9:e2200298. [PMID: 37141562 DOI: 10.1200/go.22.00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
PURPOSE Global increases in cancer, coupled with a shortage of cancer specialists, has led to an increasing role for primary care providers (PCP) in cancer care. This review aimed to examine all extant cancer curricula for PCPs and to analyze the motivations for curriculum development. METHODS A comprehensive literature search was conducted from inception to October 13, 2021, with no language restrictions. The initial search yielded 11,162 articles and 10,902 articles underwent title and abstract review. After full-text review, 139 articles were included. Numeric and thematic analyses were conducted and education programs were evaluated using Bloom's taxonomy. RESULTS Most curricula were developed in high-income countries (HICs), with 58% in the United States. Cancer-specific curricula focused on HIC priority cancers, such as skin/melanoma, and did not represent the global cancer burden. Most (80%) curricula were developed for staff physicians and 73% focused on cancer screening. More than half (57%) of programs were delivered in person, with a shift toward online delivery over time. Less than half (46%) of programs were codeveloped with PCPs and 34% did not involve PCPs in the program design and development. Curricula were primarily developed to improve cancer knowledge, and 72 studies assessed multiple outcome measures. No studies included the top two levels of Bloom's taxonomy of learning (evaluating; creating). CONCLUSION To our knowledge, this is the first review to assess the current state of cancer curricula for PCPs with a global focus. This review shows that extant curricula are primarily developed in HICs, do not represent the global cancer burden, and focus on cancer screening. This review lays a foundation to advance the cocreation of curricula that are aligned to the global cancer burden.
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Affiliation(s)
| | - Vivien Jones
- Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Bhajan Gill
- Cancer Education, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Nardeen Kodous
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Rouhi Fazelzad
- Library and Information Services, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Danielle Rodin
- Royal College of Surgeons in Ireland, Dublin, Ireland
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Ben Umakanthan
- Cancer Education, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Janet Papadakos
- Cancer Education, Princess Margaret Cancer Centre, Toronto, ON, Canada
- The Institute for Education Research, University Health Network, Toronto, ON, Canada
| | - Meredith Elana Giuliani
- Cancer Education, Princess Margaret Cancer Centre, Toronto, ON, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, ON, Canada
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7
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Bhadelia A, Oldfield LE, Cruz JL, Singh R, Finkelstein EA. Identifying Core Domains to Assess the "Quality of Death": A Scoping Review. J Pain Symptom Manage 2022; 63:e365-e386. [PMID: 34896278 DOI: 10.1016/j.jpainsymman.2021.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/18/2021] [Accepted: 11/28/2021] [Indexed: 01/13/2023]
Abstract
CONTEXT There is growing recognition of the value to patients, families, society, and health systems in providing healthcare, including end-of-life care, that is consistent with both patient preferences and clinical guidelines. OBJECTIVES Identify the core domains and subdomains that can be used to evaluate the performance of end-of-life care within and across health systems. METHODS PubMed/MEDLINE (NCBI), PsycINFO (ProQuest), and CINAHL (EBSCO) databases were searched for peer-reviewed journal articles published prior to February 22, 2020. The SPIDER tool was used to determine search terms. A priori criteria were followed with independent review to identify relevant articles. RESULTS A total of 309 eligible articles were identified out of 2728 discrete results. The articles represent perspectives from the broader health system (11), patients (70), family and informal caregivers (65), healthcare professionals (43), multiple viewpoints (110), and others (10). The most common condition of focus was cancer (103) and the majority (245) of the studies concentrated on high-income country contexts. The review identified five domains and 11 subdomains focused on structural factors relevant to end-of-life care at the broader health system level, and two domains and 22 subdomains focused on experiential aspects of end-of-life care from the patient and family perspectives. The structural health system domains were: 1) stewardship and governance, 2) resource generation, 3) financing and financial protection, 4) service provision, and 5) access to care. The experiential domains were: 1) quality of care, and 2) quality of communication. CONCLUSION The review affirms the need for a people-centered approach to managing the delicate process and period of accepting and preparing for the end of life. The identified structural and experiential factors pertinent to the "quality of death" will prove invaluable for future efforts aimed to quantify health system performance in the end-of-life period.
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Affiliation(s)
- Afsan Bhadelia
- Department of Global Health and Population (A.B.), Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
| | | | - Jennifer L Cruz
- Department of Social and Behavioral Sciences (J.L.C.), Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Ratna Singh
- Lien Centre for Palliative Care (R.S., E.A.F.), Duke-NUS Medical School, Singapore, Singapore
| | - Eric A Finkelstein
- Lien Centre for Palliative Care (R.S., E.A.F.), Duke-NUS Medical School, Singapore, Singapore
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8
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Wong D, Znassi N, Luo P, Oldfield LE, Bruce J, Danesh A, Prokopec S, Basra P, Pederson S, Wellum J, Chan C, Farncombe K, Norman M, Brunga L, Light N, Shien A, Subasri V, Malkin D, Kim R, Pugh T. OP015: Multi-omic analysis of circulating tumour DNA for the early detection of cancer in patients with Li-Fraumeni syndrome. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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9
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Shickh S, Oldfield LE, Clausen M, Mighton C, Sebastian A, Calvo A, Baxter NN, Dawson L, Penney LS, Foulkes W, Basik M, Sun S, Schrader KA, Regier DA, Karsan A, Pollett A, Pugh TJ, Kim RH, Bombard Y. OUP accepted manuscript. Oncologist 2022; 27:e393-e401. [PMID: 35385106 PMCID: PMC9075003 DOI: 10.1093/oncolo/oyac039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 01/14/2022] [Indexed: 11/29/2022] Open
Abstract
Background We explored health professionals’ views on the utility of circulating tumor DNA (ctDNA) testing in hereditary cancer syndrome (HCS) management. Materials and Methods A qualitative interpretive description study was conducted, using semi-structured interviews with professionals across Canada. Thematic analysis employing constant comparison was used for analysis. 2 investigators coded each transcript. Differences were reconciled through discussion and the codebook was modified as new codes and themes emerged from the data. Results Thirty-five professionals participated and included genetic counselors (n = 12), geneticists (n = 9), oncologists (n = 4), family doctors (n = 3), lab directors and scientists (n = 3), a health-system decision maker, a surgeon, a pathologist, and a nurse. Professionals described ctDNA as “transformative” and a “game-changer”. However, they were divided on its use in HCS management, with some being optimistic (optimists) while others were hesitant (pessimists). Differences were driven by views on 3 factors: (1) clinical utility, (2) ctDNA’s role in cancer screening, and (3) ctDNA’s invasiveness. Optimists anticipated ctDNA testing would have clinical utility for HCS patients, its role would be akin to a diagnostic test and would be less invasive than standard screening (eg imaging). Pessimistic participants felt ctDNA testing would add limited utility; it would effectively be another screening test in the pathway, likely triggering additional investigations downstream, thereby increasing invasiveness. Conclusions Providers anticipated ctDNA testing will transform early cancer detection for HCS families. However, the contrasting positions on ctDNA’s role in the care pathway raise potential practice variations, highlighting a need to develop evidence to support clinical implementation and guidelines to standardize adoption.
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Affiliation(s)
- Salma Shickh
- St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - Leslie E Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Marc Clausen
- St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - Agnes Sebastian
- St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - Alessia Calvo
- St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- McMaster University, Hamilton, ON, Canada
| | - Nancy N Baxter
- St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Lesa Dawson
- Memorial University, St. John’s, NL, Canada
- Eastern Health Authority, St. John’s, NL, Canada
| | | | - William Foulkes
- McGill University, Montréal, QC, Canada
- Jewish General Hospital, Montréal, QC, Canada
| | - Mark Basik
- McGill University, Montréal, QC, Canada
- Jewish General Hospital, Montréal, QC, Canada
| | - Sophie Sun
- BC Cancer, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | - Kasmintan A Schrader
- BC Cancer, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | - Dean A Regier
- BC Cancer, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | - Aly Karsan
- BC Cancer, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | | | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Raymond H Kim
- University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Mount Sinai Hospital, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Bombard
- St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Corresponding author: Yvonne Bombard, University of Toronto, Li Ka Shing Knowledge Institute of St. Michael’s Hospital, 30 Bond Street, Toronto, ON, Canada M5B 1W8. Tel: +1 416 864 6060, 77378;
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10
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El Ghamrasni S, Quevedo R, Hawley J, Mazrooei P, Hanna Y, Cirlan I, Zhu H, Bruce JP, Oldfield LE, Yang SYC, Guilhamon P, Reimand J, Cescon DW, Done SJ, Lupien M, Pugh TJ. Mutations in Noncoding Cis-Regulatory Elements Reveal Cancer Driver Cistromes in Luminal Breast Cancer. Mol Cancer Res 2022; 20:102-113. [PMID: 34556523 PMCID: PMC9398156 DOI: 10.1158/1541-7786.mcr-21-0471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/31/2021] [Accepted: 09/17/2021] [Indexed: 01/07/2023]
Abstract
Whole-genome sequencing of primary breast tumors enabled the identification of cancer driver genes and noncoding cancer driver plexuses from somatic mutations. However, differentiating driver from passenger events among noncoding genetic variants remains a challenge. Herein, we reveal cancer-driver cis-regulatory elements linked to transcription factors previously shown to be involved in development of luminal breast cancers by defining a tumor-enriched catalogue of approximately 100,000 unique cis-regulatory elements from 26 primary luminal estrogen receptor (ER)+ progesterone receptor (PR)+ breast tumors. Integrating this catalog with somatic mutations from 350 publicly available breast tumor whole genomes, we uncovered cancer driver cistromes, defined as the sum of binding sites for a transcription factor, for ten transcription factors in luminal breast cancer such as FOXA1 and ER, nine of which are essential for growth in breast cancer with four exclusive to the luminal subtype. Collectively, we present a strategy to find cancer driver cistromes relying on quantifying the enrichment of noncoding mutations over cis-regulatory elements concatenated into a functional unit. IMPLICATIONS: Mapping the accessible chromatin of luminal breast cancer led to discovery of an accumulation of mutations within cistromes of transcription factors essential to luminal breast cancer. This demonstrates coopting of regulatory networks to drive cancer and provides a framework to derive insight into the noncoding space of cancer.
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Affiliation(s)
- Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rene Quevedo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - James Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Parisa Mazrooei
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Genentech, South San Francisco, California
| | - Youstina Hanna
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Iulia Cirlan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Helen Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeff P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Leslie E Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - S Y Cindy Yang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Paul Guilhamon
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jüri Reimand
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Dave W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Susan J Done
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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11
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Oldfield LE, Li T, Tone A, Aronson M, Edwards M, Holter S, Quevedo R, Van de Laar E, Lerner-Ellis J, Pollett A, Clarke B, Tabori U, Gallinger S, Ferguson SE, Pugh TJ. An Integrative DNA Sequencing and Methylation Panel to Assess Mismatch Repair Deficiency. J Mol Diagn 2020; 23:242-252. [PMID: 33259954 DOI: 10.1016/j.jmoldx.2020.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/09/2020] [Accepted: 11/09/2020] [Indexed: 12/30/2022] Open
Abstract
Clinical testing for mismatch repair (MMR) deficiency often entails serial testing of tumor and constitutional DNA using multiple assays. To minimize cost and specimen requirements of MMR testing, we developed an integrated targeted sequencing protocol (termed MultiMMR) that tests for promoter methylation, mutations, copy number alterations, copy neutral loss of heterozygosity, and microsatellite instability from a single aliquot of DNA. Hybrid capture of DNA-sequencing libraries constructed with methylated adapters was performed on 142 samples (60 tumors and 82 constitutional samples) from 82 patients with MMR-associated colorectal, endometrial, and brain cancers as well as a synthetic DNA mix with 11 known mutations. The captured material was split to enable parallel bisulfite and conventional sequence analysis. The panel targeted microsatellite regions and 13 genes associated with MMR, hypermutation, and hereditary colorectal cancer. MultiMMR recapitulated clinical testing results in 23 of 24 cases, was able to explain MMR loss in an additional 29 of 48 patients with incomplete or inconclusive testing, and identified all 11 MMR variants within the synthetic DNA mix. Promoter methylation and microsatellite instability analysis found 95% and 97% concordance with clinical testing, respectively. We report the feasibility for amalgamation of the current stepwise and complex clinical testing workflow into an integrated test for hereditary and somatic causes of MMR deficiency.
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Affiliation(s)
- Leslie E Oldfield
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tiantian Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alicia Tone
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Spring Holter
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Rene Quevedo
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Emily Van de Laar
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Aaron Pollett
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Blaise Clarke
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Uri Tabori
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sarah E Ferguson
- Division of Gynecologic Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
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12
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Kim RS, Oldfield LE, Tone A, Pollett A, Van de Laar E, Pedersen S, Wellum J, Clarke B, Pugh TJ, Ferguson S. Comprehensive molecular assessment of mismatch repair deficiency in Lynch-associated ovarian cancers using next-generation sequencing (NGS) panel. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.1523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1523 Background: Abnormalities in mismatch repair (MMR) gene may be the result of pathogenic germline (Lynch syndrome) and somatic mutations as well as epigenetic events. Abnormalities in MMR have been described in non-serous/non-mucinous ovarian cancer (OC) but few studies have examined the causes of these MMR defects (MMRd). To address this, we have completed targeted mutational and methylation sequencing on MMRd OC cases. Methods: Women with newly diagnosed non-serous/mucinous OC (N = 215) were prospectively recruited from three cancer centers in Ontario, Canada between 2015-18. Tumors were reflexively assessed for MMR protein expression by immunohistochemistry. Tumor DNA was extracted from macrodissected MMRd cases and MMR-intact (MMRi) controls following pathology review. Matched tumor-normal samples were run on a custom NGS panel to identify germline and somatic mutations, copy number variants, rearrangements and promoter methylation in MMR and associated genes. Results: Of the 215 women enrolled in our study, 185 (86%) had OC alone and 30 (14%) had synchronous OC and endometrial cancer. Twenty-eight (13%) cases were MMRd, 11 of which were synchronous. The MMRd cohort had median age of 52.5 years, with mostly stage I (N = 14; 50%), grade 1 or 2 disease (N = 18; 64%) with endometrioid histotype (N = 18; 64%). One patient had recurrence after median follow-up of 33.6 months (13.2-93.6). There was no significant difference in overall/progression-free survival between the MMRd and MMRi patients. Using the NGS panel, Lynch syndrome (LS) was detected in 39% of MMRd cases (11/28; 7 OC and 4 synchronous): 7 MSH6, 2 MLH1, 1 PMS2, and 1 MSH2. Clinical germline sequencing was performed on all cases and verified panel findings. An explanation for the observed MMR phenotype was available for 18/20 deficient cases, including 9/10 MLH1−/PMS2− (7 somatic methylation, 1 bi-allelic somatic deletion, 1 germline mutation), 0/1 PMS2−, 6/7 MSH6− (6 germline mutations) and 2/2 MSH2−/MSH6− (1 germline mutation, 1 bi-allelic somatic mutation). Concordance between clinical and research panel sequencing results was 90%. None of the germline mutations were missed by the panel. Conclusions: Use of our custom NGS panel allows for the streamlined assessment of hereditary and somatic causes of MMR deficiency in OC and may be an attractive screening strategy for LS in this population.
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Affiliation(s)
| | | | - Alicia Tone
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Emily Van de Laar
- Princess Margaret Cancer Centre, Univeristy Health Network, Toronto, ON, Canada
| | | | | | - Blaise Clarke
- Department of Pathology and Laboratory Medicine, University Health Network, Toronto, ON, Canada
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13
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Oldfield LE, Connor AA, Gallinger S. Molecular Events in the Natural History of Pancreatic Cancer. Trends Cancer 2017; 3:336-346. [PMID: 28718411 DOI: 10.1016/j.trecan.2017.04.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 12/12/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest epithelial malignancies. Improvements in our understanding of PDAC carcinogenesis will hopefully improve its detection, management, and outcomes, as has been achieved with other malignancies. Here we review the literature on the natural history of PDAC, including its cell of origin, the initiating somatic mutational events, pathways deranged in the mature tumor, its biological heterogeneity, and the relationship of the primary tumor with metastases. We also suggest areas for further research and highlight translatable findings that are beginning to make clinical inroads.
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Affiliation(s)
- Leslie E Oldfield
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Ashton A Connor
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Canada.
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