1
|
Sharma P, Mahadevia H, Donepudi S, Kujtan L, Gustafson B, Ponvilawan B, Al-Obaidi A, Subramanian J, Bansal D. A Novel EGFR Germline Mutation in Lung Adenocarcinoma: Case Report and Literature Review. Clin Lung Cancer 2024; 25:479-482. [PMID: 38777674 DOI: 10.1016/j.cllc.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/14/2024] [Indexed: 05/25/2024]
Affiliation(s)
- Parth Sharma
- Department of Internal Medicine, University of Missouri-Kansas City, Kansas City, MO.
| | - Himil Mahadevia
- Department of Internal Medicine, University of Missouri-Kansas City, Kansas City, MO
| | - Sreekanth Donepudi
- Department of Hematology-Oncology, Saint Luke's Cancer Institute, Kansas City, MO
| | - Lara Kujtan
- Department of Hematology-Oncology, University of Missouri-Kansas City, Kansas City, MO
| | - Beth Gustafson
- Department of Pharmacology, Saint Luke's Cancer Institute, Kansas City, MO
| | - Ben Ponvilawan
- Department of Internal Medicine, University of Missouri-Kansas City, Kansas City, MO
| | - Ammar Al-Obaidi
- Department of Hematology-Oncology, University of Missouri-Kansas City, Kansas City, MO
| | | | - Dhruv Bansal
- Department of Hematology-Oncology, Saint Luke's Cancer Institute, Kansas City, MO
| |
Collapse
|
2
|
Fairley R, Lillard JW, Berk A, Cornew S, Gaspero J, Gillespie J, Horne LL, Kidane S, Munro SB, Parsons M, Powers ER, Rizzo SE, Tishcler A, Wohl H, Weiss MC. Increasing Clinical Trial Participation of Black Women Diagnosed with Breast Cancer. J Racial Ethn Health Disparities 2024; 11:1701-1717. [PMID: 37314691 PMCID: PMC11101578 DOI: 10.1007/s40615-023-01644-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 06/15/2023]
Abstract
Despite racial disparities in breast cancer mortality, Black women remain underrepresented in clinical trials. In this mixed methods research, 48 Black women were engaged via focus group discussions and in-depth interviews to better understand the lived experience of women with breast cancer. The results of this qualitative study informed the development of a subsequent online survey to identify barriers, motivators, and other factors that influence decision-making by Black women diagnosed with breast cancer when considering clinical trial participation. Among the 257 Black survey participants, most (95%) were aware of clinical trials; of those, most viewed them as lifesaving (81%) and/or benefiting others (90%). Negative perceptions such as serious side effects (58%), not receiving real treatment (52%), or risk of potential harm (62%) were indicated. Barriers included financial expenses (49%), concerns that their condition could be made worse (29%), that they would receive a placebo (28%), or that treatment was unapproved (28%). Participants were more likely than their health care providers (HCPs) to initiate discussions of clinical trials (53% versus 33%), and 29% of participants indicated a need for more information about risks and benefits, even after having those conversations. The most trustworthy sources of information on clinical trials were HCPs (66%) and breast cancer support groups (64%). These results suggest that trusted communities are key for providing education on clinical trials. However, there is also a need for HCPs to proactively discuss clinical trials with patients to ensure that they are adequately informed about all aspects of participation.
Collapse
Affiliation(s)
- Ricki Fairley
- TOUCH, The Black Breast Cancer Alliance, Annapolis, MD, USA
| | - James W Lillard
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA
| | | | - Sophia Cornew
- Patient Network and Data, Invitae, San Francisco, CA, USA
| | | | | | - LaTrisha L Horne
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA
| | | | | | | | - Emily R Powers
- TOUCH, The Black Breast Cancer Alliance, Annapolis, MD, USA.
| | | | | | | | - Marisa C Weiss
- Breastcancer.org, Ardmore, PA, USA
- Lankenau Medical Center, Wynnewood, PA, USA
| |
Collapse
|
3
|
Calzone KA, Stokes L, Peterson C, Badzek L. Update to the essential genomic nursing competencies and outcome indicators. J Nurs Scholarsh 2024. [PMID: 38797885 DOI: 10.1111/jnu.12993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
INTRODUCTION Genomic healthcare applications have relevance to all healthcare professionals including nursing, and most evidence-based clinical applications impact the quality and safety of healthcare. To guide nursing genomic competency initiatives, the Essential Nursing Competencies and Curricula Guidelines for Genetics and Genomics were established through a process of consensus in 2005. A 2009 update incorporated outcome indicators consisting of specific areas of knowledge and clinical performance indicators, to help support academic integration. Almost 20 years have elapsed since these competencies were first established, yet incorporating the competencies into general and specialty scope and standards of nursing practice is inconsistent, competency integration into curricula is highly uneven, continuing education in genomics for nurses is limited, and the genomic capacity of the nursing workforce remains low. These deficits have persisted despite substantial advances in genomic technology which substantially reduced costs and increased evidence-based clinical applications, including direct to consumer genomic tests, the integration of genomics into evidence-based guidelines, and evidence that genomics impacts the quality and safety of healthcare. DESIGN The aim of this project was to update and achieve consensus on genomic competencies applicable to all registered nurses. This was a mixed methods study. METHODS The update to the competencies was performed based first on a literature review to update the competencies based on the current state of the evidence. Using the updated content, a modified Delphi study was conducted with registered nurse panelists from clinical, academic, and research settings. Once consensus was achieved, the competencies were made available through the American Nurses Association for public comment. Public comments were then reviewed and integrated as needed. RESULTS The literature review resulted in a transition from genetics to genomics, given the reduction in costs, which resulted in an expansion of the scope of testing in both the germline and somatic contexts. Two Delphi rounds were required to reach consensus prior to the public comment period. Public comments were solicited through the American Nurses Association, and each comment was reviewed by the authors and addressed as indicated. CONCLUSION The Essentials of Genomic Nursing: Competencies and Outcome Indicators constitute the minimum competency in genomics required of all registered nurses regardless of the level of academic training, role, or specialty. CLINICAL RELEVANCE Evidence-based genomic applications span the entire healthcare continuum and, therefore, are relevant for all registered nurses regardless of academic training, role, practice setting, or clinical expertise. These competencies serve as the guide for the minimum requirements for registered nurse practice as well as guide curricula and continuing education for all registered nurses, including but not limited to administrators, educators, nursing leaders, practicing nurses, and researchers.
Collapse
Affiliation(s)
- Kathleen A Calzone
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Liz Stokes
- Center for Ethics and Human Rights, American Nurses Association, Silver Spring, Maryland, USA
| | - Cheryl Peterson
- Nursing Programs, American Nurses Association, Silver Spring, Maryland, USA
| | - Laurie Badzek
- Penn State University, State College, Pennsylvania, USA
| |
Collapse
|
4
|
Sanabria-Salas MC, Pedroza-Duran A, Díaz-Casas SE, Nuñez Lemus M, Grillo-Ardila CF, Briceño-Morales X, García-Mora M, Ángel-Aristizábal J, Mariño Lozano IF, Suarez Rodríguez RA, Guzmán Abisaab LH. Management and Clinical Outcomes of Breast Cancer in Women Diagnosed with Hereditary Cancer Syndromes in a Clinic-Based Sample from Colombia. Cancers (Basel) 2024; 16:2020. [PMID: 38893140 PMCID: PMC11171067 DOI: 10.3390/cancers16112020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024] Open
Abstract
This study aimed to investigate prognosis and survival differences in 82 breast cancer patients with germline pathogenic/likely pathogenic variants (PVs) treated and followed at the Breast Unit of the Instituto Nacional de Cancerología, Colombia (INC-C) between 2018 and 2021. Median age at diagnosis was 46 years, with 62.2% presenting locally advanced tumors, 47.6% histological grade 3, and 35.4% with triple-negative breast cancer (TNBC) subtype. Most carriers, 74.4% (61/82), had PVs in known breast cancer susceptibility genes (i.e., "associated gene carriers" group, considered inherited breast cancer cases): BRCA2 (30), BRCA1 (14), BARD1 (4), RAD51D (3), TP53 (2), PALB2 (2), ATM (2), CHEK2 (1), RAD51C (1), NF1 (1), and PTEN (1). BRCA1-2 represented 53.7%, and homologous recombination DNA damage repair (HR-DDR) genes associated with breast cancer risk accounted for 15.9%. Patients with PVs in non-breast-cancer risk genes were combined in a different category (21/82; 25.6%) (i.e., "non-associated gene carriers" group, considered other breast cancer cases). Median follow-up was 38.1 months, and 24% experienced recurrence, with 90% being distant. The 5-year Disease-Free Survival (DFS) for inherited breast cancer cases was 66.5%, and for other breast cancer cases it was 88.2%. In particular, for carriers of PVs in the BRCA2 gene, it was 37.6%. The 5-year Overall Survival (OS) rates ranged from 68.8% for those with PVs in BRCA2 to 100% for those with PVs in other HR-DDR genes. Further studies are crucial for understanding tumor behavior and therapy response differences among Colombian breast cancer patients with germline PVs.
Collapse
Affiliation(s)
- María Carolina Sanabria-Salas
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2C1, Canada
| | - Ana Pedroza-Duran
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Sandra E. Díaz-Casas
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Marcela Nuñez Lemus
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Carlos F. Grillo-Ardila
- Department of Obstetrics & Gynecology, School of Medicine, Universidad Nacional de Colombia, Avenida Carrera 30 N. 45-3, Bogotá 111321, Colombia;
| | - Ximena Briceño-Morales
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Mauricio García-Mora
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Javier Ángel-Aristizábal
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Iván Fernando Mariño Lozano
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Raúl Alexis Suarez Rodríguez
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Luis Hernán Guzmán Abisaab
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| |
Collapse
|
5
|
Forrest IS, Duffy Á, Park JK, Vy HMT, Pasquale LR, Nadkarni GN, Cho JH, Do R. Genome-first evaluation with exome sequence and clinical data uncovers underdiagnosed genetic disorders in a large healthcare system. Cell Rep Med 2024; 5:101518. [PMID: 38642551 PMCID: PMC11148562 DOI: 10.1016/j.xcrm.2024.101518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 05/01/2023] [Accepted: 03/26/2024] [Indexed: 04/22/2024]
Abstract
Population-based genomic screening may help diagnose individuals with disease-risk variants. Here, we perform a genome-first evaluation for nine disorders in 29,039 participants with linked exome sequences and electronic health records (EHRs). We identify 614 individuals with 303 pathogenic/likely pathogenic or predicted loss-of-function (P/LP/LoF) variants, yielding 644 observations; 487 observations (76%) lack a corresponding clinical diagnosis in the EHR. Upon further investigation, 75 clinically undiagnosed observations (15%) have evidence of symptomatic untreated disease, including familial hypercholesterolemia (3 of 6 [50%] undiagnosed observations with disease evidence) and breast cancer (23 of 106 [22%]). These genetic findings enable targeted phenotyping that reveals new diagnoses in previously undiagnosed individuals. Disease yield is greater with variants in penetrant genes for which disease is observed in carriers in an independent cohort. The prevalence of P/LP/LoF variants exceeds that of clinical diagnoses, and some clinically undiagnosed carriers are discovered to have disease. These results highlight the potential of population-based genomic screening.
Collapse
Affiliation(s)
- Iain S Forrest
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Áine Duffy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua K Park
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ha My T Vy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Genomic Data Analytics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Eye and Vision Research Institute, New York Eye and Ear Infirmary of Mount Sinai, New York, NY 10003, USA
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Data-driven and Digital Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Genomic Data Analytics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
6
|
Vanni I, Pastorino L, Andreotti V, Comandini D, Fornarini G, Grassi M, Puccini A, Tanda ET, Pastorino A, Martelli V, Mastracci L, Grillo F, Cabiddu F, Guadagno A, Coco S, Allavena E, Barbero F, Bruno W, Dalmasso B, Bellomo SE, Marchiò C, Spagnolo F, Sciallero S, Berrino E, Ghiorzo P. Combining germline, tissue and liquid biopsy analysis by comprehensive genomic profiling to improve the yield of actionable variants in a real-world cancer cohort. J Transl Med 2024; 22:462. [PMID: 38750555 PMCID: PMC11097509 DOI: 10.1186/s12967-024-05227-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Comprehensive next-generation sequencing is widely used for precision oncology and precision prevention approaches. We aimed to determine the yield of actionable gene variants, the capacity to uncover hereditary predisposition and liquid biopsy appropriateness instead of, or in addition to, tumor tissue analysis, in a real-world cohort of cancer patients, who may benefit the most from comprehensive genomic profiling. METHODS Seventy-eight matched germline/tumor tissue/liquid biopsy DNA and RNA samples were profiled using the Hereditary Cancer Panel (germline) and the TruSight Oncology 500 panel (tumor tissue/cfDNA) from 23 patients consecutively enrolled at our center according to at least one of the following criteria: no available therapeutic options; long responding patients potentially fit for other therapies; rare tumor; suspected hereditary cancer; primary cancer with high metastatic potential; tumor of unknown primary origin. Variants were annotated for OncoKB and AMP/ASCO/CAP classification. RESULTS The overall yield of actionable somatic and germline variants was 57% (13/23 patients), and 43.5%, excluding variants previously identified by somatic or germline routine testing. The accuracy of tumor/cfDNA germline-focused analysis was demonstrated by overlapping results of germline testing. Five germline variants in BRCA1, VHL, CHEK1, ATM genes would have been missed without extended genomic profiling. A previously undetected BRAF p.V600E mutation was emblematic of the clinical utility of this approach in a patient with a liver undifferentiated embryonal sarcoma responsive to BRAF/MEK inhibition. CONCLUSIONS Our study confirms the clinical relevance of performing extended parallel tumor DNA and cfDNA testing to broaden therapeutic options, to longitudinally monitor cfDNA during patient treatment, and to uncover possible hereditary predisposition following tumor sequencing in patient care.
Collapse
Affiliation(s)
- I Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - L Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - V Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - D Comandini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - G Fornarini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - M Grassi
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Puccini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E T Tanda
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
- Medical Oncology Unit 2, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Pastorino
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - V Martelli
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - L Mastracci
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - F Grillo
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - F Cabiddu
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Guadagno
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - S Coco
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E Allavena
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - F Barbero
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - W Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - B Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - S E Bellomo
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
| | - C Marchiò
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Torino, 10060, Turin, Italy
| | - F Spagnolo
- Medical Oncology Unit 2, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Plastic Surgery, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
| | - S Sciallero
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E Berrino
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Torino, 10060, Turin, Italy
| | - P Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy.
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy.
| |
Collapse
|
7
|
Raygada M, John L, Liu A, Schultz J, Thomas BJ, Bernstein D, Miettinen M, Raffeld M, Xi L, Tyagi M, Aldape K, Glod J, Reilly KM, Widemann BC, Wedekind MF. Germline findings in cancer predisposing genes from a small cohort of chordoma patients. J Cancer Res Clin Oncol 2024; 150:227. [PMID: 38700789 PMCID: PMC11068663 DOI: 10.1007/s00432-024-05706-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/15/2024] [Indexed: 05/06/2024]
Abstract
INTRODUCTION Chordoma is a rare slow-growing tumor that occurs along the length of the spinal axis and arises from primitive notochordal remnants (Stepanek et al., Am J Med Genet 75:335-336, 1998). Most chordomas are sporadic, but a small percentage of cases are due to hereditary cancer syndromes (HCS) such as tuberous sclerosis 1 and 2 (TSC1/2), or constitutional variants in the gene encoding brachyury T (TBXT) (Pillay et al., Nat Genet 44:1185-1187, 2012; Yang et al., Nat Genet 41:1176-1178, 2009). PURPOSE The genetic susceptibility of these tumors is not well understood; there are only a small number of studies that have performed germline genetic testing in this population. METHODS We performed germline genetic in chordoma patients using genomic DNA extracted by blood or saliva. CONCLUSION We report here a chordoma cohort of 24 families with newly found germline genetic mutations in cancer predisposing genes. We discuss implications for genetic counseling, clinical management, and universal germline genetic testing for cancer patients with solid tumors.
Collapse
Affiliation(s)
- Margarita Raygada
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
- NIH Clinical Center (Building 10), 10 Center Drive, Room 1-3750, Bethesda, MD, 20892, USA.
| | - Liny John
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Anne Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Julianne Schultz
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - B J Thomas
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Donna Bernstein
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Markku Miettinen
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Mark Raffeld
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Liqiang Xi
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Manoj Tyagi
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - John Glod
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Karlyne M Reilly
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Brigitte C Widemann
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Mary Frances Wedekind
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| |
Collapse
|
8
|
Ando Y, Dbouk M, Yoshida T, Abou Diwan E, Saba H, Dbouk A, Yoshida K, Roberts NJ, Klein AP, Burkhart R, He J, Hruban RH, Goggins M. Germline Pathogenic Variants in Patients With Pancreatic and Periampullary Cancers. JCO Precis Oncol 2024; 8:e2400101. [PMID: 38781545 DOI: 10.1200/po.24.00101] [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: 02/15/2024] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
PURPOSE Inherited cancer susceptibility is often not suspected in the absence of a significant cancer family history. Pathogenic germline variants in pancreatic cancer are well-studied, and routine genetic testing is recommended in the guidelines. However, data on rare periampullary cancers other than pancreatic cancer are insufficient. We compared the prevalence of germline susceptibility variants in patients with pancreatic cancer and nonpancreatic periampullary cancers. MATERIALS AND METHODS Six hundred and eight patients who had undergone pancreaticoduodenal resection at a tertiary referral hospital were studied, including 213 with pancreatic ductal adenocarcinoma, 172 with ampullary cancer, 154 with distal common bile duct cancer, and 69 with duodenal adenocarcinoma. Twenty cancer susceptibility and candidate susceptibility genes were sequenced, and variant interpretation was assessed by interrogating ClinVar and PubMed. RESULTS Pathogenic or likely pathogenic, moderate- to high-penetrant germline variants were identified in 46 patients (7.7%), including a similar percentage of patients with pancreatic (8.5%) and nonpancreatic periampullary cancer (7.1%). Low-penetrant variants were identified in an additional 11 patients (1.8%). Eighty-nine percent of the moderate- to high-penetrant variants involved the major cancer susceptibility genes BRCA2, ATM, BRCA1, CDKN2A, MSH2/MLH1, and PALB2; the remaining 11% involved other cancer susceptibility genes such as BRIP1, BAP1, and MSH6. Almost all pathogenic variant carriers had a family history of cancer. CONCLUSION Patients with pancreatic and nonpancreatic periampullary cancer have a similar prevalence of pathogenic cancer susceptibility variants. Germline susceptibility testing should be considered for patients with any periampullary cancer.
Collapse
Affiliation(s)
- Yohei Ando
- Departments of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Mohamad Dbouk
- Departments of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Takeichi Yoshida
- Departments of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Elizabeth Abou Diwan
- Departments of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Helena Saba
- Departments of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Ali Dbouk
- Departments of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Kanako Yoshida
- Departments of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Nicholas J Roberts
- Departments of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
- Departments of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Alison P Klein
- Departments of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
- Departments of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
- The Bloomberg School of Public Health, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Richard Burkhart
- Departments of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Jin He
- Departments of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Ralph H Hruban
- Departments of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
- Departments of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
- The Bloomberg School of Public Health, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Michael Goggins
- Departments of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
- Departments of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
- Departments of Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, MD
| |
Collapse
|
9
|
Church J. The Natural History of Hereditary Colorectal Cancer Syndromes: From Phenotype to Genotype? Where Do We Stand and What Does the Future Hold? Clin Colon Rectal Surg 2024; 37:127-132. [PMID: 38606050 PMCID: PMC11006442 DOI: 10.1055/s-0043-1770380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Applying the concept of a "natural history" to hereditary colorectal cancer is an interesting exercise because the way the syndromes are approached has changed so drastically. However, the exercise is instructive as it forces us to think in depth about where we are, where we have been, and, most helpfully, about where we may be going. In this article the diagnosis, along with endoscopic and surgical management of hereditary colorectal cancer are discussed in the context of their history and the changes in genomics and technology that have occurred over the last one hundred years.
Collapse
Affiliation(s)
- James Church
- Division of Colorectal Surgery, Department of Surgery, Columbia University Medical Center, New York, New York
| |
Collapse
|
10
|
Ring KL, Duska LR. How far is too far? Cancer prevention and clinical trial enrollment in geographically underserved patient populations. Gynecol Oncol 2024; 184:8-15. [PMID: 38271774 DOI: 10.1016/j.ygyno.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/27/2024]
Abstract
Despite dedicated efforts to improve equitable access to cancer care in the United States, disparities in cancer outcomes persist, and geographically underserved patients remain at an increased risk of cancer with lower rates of survival. The critical evaluation of cancer prevention inequities and clinical trial access presents the opportunity to outline novel strategies to incrementally improve bookended access to gynecologic cancer care for geographically underserved patients. Cancer prevention strategies that can be addressed in the rural patient population mirror priorities in the Healthy People 2030 objectives and include increased identification of high risk individuals who may benefit from increased cancer screening and risk reduction, increasing the proportion of people who discuss interventions to prevent cancer, such as HPV vaccination, with their provider, and increasing the proportion of adults who complete evidence based cancer screening. Barriers to accrual to clinical trials for rural patients overlap significantly with the same barriers to obtaining health care in general. These barriers include: lack of facilities and specialized providers; lack of robust health infrastructure; inability to travel; and financial barriers. In this review, we will discuss current knowledge and opportunities to improve cancer prevention initiatives and clinical trial enrollment in geographically underserved populations with a focus on rurality.
Collapse
Affiliation(s)
- Kari L Ring
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Virginia Health System, 1215 Lee Street, Charlottesville, VA 22908, United States of America.
| | - Linda R Duska
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Virginia Health System, 1215 Lee Street, Charlottesville, VA 22908, United States of America
| |
Collapse
|
11
|
Casolino R, Beer PA, Chakravarty D, Davis MB, Malapelle U, Mazzarella L, Normanno N, Pauli C, Subbiah V, Turnbull C, Westphalen CB, Biankin AV. Interpreting and integrating genomic tests results in clinical cancer care: Overview and practical guidance. CA Cancer J Clin 2024; 74:264-285. [PMID: 38174605 DOI: 10.3322/caac.21825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The last decade has seen rapid progress in the use of genomic tests, including gene panels, whole-exome sequencing, and whole-genome sequencing, in research and clinical cancer care. These advances have created expansive opportunities to characterize the molecular attributes of cancer, revealing a subset of cancer-associated aberrations called driver mutations. The identification of these driver mutations can unearth vulnerabilities of cancer cells to targeted therapeutics, which has led to the development and approval of novel diagnostics and personalized interventions in various malignancies. The applications of this modern approach, often referred to as precision oncology or precision cancer medicine, are already becoming a staple in cancer care and will expand exponentially over the coming years. Although genomic tests can lead to better outcomes by informing cancer risk, prognosis, and therapeutic selection, they remain underutilized in routine cancer care. A contributing factor is a lack of understanding of their clinical utility and the difficulty of results interpretation by the broad oncology community. Practical guidelines on how to interpret and integrate genomic information in the clinical setting, addressed to clinicians without expertise in cancer genomics, are currently limited. Building upon the genomic foundations of cancer and the concept of precision oncology, the authors have developed practical guidance to aid the interpretation of genomic test results that help inform clinical decision making for patients with cancer. They also discuss the challenges that prevent the wider implementation of precision oncology.
Collapse
Affiliation(s)
- Raffaella Casolino
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Philip A Beer
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Hull York Medical School, York, UK
| | | | - Melissa B Davis
- Department of Surgery, Weill Cornell Medicine, New York City, New York, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Luca Mazzarella
- Laboratory of Translational Oncology and Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors IEO European Institute of Oncology, IRCCS, Milan, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS "Fondazione G. Pascale", Naples, Italy
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Vivek Subbiah
- Sarah Cannon Research Institute, Nashville, Tennessee, USA
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- National Cancer Registration and Analysis Service, National Health Service (NHS) England, London, UK
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - C Benedikt Westphalen
- Department of Medicine III, Ludwig Maximilians University (LMU) Hospital Munich, Munich, Germany
- Comprehensive Cancer Center, LMU Hospital Munich, Munich, Germany
- German Cancer Consortium, LMU Hospital Munich, Munich, Germany
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- South Western Sydney Clinical School, Liverpool, New South Wales, Australia
| |
Collapse
|
12
|
Yu Z, Zhang Z, Liu J, Wu X, Fan X, Pang J, Bao H, Yin J, Wu X, Shao Y, Liu Z, Liu F. Identification of pathogenic germline variants in a large Chinese lung cancer cohort by clinical sequencing. Mol Oncol 2024; 18:1301-1315. [PMID: 37885353 PMCID: PMC11076998 DOI: 10.1002/1878-0261.13548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/29/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023] Open
Abstract
Genetic factors play significant roles in the tumorigenicity of lung cancer; however, there is lack of systematic and large-scale characterization of pathogenic germline variants for lung cancer. In this study, germline variants in 146 preselected cancer-susceptibility genes were detected in 17 904 Chinese lung cancer patients by clinical next-generation sequencing. Among 17 904 patients, 1738 patients (9.7%) carried 1840 pathogenic/likely pathogenic (P/LP) variants from 87 cancer-susceptibility genes. SBDS (SBDS ribosome maturation factor) (1.37%), TSHR (thyroid stimulating hormone receptor) (1.20%), BLM (BLM RecQ like helicase) (0.62%), BRCA2 (BRCA2 DNA repair associated) (0.62%), and ATM (ATM serine/threonine kinase) (0.45%) were the top five genes with the highest overall prevalence. The top mutated pathways were all involved in DNA damage repair (DDR). Case-control analysis showed SBDS c.184A>T(p.K62*), TSHR c.1574T>C(p.F525S), BRIP1 (BRCA1 interacting helicase 1) c.1018C>T(p.L340F), and MUTYH (mutY DNA glycosylase) c.55C>T(p.R19*) were significantly associated with increased lung cancer risk (q value < 0.05). P/LP variants in certain genes were associated with early onset of lung cancer. Our study indicates that Chinese lung cancer patients have a higher prevalence of P/LP variants than previously reported. P/LP variants are distributed in multiple pathways and dominated by DNA damage repair-associated pathways. The association between identified P/LP variants and lung cancer risk requires further studies for verification.
Collapse
Affiliation(s)
- Zhe Yu
- Department of Respiratory MedicineNingbo NO.2 HospitalChina
| | - Zirui Zhang
- Department of Cardiovascular and Thoracic SurgeryNanjing Drum Tower Hospital Affiliated to Nanjing University School of MedicineChina
| | - Jun Liu
- Department of ChemotherapyAffiliated Hospital of Nantong UniversityChina
| | | | | | | | - Hua Bao
- Nanjing Geneseeq Technology Inc.China
| | - Jiani Yin
- Nanjing Geneseeq Technology Inc.China
| | - Xue Wu
- Nanjing Geneseeq Technology Inc.China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc.China
- School of Public HealthNanjing Medical UniversityChina
| | - Zhengcheng Liu
- Department of Cardiovascular and Thoracic SurgeryNanjing Drum Tower Hospital Affiliated to Nanjing University School of MedicineChina
| | - Fang Liu
- Senior Department of OncologyThe Fifth Medical Center of PLA General HospitalBeijingChina
| |
Collapse
|
13
|
Klatte DCF, Starr JS, Clift KE, Hardway HD, van Hooft JE, van Leerdam ME, Potjer TP, Presutti RJ, Riegert-Johnson DL, Wallace MB, Bi Y. Utilization and Outcomes of Multigene Panel Testing in Patients With Pancreatic Ductal Adenocarcinoma. JCO Oncol Pract 2024:OP2300447. [PMID: 38621197 DOI: 10.1200/op.23.00447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/28/2023] [Accepted: 03/07/2024] [Indexed: 04/17/2024] Open
Abstract
PURPOSE Guidelines recommend germline genetic testing (GT) for patients with pancreatic ductal adenocarcinoma (PDAC). This study aims to evaluate the utilization and outcomes of multigene panel GT in patients with PDAC. METHODS This retrospective, multisite study included patients with PDAC diagnosed between May 2018 and August 2020 at Mayo Clinic Arizona, Florida, and Minnesota. Discussion, uptake, and outcomes of GT were compared before (May 1, 2018-May 1, 2019) and after (August 1, 2019-August 1, 2020) the guideline update, accounting for a transition period. RESULTS The study identified 533 patients with PDAC, with 321 (60.2%) preguideline and 212 (39.8%) postguideline. Patient characteristics did not differ between the preguideline and postguideline periods. GT was discussed in 34.3% (110 of 321) of preguideline and 39.6% (84 of 212) of postguideline patients (odds ratio [OR], 1.26 [95% CI, 0.88 to 1.80]) and subsequently performed in 80.9% (89 of 110) of preguideline and 75.0% (63 of 84) of postguideline patients (OR, 1.10 [95% CI, 0.75 to 1.61]). Of 152 tested patients, 26 (17.1%) had a pathogenic variant (PV), of whom 17 (11.2%; 17 of 152) were PDAC-associated. Over the entire study period, GT was more likely in younger patients (65 v 70 years; P < .001), those seen by a medical oncologist (82.9% v 69.0%; P < .001), and those surviving more than 12 months from diagnosis (70.4% v 43.4%; P < .001). Demographics and personal/family cancer history were comparable between patients with and without a PDAC PV. CONCLUSION GT remains underutilized despite National Comprehensive Cancer Network guideline recommendations. Given the poor prognosis of PDAC and potential implications of GT, efforts to increase utilization are needed to provide surveillance and support to both patients with PDAC and at-risk family members.
Collapse
Affiliation(s)
- Derk C F Klatte
- Department of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jason S Starr
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL
| | - Kristin E Clift
- Department of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL
| | - Heather D Hardway
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL
| | - Jeanin E van Hooft
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Monique E van Leerdam
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Thomas P Potjer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - R John Presutti
- Department of Family Medicine, Mayo Clinic, Jacksonville, FL
| | | | - Michael B Wallace
- Department of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL
- Department of Gastroenterology, Sheikh Shakhbout Medical City, Abu Dhabi, United Arab Emirates
| | - Yan Bi
- Department of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL
| |
Collapse
|
14
|
Chiang J, Chua Z, Chan JY, Sule AA, Loke WH, Lum E, Ong MEH, Graves N, Ngeow J. Strategies to improve implementation of cascade testing in hereditary cancer syndromes: a systematic review. NPJ Genom Med 2024; 9:26. [PMID: 38570510 PMCID: PMC10991315 DOI: 10.1038/s41525-024-00412-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
Hereditary cancer syndromes constitute approximately 10% of all cancers. Cascade testing involves testing of at-risk relatives to determine if they carry the familial pathogenic variant. Despite growing efforts targeted at improving cascade testing uptake, current literature continues to reflect poor rates of uptake, typically below 30%. This study aims to systematically review current literature on intervention strategies to improve cascade testing, assess the quality of intervention descriptions and evaluate the implementation outcomes of listed interventions. We searched major databases using keywords and subject heading of "cascade testing". Interventions proposed in each study were classified according to the Effective Practice and Organization of Care (EPOC) taxonomy. Quality of intervention description was assessed using the TIDieR checklist, and evaluation of implementation outcomes was performed using Proctor's Implementation Outcomes Framework. Improvements in rates of genetic testing uptake was seen in interventions across the different EPOC taxonomy strategies. The average TIDieR score was 7.3 out of 12. Items least reported include modifications (18.5%), plans to assess fidelity/adherence (7.4%) and actual assessment of fidelity/adherence (7.4%). An average of 2.9 out of 8 aspects of implementation outcomes were examined. The most poorly reported outcomes were cost, fidelity and sustainability, with only 3.7% of studies reporting them. Most interventions have demonstrated success in improving cascade testing uptake. Uptake of cascade testing was highest with delivery arrangement (68%). However, the quality of description of interventions and assessment of implementation outcomes are often suboptimal, hindering their replication and implementation downstream. Therefore, further adoption of standardized guidelines in reporting of interventions and formal assessment of implementation outcomes may help promote translation of these interventions into routine practice.
Collapse
Affiliation(s)
- Jianbang Chiang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore, 169857, Singapore
| | - Ziyang Chua
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Jia Ying Chan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Ashita Ashish Sule
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Wan Hsein Loke
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Elaine Lum
- Health Services & Systems Research, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Marcus Eng Hock Ong
- Health Services & Systems Research, Duke-NUS Medical School, Singapore, 169857, Singapore
- Department of Emergency Medicine, Singapore General Hospital, Singapore, 169608, Singapore
| | - Nicholas Graves
- Health Services & Systems Research, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore.
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore, 169857, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
| |
Collapse
|
15
|
Pensabene M, Calabrese A, von Arx C, Caputo R, De Laurentiis M. Cancer genetic counselling for hereditary breast cancer in the era of precision oncology. Cancer Treat Rev 2024; 125:102702. [PMID: 38452709 DOI: 10.1016/j.ctrv.2024.102702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/09/2024]
Abstract
A relevant percentage of breast cancers (BCs) are tied to pathogenetic (P)/likely pathogenetic (LP) variants in predisposing genes. The knowledge of P/LP variants is an essential element in the management of BC patients since the first diagnosis because it influences surgery and subsequent oncological treatments and follow-up. Moreover, patients with metastatic BCs can benefit from personalized treatment if carriers of P/LP in BRCA1/2 genes. Multigene panels allow the identification of other predisposing genes with an impact on management. Cascade genetic testing for healthy family members allows personalized preventive strategies. Here, we review the advances and the challenges of Cancer Genetic Counseling (CGC). We focus on the area of oncology directed to hereditary BC management describing the peculiar way to lead CGC and how CGC changes over time. The authors describe the impact of genetic testing by targeted approach or universal approach on the management of BC according to the stage at diagnosis. Moreover, they describe the burden of CGC and testing and future perspectives to widely offer testing. A new perspective is needed for models of service delivery of CGC and testing, beyond formal genetic counselling. A broader genetic test can be quickly usable in clinical practice for comprehensive BC management and personalized prevention in the era of precision oncology.
Collapse
Affiliation(s)
- M Pensabene
- Clinical and Experimental Unit of Breast Cancer, National Cancer Institute, IRCCS "Fondazione G. Pascale", Naples, Italy.
| | - A Calabrese
- Clinical and Experimental Unit of Breast Cancer, National Cancer Institute, IRCCS "Fondazione G. Pascale", Naples, Italy.
| | - C von Arx
- Clinical and Experimental Unit of Breast Cancer, National Cancer Institute, IRCCS "Fondazione G. Pascale", Naples, Italy.
| | - R Caputo
- Clinical and Experimental Unit of Breast Cancer, National Cancer Institute, IRCCS "Fondazione G. Pascale", Naples, Italy.
| | - M De Laurentiis
- Clinical and Experimental Unit of Breast Cancer, National Cancer Institute, IRCCS "Fondazione G. Pascale", Naples, Italy.
| |
Collapse
|
16
|
Capasso A, Nehoray B, Gorman N, Quinn EA, Bucio D, Blazer KR. Genetic counselors' and community clinicians' implementation and perceived barriers to informed consent during pre-test counseling for hereditary cancer risk. J Genet Couns 2024. [PMID: 38480478 DOI: 10.1002/jgc4.1887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 04/21/2024]
Abstract
As demand for genetic cancer risk assessment (GCRA) continues to increase, so does the sense of urgency to scale up efforts to triage patients, facilitate informed consent, and order genetic testing for cancer risk. The National Society of Genetic Counselors outlines the elements of informed consent that should be addressed in a GCRA session. While this practice resource aims to improve health equity, research on how well the elements of informed consent are implemented in practice is lacking. This retrospective and prospective mixed-methods study assessed how adequately the elements of informed consent are addressed during pre-test GCRA among 307 community clinicians (CC) and 129 cancer genetic counselors (GC), and barriers they face to addressing these elements. Results revealed that more than 90% of both cohorts consistently addressed components of at least 5 of the 10 elements of informed consent during a pre-test consultation. Technical aspects and accuracy of the test and utilization of test results were the most similarly addressed elements. Notably, GCs more often review the purpose of the test and who to test, general information about the gene(s), and economic considerations whereas CCs more often review alternatives to testing. Both cohorts reported psychosocial aspects of the informed consent process as the least adequately addressed element. Time constraints and patient-related concerns were most often cited by both cohorts as barriers to optimal facilitation of informed consent. Additional barriers reported by CCs included provider lack of awareness, experience, or education, and availability of resources and institutional support. Findings from this study may contribute to the development of alternative delivery models that incorporate supplementary educational tools to enhance patient understanding about the utility of genetic testing, while helping to mitigate the barrier of time constraints. Equally important is the use of this information to develop continuing education tools for providers.
Collapse
Affiliation(s)
- Alexandra Capasso
- School of Pharmacy and Health Sciences, Keck Graduate Institute, Claremont, California, USA
- Division of Clinical Cancer Genomics, City of Hope National Medical Center, Duarte, California, USA
| | - Bita Nehoray
- Division of Clinical Cancer Genomics, City of Hope National Medical Center, Duarte, California, USA
| | - Nicholas Gorman
- School of Pharmacy and Health Sciences, Keck Graduate Institute, Claremont, California, USA
| | - Emily A Quinn
- School of Pharmacy and Health Sciences, Keck Graduate Institute, Claremont, California, USA
| | - Daiana Bucio
- Clinical Consultation Services, Invitae Corporation, San Francisco, California, USA
| | - Kathleen R Blazer
- Division of Clinical Cancer Genomics, City of Hope National Medical Center, Duarte, California, USA
| |
Collapse
|
17
|
Jerez J, Santiago M. Unraveling germline predisposition in hematological neoplasms: Navigating complexity in the genomic era. Blood Rev 2024; 64:101143. [PMID: 37989620 DOI: 10.1016/j.blre.2023.101143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/14/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023]
Abstract
Genomic advancements have yielded pivotal insights into hematological neoplasms, particularly concerning germline predisposition mutations. Following the WHO 2016 revisions, dedicated segments were proposed to address these aspects. Current WHO 2022, ICC 2022, and ELN 2022 classifications recognize their significance, introducing more mutations and prompting integration into clinical practice. Approximately 5-10% of hematological neoplasm patients show germline predisposition gene mutations, rising with risk factors such as personal cancer history and familial antecedents, even in older adults. Nevertheless, technical challenges persist. Optimal DNA samples are skin fibroblast-extracted, although not universally applicable. Alternatives such as hair follicle use are explored. Moreover, the scrutiny of germline genomics mandates judicious test selection to ensure precise and accurate interpretation. Given the significant influence of genetic counseling on patient care and post-assessment procedures, there arises a demand for dedicated centers offering specialized services.
Collapse
Affiliation(s)
- Joaquín Jerez
- Hematology Department, Fundación Arturo López Pérez, Chile; Resident of Hematology, Universidad de los Andes, Chile.
| | - Marta Santiago
- Hematology Department, Hospital La Fe, 46026, Valencia, Spain; Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026, Valencia, Spain.
| |
Collapse
|
18
|
Wang M, Lan S, Zhang W, Jin Q, Du H, Sun X, He L, Meng X, Su L, Liu G. Anti-Cancer Potency of Copper-Doped Carbon Quantum Dots Against Breast Cancer Progression. Int J Nanomedicine 2024; 19:1985-2004. [PMID: 38435754 PMCID: PMC10908338 DOI: 10.2147/ijn.s449887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/20/2024] [Indexed: 03/05/2024] Open
Abstract
Introduction The anti-cancer potency of copper-doped carbon quantum dots (Cu-CDs) against breast cancer progression needs more detailed investigations. Methods With urea and ethylene glycol applied as carbon sources and copper sulfate used as a reactive dopant, Cu-CDs were synthesized in the current study by a one-step hydrothermal synthesis method, followed by the characterization and biocompatibility evaluations of Cu-CDs. Subsequently, the anti-cancer potency of Cu-CDs against breast cancer progression was confirmed by these biochemical, molecular, and transcriptomic assessments, including viability, proliferation, migration, invasion, adhesion, clonogenicity, cell cycle distribution, apoptosis, redox homeostasis, and transcriptomic assays of MDA-MB-231 cells. Results The biocompatibility of Cu-CDs was confirmed based on the non-significant changes in the pathological and physiological parameters in the Cu-CDs treated mice, as well as the noncytotoxic effect of Cu-CDs on normal cells. Moreover, the Cu-CDs treatments not only decreased the viability, proliferation, migration, invasion, adhesion, and clonogenicity of MDA-MB-231 cells but also induced the redox imbalance, cell cycle arrest, and apoptosis of MDA-MB-231 cells via ameliorating the mitochondrial dysfunctions and regulating the MAPK signaling pathway. Conclusion Our findings confirmed the biosafety and excellent anti-cancer potency of Cu-CDs against breast cancer progression by tapping into mechanisms that disrupt malignant behaviors and oxidative homeostasis of breast cancer cells.
Collapse
Affiliation(s)
- Mengqi Wang
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Shuting Lan
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Wenqi Zhang
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Qin Jin
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People’s Republic of China
| | - Hua Du
- Department of Pathology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Xiaomei Sun
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Lijun He
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Xiangyun Meng
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Liya Su
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Gang Liu
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, People’s Republic of China
| |
Collapse
|
19
|
Cheng SM, Su YY, Chiang NJ, Wang CJ, Chao YJ, Huang CJ, Tsai HJ, Chen SH, Chang CY, Tsai CR, Li YJ, Yen CJ, Chuang SC, Chang JSM, Shan YS, Hwang DY, Chen LT. Germline mutations of homologous recombination genes and clinical outcomes in pancreatic cancer: a multicenter study in Taiwan. J Biomed Sci 2024; 31:21. [PMID: 38350919 PMCID: PMC10865564 DOI: 10.1186/s12929-024-01008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/28/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Cancer susceptibility germline mutations are associated with pancreatic ductal adenocarcinoma (PDAC). However, the hereditary status of PDAC and its impact on survival is largely unknown in the Asian population. METHODS Exome sequencing was performed on 527 blood samples from PDAC individuals and analyzed for mutations in 80 oncogenic genes. Pathogenic and likely pathogenic (P/LP) germline variants were diagnosed according to the ACMG variant classification categories. The association between germline homologous recombination gene mutations (gHRmut, including BAP1, BRCA1, BRCA2, PALB2, ATM, BLM, BRIP1, CHEK2, NBN, MUTYH, FANCA and FANCC) and the treatment outcomes was explored in patients with stage III/IV diseases treated with first-line (1L) platinum-based versus platinum-free chemotherapy. RESULTS Overall, 104 of 527 (19.7%) patients carried germline P/LP variants. The most common mutated genes were BRCA2 (3.60%), followed by ATR (2.66%) and ATM (1.9%). After a median follow-up duration of 38.3-months (95% confidence interval, 95% CI 35.0-43.7), the median overall survival (OS) was not significantly different among patients with gHRmut, non-HR germline mutations, or no mutation (P = 0.43). Among the 320 patients with stage III/IV disease who received 1L combination chemotherapy, 32 (10%) had gHRmut. Of them, patients receiving 1L platinum-based chemotherapy exhibited a significantly longer median OS compared to those with platinum-free chemotherapy, 26.1 months (95% CI 12.7-33.7) versus 9.6 months (95% CI 5.9-17.6), P = 0.001. However, the median OS of patients without gHRmut was 14.5 months (95% CI 13.2-16.9) and 12.6 months (95% CI 10.8-14.7) for patients receiving 1L platinum-based and platinum-free chemotherapy, respectively (P = 0.22). These results were consistent after adjusting for potential confounding factors including age, tumor stage, performance status, and baseline CA 19.9 in the multivariate Cox regression analysis. CONCLUSIONS Our study showed that nearly 20% of Taiwanese PDAC patients carried germline P/LP variants. The longer survival observed in gHRmut patients treated with 1L platinum-based chemotherapy highlights the importance of germline testing for all patients with advanced PDAC at diagnosis.
Collapse
Affiliation(s)
- Siao Muk Cheng
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Yung-Yeh Su
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Deparment of Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Internal Medicine, Kaohsiung Medical University Hospital and Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Nai-Jung Chiang
- Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chih-Jung Wang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Surgery, National Cheng-Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ying-Jui Chao
- Department of Surgery, National Cheng-Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Jui Huang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hui-Jen Tsai
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
- Deparment of Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Internal Medicine, Kaohsiung Medical University Hospital and Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shang-Hung Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
- Deparment of Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chi-Yen Chang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Chia-Rung Tsai
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Yi-Jie Li
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Chia-Jui Yen
- Deparment of Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Chang Chuang
- Division of General and Digestive Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Surgery, Faculty of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jeffrey Shu-Ming Chang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Yan-Shen Shan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Department of Surgery, National Cheng-Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Daw-Yang Hwang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan.
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Center for Biomarkers and Biotech Drugs, Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Precision Medicine Ph.D. Program, National Tsing Hua University, Hsinchu, Taiwan.
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan.
- Deparment of Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Department of Internal Medicine, Kaohsiung Medical University Hospital and Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.
| |
Collapse
|
20
|
Horton C, Hoang L, Zimmermann H, Young C, Grzybowski J, Durda K, Vuong H, Burks D, Cass A, LaDuca H, Richardson ME, Harrison S, Chao EC, Karam R. Diagnostic Outcomes of Concurrent DNA and RNA Sequencing in Individuals Undergoing Hereditary Cancer Testing. JAMA Oncol 2024; 10:212-219. [PMID: 37924330 PMCID: PMC10625669 DOI: 10.1001/jamaoncol.2023.5586] [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: 07/12/2023] [Accepted: 09/04/2023] [Indexed: 11/06/2023]
Abstract
Importance Personalized surveillance, prophylaxis, and cancer treatment options for individuals with hereditary cancer predisposition are informed by results of germline genetic testing. Improvements to genomic technology, such as the availability of RNA sequencing, may increase identification of individuals eligible for personalized interventions by improving the accuracy and yield of germline testing. Objective To assess the cumulative association of paired DNA and RNA testing with detection of disease-causing germline genetic variants and resolution of variants of uncertain significance (VUS). Design, Setting, and Participants Paired DNA and RNA sequencing was performed on individuals undergoing germline testing for hereditary cancer indication at a single diagnostic laboratory from March 2019 through April 2020. Demographic characteristics, clinical data, and test results were curated as samples were received, and changes to variant classification were assessed over time. Data analysis was performed from May 2020 to June 2023. Main Outcomes and Measures Main outcomes were increase in diagnostic yield, decrease in VUS rate, the overall results by variant type, the association of RNA evidence with variant classification, and the corresponding predicted effect on cancer risk management. Results A total of 43 524 individuals were included (median [range] age at testing, 54 [2-101] years; 37 373 female individuals [85.7%], 6224 male individuals [14.3%], and 2 individuals of unknown sex [<0.1%]), with 43 599 tests. A total of 2197 (5.0%) were Ashkenazi Jewish, 1539 (3.5%) were Asian, 3077 (7.1%) were Black, 2437 (5.6%) were Hispanic, 27 793 (63.7%) were White, and 2049 (4.7%) were other race, and for 4507 individuals (10.3%), race and ethnicity were unknown. Variant classification was impacted in 549 individuals (1.3%). Medically significant upgrades were made in 97 individuals, including 70 individuals who had a variant reclassified from VUS to pathogenic/likely pathogenic (P/LP) and 27 individuals who had a novel deep intronic P/LP variant that would not have been detected using DNA sequencing alone. A total of 93 of 545 P/LP splicing variants (17.1%) were dependent on RNA evidence for classification, and 312 of 439 existing splicing VUS (71.1%) were resolved by RNA evidence. Notably, the increase in positive rate (3.1%) and decrease in VUS rate (-3.9%) was higher in Asian, Black, and Hispanic individuals combined compared to White individuals (1.6%; P = .02; and -2.5%; P < .001). Conclusions and Relevance Findings of this diagnostic study demonstrate that the ability to perform RNA sequencing concurrently with DNA sequencing represents an important advancement in germline genetic testing by improving detection of novel variants and classification of existing variants. This expands the identification of individuals with hereditary cancer predisposition and increases opportunities for personalization of therapeutics and surveillance.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Huy Vuong
- Ambry Genetics, Aliso Viejo, California
| | | | | | | | | | | | - Elizabeth C Chao
- Ambry Genetics, Aliso Viejo, California
- University of California, Irvine, School of Medicine
| | | |
Collapse
|
21
|
Shane-Carson KP, Smith D, Smith A, Seeley C. Retrospective chart analysis to determine the impact of a patient-facing digital risk stratification tool combined with a clinical screener for hereditary cancer genetic risk assessment triage in a community oncology clinic. J Community Genet 2024; 15:25-31. [PMID: 37889419 PMCID: PMC10857995 DOI: 10.1007/s12687-023-00687-3] [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: 05/30/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
The purpose of this study was to evaluate the utility of adding a clinical screener to the patient-facing digital risk stratification tool triage process for the identification of patients eligible for a genetic risk assessment for hereditary cancer. Digital risk stratification entries were retrospectively reviewed to determine the overall number of patients eligible for genetic risk assessment. These were also analyzed to determine how many patients were re-contacted by the clinical screener, and how many of those recontacted patients met criteria after their personal and family history was revised by the clinical screener. There was an 89.9% digital risk stratification triage tool completion rate, with 22.6% requiring contact from the clinical screener. Of the 640 patients who completed the digital tool, 5.9% met criteria for testing after their personal and/or family history was revised by the clinical screener. Overall, 51.1% of patients met criteria for a genetic risk assessment. The addition of a clinical screener further increased identification of patients eligible for genetic risk assessment. About half of patients who met criteria after being contacted by the clinical screener met criteria based on their personal diagnosis of cancer alone. Incorporation of a clinical screener to the digital screening process may serve to reduce barriers to patient completion of the tool and increase rates of patient identification for cancer genetic services.
Collapse
Affiliation(s)
- Kate P Shane-Carson
- Division of Human Genetics, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Douglas Smith
- Division of Adena Health, Adena Cancer Center, Chillicothe, OH, USA
| | - Angie Smith
- Division of Adena Health, Adena Cancer Center, Chillicothe, OH, USA
| | - Caroline Seeley
- Division of Human Genetics, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
22
|
Gressel GM, Frey MK, Norquist B, Senter L, Blank SV, Urban RR. Germline and somatic testing for ovarian Cancer: An SGO clinical practice statement. Gynecol Oncol 2024; 181:170-178. [PMID: 38215513 DOI: 10.1016/j.ygyno.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/09/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Germline and somatic genetic testing have become critical components of care for people with ovarian cancer. The identification of germline and somatic pathogenic variants as well as homologous recombination deficiency can contribute to the prediction of treatment response, prognostic outcome, and suitability for targeted agents (e.g. poly (ADP-ribose) polymerase (PARP) inhibitors). Furthermore, identifying germline pathogenic variants can prompt cascade genetic testing for at-risk relatives. Despite the clinical benefits and consensus recommendations from several organizations calling for universal genetic testing in ovarian cancer, only about one third of patients complete germline or somatic genetic testing. The members of the Society of Gynecologic Oncology (SGO) Clinical Practice Committee have composed this statement to provide an overview of germline and somatic genetic testing for patients with epithelial ovarian cancer, focusing on available testing modalities and options for care delivery.
Collapse
Affiliation(s)
- G M Gressel
- Corewell Health Cancer Center, Division of Gynecologic Oncology, Michigan State University- College of Human Medicine, United States.
| | - M K Frey
- Weill Cornell Medicine, Division of Gynecologic Oncology, United States
| | - B Norquist
- University of Washington School of Medicine, Division of Gynecologic Oncology, United States
| | - L Senter
- The Ohio State University, Comprehensive Cancer Center,United States
| | - S V Blank
- Icahn School of Medicine at Mount Sinai, United States
| | - R R Urban
- University of Washington School of Medicine, Division of Gynecologic Oncology, United States
| |
Collapse
|
23
|
Shelton C, Ruiz A, Shelton L, Montgomery H, Freas K, Ellsworth RE, Poll S, Pineda-Alvarez D, Heald B, Esplin ED, Nielsen SM. Universal Germline-Genetic Testing for Breast Cancer: Implementation in a Rural Practice and Impact on Shared Decision-Making. Ann Surg Oncol 2024; 31:325-334. [PMID: 37814187 PMCID: PMC10695880 DOI: 10.1245/s10434-023-14394-3] [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: 08/11/2023] [Accepted: 09/15/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Whereas the National Comprehensive Cancer Network (NCCN) criteria restrict germline-genetic testing (GGT) to a subset of breast cancer (BC) patients, the American Society of Breast Surgeons recommends universal GGT. Although the yield of pathogenic germline variants (PGV) in unselected BC patients has been studied, the practicality and utility of incorporating universal GGT into routine cancer care in community and rural settings is understudied. This study reports real-world implementation of universal GGT for patients with breast cancer and genetics-informed, treatment decision-making in a rural, community practice with limited resources. METHODS From 2019 to 2022, all patients with breast cancer at a small, rural hospital were offered GGT, using a genetics-extender model. Statistical analyses included Fisher's exact test, t-tests, and calculation of odds ratios. Significance was set at p < 0.05. RESULTS Of 210 patients with breast cancer who were offered GGT, 192 (91.4%) underwent testing with 104 (54.2%) in-criteria (IC) and 88 (45.8%) out-of-criteria (OOC) with NCCN guidelines. Pathogenic germline variants were identified in 25 patients (13.0%), with PGV frequencies of 15 of 104 (14.4%) in IC and ten of 88 (11.4%) in OOC patients (p = 0.495). GGT informed treatment for 129 of 185 (69.7%) patients. CONCLUSIONS Universal GGT was successfully implemented in a rural, community practice with > 90% uptake. Treatment was enhanced or de-escalated in those with and without clinically actionable PGVs, respectively. Universal GGT for patients with breast cancer is feasible within rural populations, enabling optimization of clinical care to patients' genetic profile, and may reduce unnecessary healthcare, resource utilization.
Collapse
Affiliation(s)
| | | | | | | | - Karen Freas
- The Outer Banks Hospital, Nags Head, NC, USA
| | | | - Sarah Poll
- Invitae Corporation, San Francisco, CA, USA
| | | | | | | | | |
Collapse
|
24
|
Hutchcraft ML, Zhang S, Lin N, Pickarski JC, Belcher EA, Wei S, Bocklage T, Miller RW, Villano JL, Cavnar MJ, Kim J, Arnold SM, Ueland FR, Kolesar JM. Feasibility and Clinical Utility of Reporting Hereditary Cancer Predisposition Pathogenic Variants Identified in Research Germline Sequencing: A Prospective Interventional Study. JCO Precis Oncol 2024; 8:e2300266. [PMID: 38295319 PMCID: PMC10843325 DOI: 10.1200/po.23.00266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/02/2023] [Accepted: 12/04/2023] [Indexed: 02/02/2024] Open
Abstract
PURPOSE Patients with cancer frequently undergo research-grade germline sequencing but clinically actionable results are not routinely disclosed. The objective of this study is to evaluate the feasibility of reporting clinically relevant secondary findings (SF) identified in germline research sequencing using the institutional molecular tumor board (MTB) and the treating oncology physician. METHODS This prospective, interventional cohort study enrolled Total Cancer Care participants with any cancer diagnosis at a single institution. Patients underwent research-grade germline whole-exome sequencing, with bioinformatic analysis in a Clinical Laboratory Improvement Amendments-certified laboratory to verify pathogenic/likely pathogenic germline variants (PGVs) in any American College of Medical Genomics and Genetics SF v2.0 genes. After a protocol modification in consenting patients, the MTB reported PGVs to treating oncology physicians with recommendations for referral to a licensed genetic counselor and clinical confirmatory testing. RESULTS Of the 781 enrolled participants, 32 (4.1%) harbored cancer predisposition PGVs, 24 (3.1%) were heterozygous carriers of an autosomal recessive cancer predisposition syndrome, and 14 (1.8%) had other hereditary disease PGVs. Guideline-directed testing would have missed 37.5% (12/32) of the inherited cancer predisposition PGVs, which included BRCA1, BRCA2, MSH6, SDHAF2, SDHB, and TP53 variants. Three hundred fifteen participants consented to reporting results; results for all living patients were reported to the clinical team with half referred to a licensed genetic counselor. There was concordance between all research variants identified in patients (n = 9) who underwent clinical confirmatory sequencing. CONCLUSION MTB reporting of research-grade germline sequencing to the clinical oncology team is feasible. Over a third of PGVs identified using a universal testing strategy would have been missed by guideline-based approach, suggesting a role for expanding germline testing.
Collapse
Affiliation(s)
- Megan L. Hutchcraft
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Shulin Zhang
- Department of Pathology and Laboratory Medicine University of Kentucky Chandler Medical Center, Lexington, KY
- Markey Comprehensive Cancer Center, University of Kentucky, Lexington, KY
| | - Nan Lin
- Department of Pharmacy Practice and Science, University of Kentucky College of Pharmacy, Lexington, KY
| | | | - Elizabeth A. Belcher
- Department of Clinical Research, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Sainan Wei
- Department of Pathology and Laboratory Medicine University of Kentucky Chandler Medical Center, Lexington, KY
| | - Thèrése Bocklage
- Department of Pathology and Laboratory Medicine University of Kentucky Chandler Medical Center, Lexington, KY
| | - Rachel W. Miller
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - John L. Villano
- Division of Medical Oncology, Department of Internal Medicine, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Michael J. Cavnar
- Division of Surgical Oncology, Department of Surgery, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Joseph Kim
- Division of Surgical Oncology, Department of Surgery, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Susanne M. Arnold
- Division of Medical Oncology, Department of Internal Medicine, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Frederick R. Ueland
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Jill M. Kolesar
- Markey Comprehensive Cancer Center, University of Kentucky, Lexington, KY
- Department of Pharmacy Practice and Science, University of Kentucky College of Pharmacy, Lexington, KY
| |
Collapse
|
25
|
Roy B, Knapke S, Pillay-Smiley N, Zhang X, Queen K, Sisson R. Current practice of cancer predisposition testing in pediatric patients with CNS tumors in the United States. Pediatr Blood Cancer 2024; 71:e30725. [PMID: 37859593 DOI: 10.1002/pbc.30725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/10/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
An estimated 8.6% of all pediatric patients with central nervous system tumors (CNSTs) have underlying hereditary cancer predisposition (HCP). Identifying HCP affects risk assessment and medical management options for the patients and their family members. However, there is a lack of consensus on the optimal germline genetic testing (GT) approach for pediatric patients with CNSTs. As a first step in addressing the need for consensus, we surveyed oncology and genetics providers from 47 institutions in professional organizations across the United States. We investigated their current practice (e.g., GT decisions and ordering practices) when assessing pediatric patients with CNSTs for HCP. We received 60 responses from 21 pediatric oncologists, 10 neuro-oncologists, 28 genetics providers, and one neuro-oncologist/geneticist. Results demonstrate genetic counselors, followed by oncologists, most often facilitated consent, ordered testing, and selected which test to order. The most ordered test was a multi-gene panel (60%). Of 18 CNST diagnoses, choroid plexus carcinoma (CPC) was the diagnosis for which most providers (78%) reported they would offer GT. For medulloblastoma, 56% overall reported they would offer GT (64% of genetics providers, 62% of neuro-oncologists, 20% of pediatric oncologists; p = .050). Findings suggest that even for the CNSTs most commonly known to be associated with HCP regardless of family history, there was variability in providers' decisions to offer GT. The lack of consensus in GT decisions in our study indicates inconsistencies in the genetics care of pediatric patients with CNSTs, demonstrating a need for consensus guidelines to promote consistent genetics care.
Collapse
Affiliation(s)
- Baylee Roy
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- Leadership Education in Neurodevelopmental and related Disabilities, University of Cincinnati and Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Sara Knapke
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Natasha Pillay-Smiley
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Xue Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Kate Queen
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Rebecca Sisson
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| |
Collapse
|
26
|
Xiong M, Wang X, Liu D, Xiu B, Zhang Q, Chi W, Goh CW, Zhang L, Chen M, Ren H, Shao Z, Yang B, Wu J. Somatic mutations in a multigene panel and impact on prognosis based on TP53 status in Chinese HER2-positive patients undergoing neoadjuvant therapy: A single-institution retrospective cohort. Cancer Med 2024; 13:e6955. [PMID: 38379328 PMCID: PMC10832311 DOI: 10.1002/cam4.6955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 12/27/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Gene mutations play a crucial role in the occurrence and development of tumors, particularly in breast cancer (BC). Neoadjuvant therapy (NAT) has shown greater clinical benefit in HER2-positive breast cancer. However, further clinical investigation is needed to fully understand the correlation between genetic mutations and NAT efficacy and the long-term prognosis in HER2-positive BC. METHODS This was a retrospective cohort study of 222 patients receiving NAT between 2017 and 2021 in the Department of Breast Surgery of Fudan University Shanghai Cancer Center. Tumor samples from these patients were subjected to Next Generation Sequencing (NGS) to analyze mutations in 513 cancer-related genes. This study aimed to investigate the association between these genetic mutations and postoperative pathological complete response (pCR), as well as their impact on disease-free survival (DFS). RESULTS In total, 48.65% patients reached pCR, ER-negative status (p < 0.001), PR-negative status (p < 0.001), Ki67 ≥ 20 (p = 0.011), and dual-targeted therapy (p < 0.001) were all associated with enhanced pCR rates. The frequency of somatic alterations in TP53 (60%), PIK3CA (15%), and ERBB2 (11%) was highest. In the HER2+/HR- cohort, patients who achieved pCR had a significant benefit in prognosis (HR = 3.049, p = 0.0498). KMT2C (p = 0.036) and TP53 (p = 0.037) mutations were significantly increased in patients with DFS events. Moreover, TP53 mutations had prognostic significance in HER2-positive BC patients with HR-negative (HR = 3.712, p = 0.027) and pCR (HR = 6.253, p = 0.027) status and who received herceptin-only targeted therapy (HR = 4.145, p = 0.011). CONCLUSIONS The genetic mutation profiles of Chinese HER2+ patients who received NAT were discrepant with respect to HR status or DFS events. TP53 mutations have significant prognostic value in patients with NAT for HER2-positive BC and patients benefit differently depending on HR status, the neoadjuvant regimen and response, which highlights the significance of genetic factors in treatment customization based on individual genetic and clinical characteristics.
Collapse
Affiliation(s)
- Min Xiong
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Xuliren Wang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Douwaner Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Bingqiu Xiu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Qi Zhang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Weiru Chi
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Chih Wan Goh
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Liyi Zhang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Ming Chen
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Hengyu Ren
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Zhi‐Ming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Benlong Yang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
| | - Jiong Wu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in ShanghaiFudan University Shanghai Cancer CenterShanghaiChina
- Collaborative Innovation Center for Cancer MedicineShanghaiChina
| |
Collapse
|
27
|
Chotiprasidhi P, Sato-Espinoza AK, Wangensteen KJ. Germline Genetic Associations for Hepatobiliary Cancers. Cell Mol Gastroenterol Hepatol 2023; 17:623-638. [PMID: 38163482 PMCID: PMC10899027 DOI: 10.1016/j.jcmgh.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Hepatobiliary cancers (HBCs) include hepatocellular carcinoma, cholangiocarcinoma, and gallbladder carcinoma, which originate from the liver, bile ducts, and gallbladder, respectively. They are responsible for a substantial burden of cancer-related deaths worldwide. Despite knowledge of risk factors and advancements in therapeutics and surgical interventions, the prognosis for most patients with HBC remains bleak. There is evidence from familial aggregation and case-control studies to suggest a familial risk component in HBC susceptibility. Recent progress in genomics research has led to the identification of germline variants including single nucleotide polymorphisms (SNPs) and pathogenic or likely pathogenic (P/LP) variants in cancer-associated genes associated with HBC risk. These findings emerged from genome-wide association studies and next-generation sequencing techniques such as whole-exome sequencing. Patients with other cancer types, including breast, colon, ovarian, prostate, and pancreatic cancer, are recommended by guidelines to undergo germline genetic testing, but similar recommendations are lagging in HBC. This prompts the question of whether multi-gene panel testing should be integrated into clinical guidelines for HBC management. Here, we review the hereditary genetics of HBC, explore studies investigating SNPs and P/LP variants in HBC patients, discuss the clinical implications and potential for personalized treatments and impact on patient's family members, and conclude that additional studies are needed to examine how genetic testing can be applied clinically.
Collapse
Affiliation(s)
- Perapa Chotiprasidhi
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Kirk J Wangensteen
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
28
|
Shain J, Michel A, May MS, Qunaj L, El-Sadr W, Chung WK, Appelbaum PS, Jacobson JS, Justman J, Neugut AI. Cancer genetic mutation prevalence in sub-Saharan Africa: A review of existing data. Semin Oncol 2023; 50:123-130. [PMID: 38171987 DOI: 10.1053/j.seminoncol.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Cancer represents a leading cause of death worldwide. Germline mutations in several genes increase the risk of developing several cancers, including cancers of the breast, ovary, pancreas, colorectum, and melanoma. An understanding of the population prevalence of pathogenic germline variants can be helpful in the design of public health interventions, such as genetic testing, which has downstream implications for cancer screening, prevention, and treatment. While population-based studies of pathogenic germline variants exist, most such studies have been conducted in White populations. Limited data exist regarding the prevalence of germline mutations within sub-Saharan African populations. MATERIALS AND METHODS We identified countries defined as sub-Saharan Africa by the World Bank and conducted a scoping literature review using PubMed. For each country, we identified and summarized studies that focused on the prevalence of germline genetic mutations with sample sizes >10 and in a population directly from sub-Saharan Africa, either with or without diseases associated with the relevant genetic mutations. Studies that evaluated the prevalence of somatic or likely benign variants were excluded. RESULTS Within the 48 countries in sub-Saharan Africa, we identified 34 studies which meet the inclusion criteria. Twenty studies were conducted in South Africa, Nigeria, or Burkina Faso; four countries had more than two published papers. We found that 33 of 48 countries in sub-Saharan Africa lacked any genetic studies. Notably, there has been an increase in relevant studies starting in 2020. Importantly, of the 34 studies identified, 29 included data on BRCA1 or BRCA2. Data on the prevalence of mutations contributing to familial cancer syndromes other than BRCA1 and BRCA2 was limited. CONCLUSIONS While some progress has been made towards understanding the prevalence of germline mutations in cancer susceptibility genes, the characterization of genetic mutations among sub-Saharan African populations remains strikingly incomplete. Given the genetic diversity in the region, there remains a great need for large-scale, population-based studies to understand the prevalence of germline pathogenic variants and adequately capture all the subpopulations in this part of the world.
Collapse
Affiliation(s)
- Joshua Shain
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Alissa Michel
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Michael S May
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Lindor Qunaj
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Wafaa El-Sadr
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Wendy K Chung
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Psychiatry, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Paul S Appelbaum
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Judith S Jacobson
- Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Jessica Justman
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY
| | - Alfred I Neugut
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY; Department of Epidemiology and ICAP, Mailman School of Public Health, Columbia University, New York, NY.
| |
Collapse
|
29
|
Wei B, Zhao J, Li J, Feng J, Sun M, Wang Z, Shi C, Yang K, Qin Y, Zhang J, Ma J, Dong H. Pathogenic germline variants in BRCA1 and TP53 increase lung cancer risk in Chinese. Cancer Med 2023; 12:21219-21228. [PMID: 37930190 PMCID: PMC10726856 DOI: 10.1002/cam4.6692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/07/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUD Multiple studies have identified pathogenic germline variants in cancer susceptibility genes (CSGs) in Chinese lung cancer patients; however, accurate assessment of these variants' contributions to cancer predisposition is always hampered by the absence of data on the prevalence of these variants in the general population. It is necessary to conduct a large-scale case-control study to identify CSGs that significantly increase the risk of lung cancer. MATERIALS AND METHODS We performed targeted sequencing of a CSGs panel in 1117 lung cancer patients and 16,327 controls from the general Chinese population. RESULTS In comparison to controls, lung cancer patients had a considerably higher prevalence of pathogenic and likely pathogenic (P/LP) variations. Among lung cancer patients, 72% of P/LP variants carriers did not have a family cancer history, who would be ignored if germline testing was only provided for patients meeting family history-based criteria. Furthermore, compared to individuals with late-onset lung cancer, patients with early-onset lung cancer had a considerably higher prevalence of P/LP variations. With odds ratios (ORs) ranging from 4-fold (BRCA1: OR, 4.193; 95%CI, 1.382-10.768) to 29-fold (TP53: OR, 29.281; 95%CI, 1.523-1705.506), P/LP variants in the BRCA1 and TP53 genes were discovered to be strongly related to increased lung cancer risk. Additionally, with ORs ranging from 7.322-fold to infinity, we discovered 23 variations previously categorized as non-P/LP variants were highly enriched in lung cancer patients. CONCLUSION Our findings indicated that P/LP variants in BRCA1 and TP53 conferred increased risk of lung cancer in Chinese.
Collapse
Affiliation(s)
- Bing Wei
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Jiadong Zhao
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jun Li
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Junnan Feng
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Manman Sun
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Zhizhong Wang
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Chao Shi
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Ke Yang
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Yue Qin
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jing Zhang
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jie Ma
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Hui Dong
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic DiseasesShanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| |
Collapse
|
30
|
Erali RA, Pu T, Vu TM, Mangieri CW, Jee Y, Wise JS, Perry KC, Hsu FC, Levine EA, McNatt MH, Chiba A. Pivotal Role of Genetic Counselors in the Uptake of Germline Genetic Testing in Non-Metastatic Breast Cancer and the Impact of Testing on Surgical Decision Making. Am Surg 2023; 89:5842-5849. [PMID: 37183417 DOI: 10.1177/00031348231175097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND Genetic testing is increasingly utilized in breast cancer patients; however, testing rates remain low. We aimed to evaluate the rate of genetic testing at a tertiary academic medical center utilizing a multidisciplinary clinic model including genetic counselor. METHODS A single-center retrospective chart review was performed on a cohort of newly diagnosed breast cancer patients from January 2018 through February 2019. Patients were reviewed for genetic screening eligibility, consultation with a genetic counselor, and test results. RESULTS Final analysis included 426 patients. 261 (61.3%) were found to meet National Comprehensive Cancer Network guidelines for genetic testing, of which 178 patient (68.2%) underwent testing and 32 patients (12.3%) declined testing. Of the 165 not eligible for testing, 5 patients were tested. A total of 183 patients underwent testing and 116 (63.4%) had a negative result, 17 (9.3%) were positive for at least one gene mutation and 50 (27.3%) were identified to have a variant of unknown significance (VUS). There was a positive association between those patients who met with a genetic counselor and eligibility for testing (OR 31.1, 95% CI 16.0-60.5). CONCLUSIONS Genetic testing result has become an increasingly important factor when defining optimal surgical treatment for breast cancer patients. Increasing the availability of genetic consultation for breast cancer patients can improve testing rates and patient selection.
Collapse
Affiliation(s)
- Richard A Erali
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Tracey Pu
- Department of Surgery, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Thuy M Vu
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Christopher W Mangieri
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Yoonsun Jee
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jordan S Wise
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Kathleen C Perry
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Fang-Chi Hsu
- Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Edward A Levine
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Marissa H McNatt
- Division of Surgical Oncology, Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Akiko Chiba
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| |
Collapse
|
31
|
Brake DA, Idler BM, Kunze KL, Golafshar MA, Heald B, Young S, Klint M, Barrus K, Esplin ED, Nussbaum RL, Samadder NJ, Hinni ML, Chang BA. Germline Genetic Testing in Unselected Squamous and Non-Squamous Head and Neck Cancers. Laryngoscope 2023; 133:3378-3388. [PMID: 37132629 DOI: 10.1002/lary.30720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/20/2023] [Accepted: 04/10/2023] [Indexed: 05/04/2023]
Abstract
OBJECTIVE This study describes the prevalence of pathogenic germline variants (PGVs) in head and neck cancer patients, the incremental yield compared to a guideline-based approach to genetic evaluation, and the uptake of family variant testing. STUDY DESIGN Prospective cohort study. SETTING Three tertiary academic medical centers. METHODS Germline sequencing using an 84-gene screening platform among unselected head and neck cancer patients who received care at Mayo Clinic Cancer Centers between April 2018 and March 2020. RESULTS Amongst 200 patients, the median age was 62.0 years (Q1, Q3: 55, 71), 23.0% were female, 89.0% white/non-Hispanic, 5.0% Hispanic/Latinx, 6% of another race, and 42.0% had prognostic stage IV disease. The most common subsites were the oropharyngeal (45.0%) and salivary glands (12.0%). The most common histology was squamous cell carcinoma (74.5%). Twenty-one patients (10.5%) had a total of 22 PGVs; 20 of the 21 patients (95.2%) did not meet criteria for testing by current guidelines. Regarding penetrance of the 22 PGVs, 11 were high or moderate (most common PMS2 or HOXB13), and 11 were low or recessive (most common MUTYH, WNR, or RECQL4). One patient had a change in care based on an identified PGV. Family variant testing was completed at a rate of 4.8%. CONCLUSIONS Universal gene panel testing identified a PGV in 10.5% of head and neck cancer patients; almost all would have been missed by current guideline-based testing. One of 21 patients had a treatment change due to their PGV, indicating that head and neck cancer treatment decisions are not yet widely informed by germline alterations. LEVEL OF EVIDENCE 3 Laryngoscope, 133:3378-3388, 2023.
Collapse
Affiliation(s)
- Daniela A Brake
- Department of Otolaryngology Head & Neck Surgery, Mayo Clinic, Phoenix, Arizona, USA
| | - Beau M Idler
- Department of Otolaryngology Head & Neck Surgery, Mayo Clinic, Phoenix, Arizona, USA
| | - Katie L Kunze
- Department of Quantitative Health Sciences, Mayo Clinic, Scottsdale, Arizona, USA
| | - Michael A Golafshar
- Department of Quantitative Health Sciences, Mayo Clinic, Scottsdale, Arizona, USA
| | - Brandie Heald
- Invitae Corporation, San Francisco, California, U.S.A
| | - Sarah Young
- Invitae Corporation, San Francisco, California, U.S.A
| | - Margaret Klint
- Department of Clinical Genomics, Mayo Clinic, Phoenix, Arizona, USA
| | - Kathleen Barrus
- Department of Clinical Genomics, Mayo Clinic, Phoenix, Arizona, USA
| | | | | | - N Jewel Samadder
- Department of Clinical Genomics, Mayo Clinic, Phoenix, Arizona, USA
- Center for Individualized Medicine, Mayo Clinic, Phoenix, Arizona, U.S.A
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Phoenix, Arizona, USA
| | - Michael L Hinni
- Department of Otolaryngology Head & Neck Surgery, Mayo Clinic, Phoenix, Arizona, USA
| | - Brent A Chang
- Department of Otolaryngology Head & Neck Surgery, Mayo Clinic, Phoenix, Arizona, USA
| |
Collapse
|
32
|
Hsu DS, Jiang SF, Habel LA, Hoodfar E, Karlea A, Manace-Brenman L, Dzubnar JM, Shim VC. Germline Genetic Testing Among Women ≤ 45 Years of Age with Ductal Carcinoma In Situ Versus Invasive Breast Cancer in a Large Integrated Health Care System. Ann Surg Oncol 2023; 30:6454-6461. [PMID: 37386303 DOI: 10.1245/s10434-023-13745-4] [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: 01/26/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND We compared the results of hereditary cancer multigene panel testing among patients ≤ 45 years of age diagnosed with ductal carcinoma in situ (DCIS) versus invasive breast cancer (IBC) in a large integrated health care system. METHODS A retrospective cohort study of hereditary cancer gene testing among women ≤ 45 years of age diagnosed with DCIS or IBC at Kaiser Permanente Northern California between September 2019 and August 2020 was performed. During the study period, institutional guidelines recommended the above population be referred to genetic counselors for pretesting counseling and testing. RESULTS A total of 61 DCIS and 485 IBC patients were identified. Genetic counselors met with 95% of both groups, and 86.4% of DCIS patients and 93.9% of IBC patients (p = 0.0339) underwent gene testing. Testing differed by race/ethnicity (p = 0.0372). Among those tested, 11.76% (n = 6) of DCIS patients and 16.71% (n = 72) of IBC patients had a pathogenic variant (PV) or likely pathogenic variant (LPV) based on the 36-gene panel (p = 0.3650). Similar trends were seen in 13 breast cancer (BC)-related genes (p = 0.0553). Family history of cancer was significantly associated with both BC-related and non-BC-related PVs in IBC, but not DCIS. CONCLUSION In our study, 95% of patients were seen by a genetic counselor when age was used as an eligibility criterion for referral. While larger studies are needed to further compare the prevalence of PVs/LPVs among DCIS and IBC patients, our data suggest that even in younger patients, the prevalence of PVs/LPVs in BC-related genes is lower in DCIS patients.
Collapse
MESH Headings
- Humans
- Female
- Breast Neoplasms/epidemiology
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Carcinoma, Intraductal, Noninfiltrating/epidemiology
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Genetic Predisposition to Disease
- Retrospective Studies
- Carcinoma, Ductal, Breast/epidemiology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Genetic Testing
Collapse
Affiliation(s)
- Diana S Hsu
- University of California San Francisco, East Bay, Oakland, CA, USA
| | | | - Laurel A Habel
- Division of Research, Kaiser Permanente, Oakland, CA, USA
| | | | - Audrey Karlea
- Department of Genetics, Kaiser Permanente, Oakland, CA, USA
| | | | | | | |
Collapse
|
33
|
Sorscher S, LoPiccolo J, Heald B, Chen E, Bristow SL, Michalski ST, Nielsen SM, Lacoste A, Keyder E, Lee H, Nussbaum RL, Martins R, Esplin ED. Rate of Pathogenic Germline Variants in Patients With Lung Cancer. JCO Precis Oncol 2023; 7:e2300190. [PMID: 37992258 PMCID: PMC10681406 DOI: 10.1200/po.23.00190] [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: 04/18/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 11/24/2023] Open
Abstract
PURPOSE Germline genetic testing (GGT) is now recommended for all patients diagnosed with ovarian or pancreatic cancer and for a large proportion of patients based solely on a diagnosis of colorectal or breast cancer. However, GGT is not yet recommended for all patients diagnosed with lung cancer (LC), primarily because of a lack of evidence that supports a significant frequency of identifying pathogenic germline variants (PGVs) in these patients. This study characterizes GGT results in a cohort of patients with LC. METHODS We reviewed deidentified data for 7,788 patients with GGT (2015-2022). PGV frequencies were compared to a control cohort of unaffected individuals. GGT results were stratified by genomic ancestry, history of cancer, and PGV clinical actionability per current guidelines. RESULTS Of all patients with LC, 14.9% (1,161/7,788) had PGVs. The rate was similar when restricted to patients with no cancer family history (FH) or personal history (PH) of other cancers (14.3%). PGVs were significantly enriched in BRCA2, ATM, CHEK2, BRCA1, and mismatch repair genes compared with controls. Patients of European (EUR) genomic ancestry had the highest PGV rate (18%) and variants of uncertain significance were significantly higher in patients of non-EUR genomic ancestry. Of the PGVs identified, 61.3% were in DNA damage repair (DDR) genes and 95% were clinically actionable. CONCLUSION This retrospective study shows a LC diagnosis identifies patients with a significant likelihood of having a cancer-predisposing PGV across genomic ancestries. Enrichment of PGVs in DDR genes suggests that these PGVs may contribute to LC cancer predisposition. The frequency of PGVs among patients with LC did not differ significantly according to FH or PH of other cancers.
Collapse
Affiliation(s)
| | - Jaclyn LoPiccolo
- Hematology/Oncology Division, Dana-Farber Cancer Center, Boston, MA
| | | | | | | | | | | | | | | | - Hayan Lee
- Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA
| | | | - Renato Martins
- Hematology, Oncology and Palliative Care Division, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA
| | | |
Collapse
|
34
|
Farinea G, Crespi V, Listì A, Righi L, Bironzo P, Merlini A, Malapelle U, Novello S, Scagliotti GV, Passiglia F. The Role of Germline Mutations in Thoracic Malignancies: Between Myth and Reality. J Thorac Oncol 2023; 18:1146-1164. [PMID: 37331604 DOI: 10.1016/j.jtho.2023.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/15/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023]
Abstract
Considering the established contribution of environmental factors to the development of thoracic malignancies, the inherited susceptibility of these tumors has rarely been explored. However, the recent introduction of next-generation sequencing-based tumor molecular profiling in the real-word setting enabled us to deeply characterize the genomic background of patients with lung cancer with or without smoking-related history, increasing the likelihood of detecting germline mutations with potential prevention and treatment implications. Pathogenic germline variants have been detected in 2% to 3% of patients with NSCLC undergoing next-generation sequencing analysis, whereas the proportion of germline mutations associated with the development of pleural mesothelioma widely varies across different studies, ranging between 5% and 10%. This review provides an updated summary of emerging evidence about germline mutations in thoracic malignancies, focusing on pathogenetic mechanisms, clinical features, therapeutic implications, and screening recommendations for high-risk individuals.
Collapse
Affiliation(s)
- Giovanni Farinea
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Veronica Crespi
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Angela Listì
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Luisella Righi
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Paolo Bironzo
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Alessandra Merlini
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Umberto Malapelle
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Silvia Novello
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | | | - Francesco Passiglia
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| |
Collapse
|
35
|
Bouras A, Legrand C, Kourda J, Ruano E, Grand‐Masson C, Lefol C, Wang Q. From variant of unknown significance to likely pathogenic: Characterization and pathogenicity determination of a large genomic deletion in the MLH1 gene. Mol Genet Genomic Med 2023; 11:e2231. [PMID: 37350751 PMCID: PMC10496038 DOI: 10.1002/mgg3.2231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/01/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND The MLH1 gene is one of the DNA mismatch repair genes (MMR), implicated in Lynch syndrome (LS), an autosomal dominant hereditary tumor susceptibility disease. The advent of next-generation sequencing (NGS) technologies has accelerated the diagnosis of inherited diseases and increased the percentage of diagnosis of inherited cancers. However, some complex genomic alterations require the combination of several analytical strategies to allow correct biological interpretations. Here, we describe a novel MLH1 deletion and its pathogenicity determination in a patient suspected of LS. METHODS The index case was a French 73-year-old man diagnosed with colorectal cancer displaying microsatellite instability and the loss of MLH1 and PMS2 expression. NGS analysis was used as the primary method for MMR genes screening. Long-range PCR and reverse transcriptase polymerase chain reaction (RT-PCR) were used for breakpoints and pathogenicity determinations. RESULTS A large genomic deletion was detected which removed the last six nucleotides of MLH1 exon 11 together with a large part of intron 11. It was initially considered as a variant of unknown significance (VUS). Genomic breakpoints were subsequently characterized defining the deletion as c.1033_1039-248del. Further RNA analysis demonstrated that this variant activated a cryptic donor splice site at the 5' of the breakpoint, leading to a premature truncated protein: p.Thr345Alafs*13. CONCLUSION Our finding suggested that although NGS technologies have increased variant detection yield, combined approaches were still needed for complex variant characterization and pathogenicity assessment.
Collapse
Affiliation(s)
- Ahmed Bouras
- Laboratory of Constitutional Genetics for Frequent Cancer HCL‐CLBCentre Léon BérardLyonFrance
| | - Clementine Legrand
- Genetic Service, Department of Genetics and ProcreationCHU Grenoble AlpesGrenobleFrance
| | | | - Eric Ruano
- Laboratory of Constitutional Genetics for Frequent Cancer HCL‐CLBCentre Léon BérardLyonFrance
| | - Chloé Grand‐Masson
- Laboratory of Constitutional Genetics for Frequent Cancer HCL‐CLBCentre Léon BérardLyonFrance
| | - Cedrick Lefol
- Laboratory of Constitutional Genetics for Frequent Cancer HCL‐CLBCentre Léon BérardLyonFrance
| | - Qing Wang
- Laboratory of Constitutional Genetics for Frequent Cancer HCL‐CLBCentre Léon BérardLyonFrance
| |
Collapse
|
36
|
Desai NV, Barrows ED, Nielsen SM, Hatchell KE, Anderson MJ, Haverfield EV, Herrera B, Esplin ED, Lucassen A, Tung NM, Isaacs C. Retrospective Cohort Study on the Limitations of Direct-to-Consumer Genetic Screening in Hereditary Breast and Ovarian Cancer. JCO Precis Oncol 2023; 7:e2200695. [PMID: 37535880 PMCID: PMC10581610 DOI: 10.1200/po.22.00695] [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: 12/16/2022] [Revised: 05/08/2023] [Accepted: 06/29/2023] [Indexed: 08/05/2023] Open
Abstract
PURPOSE Among cancer predisposition genes, most direct-to-consumer (DTC) genetic tests evaluate three Ashkenazi Jewish (AJ) founder mutations in BRCA1/2, which represent a small proportion of pathogenic or likely pathogenic variants (PLPV) in cancer predisposing genes. In this study, we investigate PLPV in BRCA1/2 and other cancer predisposition genes that are missed by testing only AJ founder BRCA1/2 mutations. METHODS Individuals were referred to genetic testing for personal diagnoses of breast and/or ovarian cancer (clinical cohort) or were self-referred (nonindication-based cohort). There were 348,692 participants in the clinical cohort and 7,636 participants in the nonindication-based cohort. Both cohorts were analyzed for BRCA1/2 AJ founder mutations. Full sequence analysis was done for PLPV in BRCA1/2, CDH1, PALB2, PTEN, STK11, TP53, ATM, BARD1, BRIP1, CHEK2 (truncating variants), EPCAM, MLH1, MSH2/6, NF1, PMS2, RAD51C/D, and 22 other genes. RESULTS BRCA1/2 AJ founder mutations accounted for 10.8% and 29.7% of BRCA1/2 PLPV in the clinical and nonindication-based cohorts, respectively. AJ founder mutations accounted for 89.9% of BRCA1/2 PLPV in those of full AJ descent, but only 69.6% of those of partial AJ descent. In total, 0.5% of all individuals had a BRCA1/2 AJ founder variant, while 7.7% had PLPV in a high-risk breast/ovarian cancer gene. For non-AJ individuals, limiting evaluation to the AJ founder BRCA1/2 mutations missed >90% of mutations in actionable cancer risk genes. Secondary analysis revealed a false-positive rate of 69% for PLPV outside of non-AJ BRCA 1/2 founder mutations. CONCLUSION DTC genetic testing misses >90% of BRCA1/2 PLPV in individuals of non-AJ ancestry and about 10% of BRCA1/2 PLPV among AJ individuals. There is a high false-positivity rate for non-AJ BRCA 1/2 PLPV with DTC genetic testing.
Collapse
Affiliation(s)
| | - Elizabeth D. Barrows
- Division of Hematology-Oncology, MedStar Georgetown University Hospital, Washington, DC
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, DC
| | | | | | | | | | | | | | - Anneke Lucassen
- Department of Clinical Ethics and Law at Southampton, University of Southampton, Southampton, United Kingdom
- Welcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nadine M. Tung
- Division of Hematology-Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Claudine Isaacs
- Division of Hematology-Oncology, MedStar Georgetown University Hospital, Washington, DC
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, DC
| |
Collapse
|
37
|
Mitchell OD, Gilliam K, del Gaudio D, McNeely KE, Smith S, Acevedo M, Gaduraju M, Hodge R, Ramsland ASS, Segal J, Das S, Hathaway F, Bryan DS, Tawde S, Galasinski S, Wang P, Tjota MY, Husain AN, Armato SG, Donington J, Ferguson MK, Turaga K, Churpek JE, Kindler HL, Drazer MW. Germline Variants Incidentally Detected via Tumor-Only Genomic Profiling of Patients With Mesothelioma. JAMA Netw Open 2023; 6:e2327351. [PMID: 37556141 PMCID: PMC10413174 DOI: 10.1001/jamanetworkopen.2023.27351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/08/2023] [Indexed: 08/10/2023] Open
Abstract
IMPORTANCE Patients with mesothelioma often have next-generation sequencing (NGS) of their tumor performed; tumor-only NGS may incidentally identify germline pathogenic or likely pathogenic (P/LP) variants despite not being designed for this purpose. It is unknown how frequently patients with mesothelioma have germline P/LP variants incidentally detected via tumor-only NGS. OBJECTIVE To determine the prevalence of incidental germline P/LP variants detected via tumor-only NGS of mesothelioma. DESIGN, SETTING, AND PARTICIPANTS A series of 161 unrelated patients with mesothelioma from a high-volume mesothelioma program had tumor-only and germline NGS performed during April 2016 to October 2021. Follow-up ranged from 18 months to 7 years. Tumor and germline assays were compared to determine which P/LP variants identified via tumor-only NGS were of germline origin. Data were analyzed from January to March 2023. MAIN OUTCOMES AND MEASURES The proportion of patients with mesothelioma who had P/LP germline variants incidentally detected via tumor-only NGS. RESULTS Of 161 patients with mesothelioma, 105 were male (65%), the mean (SD) age was 64.7 (11.2) years, and 156 patients (97%) self-identified as non-Hispanic White. Most (126 patients [78%]) had at least 1 potentially incidental P/LP germline variant. The positive predictive value of a potentially incidental germline P/LP variant on tumor-only NGS was 20%. Overall, 26 patients (16%) carried a P/LP germline variant. Germline P/LP variants were identified in ATM, ATR, BAP1, CHEK2, DDX41, FANCM, HAX1, MRE11A, MSH6, MUTYH, NF1, SAMD9L, and TMEM127. CONCLUSIONS AND RELEVANCE In this case series of 161 patients with mesothelioma, 16% had confirmed germline P/LP variants. Given the implications of a hereditary cancer syndrome diagnosis for preventive care and familial counseling, clinical approaches for addressing incidental P/LP germline variants in tumor-only NGS are needed. Tumor-only sequencing should not replace dedicated germline testing. Universal germline testing is likely needed for patients with mesothelioma.
Collapse
Affiliation(s)
- Owen D. Mitchell
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Illinois
| | - Katie Gilliam
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Illinois
| | | | - Kelsey E. McNeely
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Illinois
| | - Shaili Smith
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Illinois
| | - Maria Acevedo
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Illinois
| | - Meghana Gaduraju
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Illinois
| | - Rachel Hodge
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Illinois
| | | | - Jeremy Segal
- Department of Pathology, The University of Chicago, Illinois
| | - Soma Das
- Department of Human Genetics, The University of Chicago, Illinois
| | - Feighanne Hathaway
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Illinois
| | | | - Sanjukta Tawde
- Department of Human Genetics, The University of Chicago, Illinois
| | | | - Peng Wang
- Department of Pathology, The University of Chicago, Illinois
| | | | - Aliya N. Husain
- Department of Pathology, The University of Chicago, Illinois
| | | | | | | | - Kiran Turaga
- Department of Surgery, The University of Chicago, Illinois
| | - Jane E. Churpek
- Division of Hematology, Medical Oncology, and Palliative Care, Department of Medicine, University of Wisconsin, Madison
| | - Hedy L. Kindler
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Illinois
| | - Michael W. Drazer
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Illinois
| |
Collapse
|
38
|
Henkel J, Laner A, Locher M, Wohlfrom T, Neitzel B, Becker K, Neuhann T, Abicht A, Steinke-Lange V, Holinski-Feder E. Diagnostic yield and clinical relevance of expanded germline genetic testing for nearly 7000 suspected HBOC patients. Eur J Hum Genet 2023; 31:925-930. [PMID: 37188824 PMCID: PMC10400578 DOI: 10.1038/s41431-023-01380-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/18/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Here we report the results of a retrospective germline analysis of 6941 individuals fulfilling the criteria necessary for genetic testing of hereditary breast- and ovarian cancer (HBOC) according to the German S3 or AGO Guidelines. Genetic testing was performed by next-generation sequencing using 123 cancer-associated genes based on the Illumina TruSight® Cancer Sequencing Panel. In 1431 of 6941 cases (20.6%) at least one variant was reported (ACMG/AMP classes 3-5). Of those 56.3% (n = 806) were class 4 or 5 and 43.7% (n = 625) were a class 3 (VUS). We defined a 14 gene HBOC core gene panel and compared this to a national and different internationally recommended gene panels (German Hereditary Breast and Ovarian Cancer Consortium HBOC Consortium, ClinGen expert Panel, Genomics England PanelsApp) in regard of diagnostic yield, revealing a diagnostic range of pathogenic variants (class 4/5) from 7.8 to 11.6% depending on the panel evaluated. With the 14 HBOC core gene panel having a diagnostic yield of pathogenic variants (class 4/5) of 10.8%. Additionally, 66 (1%) pathogenic variants (ACMG/AMP class 4 or 5) were found in genes outside the 14 HBOC core gene set (secondary findings) that would have been missed with the restriction to the analysis of HBOC genes. Furthermore, we evaluated a workflow for a periodic re-evaluation of variants of uncertain clinical significance (VUS) for the improvement of clinical validity of germline genetic testing.
Collapse
Affiliation(s)
- Jan Henkel
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
| | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
| | | | | | | | | | | | - Angela Abicht
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, München, Germany
| | - Verena Steinke-Lange
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität, München, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, München, Germany.
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität, München, Germany.
| |
Collapse
|
39
|
Pinto E Vairo F, Kemppainen JL, Vitek CRR, Whalen DA, Kolbert KJ, Sikkink KJ, Kroc SA, Kruisselbrink T, Shupe GF, Knudson AK, Burke EM, Loftus EC, Bandel LA, Prochnow CA, Mulvihill LA, Thomas B, Gable DM, Graddy CB, Garzon GGM, Ekpoh IU, Porquera EMC, Fervenza FC, Hogan MC, El Ters M, Warrington KJ, Davis JM, Koster MJ, Orandi AB, Basiaga ML, Vella A, Kumar S, Creo AL, Lteif AN, Pittock ST, Tebben PJ, Abate EG, Joshi AY, Ristagno EH, Patnaik MS, Schimmenti LA, Dhamija R, Sabrowsky SM, Wierenga KJ, Keddis MT, Samadder NJJ, Presutti RJ, Robinson SI, Stephens MC, Roberts LR, Faubion WA, Driscoll SW, Wong-Kisiel LC, Selcen D, Flanagan EP, Ramanan VK, Jackson LM, Mauermann ML, Ortega VE, Anderson SA, Aoudia SL, Klee EW, McAllister TM, Lazaridis KN. Implementation of genomic medicine for rare disease in a tertiary healthcare system: Mayo Clinic Program for Rare and Undiagnosed Diseases (PRaUD). J Transl Med 2023; 21:410. [PMID: 37353797 PMCID: PMC10288779 DOI: 10.1186/s12967-023-04183-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/05/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND In the United States, rare disease (RD) is defined as a condition that affects fewer than 200,000 individuals. Collectively, RD affects an estimated 30 million Americans. A significant portion of RD has an underlying genetic cause; however, this may go undiagnosed. To better serve these patients, the Mayo Clinic Program for Rare and Undiagnosed Diseases (PRaUD) was created under the auspices of the Center for Individualized Medicine (CIM) aiming to integrate genomics into subspecialty practice including targeted genetic testing, research, and education. METHODS Patients were identified by subspecialty healthcare providers from 11 clinical divisions/departments. Targeted multi-gene panels or custom exome/genome-based panels were utilized. To support the goals of PRaUD, a new clinical service model, the Genetic Testing and Counseling (GTAC) unit, was established to improve access and increase efficiency for genetic test facilitation. The GTAC unit includes genetic counselors, genetic counseling assistants, genetic nurses, and a medical geneticist. Patients receive abbreviated point-of-care genetic counseling and testing through a partnership with subspecialty providers. RESULTS Implementation of PRaUD began in 2018 and GTAC unit launched in 2020 to support program expansion. Currently, 29 RD clinical indications are included in 11 specialty divisions/departments with over 142 referring providers. To date, 1152 patients have been evaluated with an overall solved or likely solved rate of 17.5% and as high as 66.7% depending on the phenotype. Noteworthy, 42.7% of the solved or likely solved patients underwent changes in medical management and outcome based on genetic test results. CONCLUSION Implementation of PRaUD and GTAC have enabled subspecialty practices advance expertise in RD where genetic counselors have not historically been embedded in practice. Democratizing access to genetic testing and counseling can broaden the reach of patients with RD and increase the diagnostic yield of such indications leading to better medical management as well as expanding research opportunities.
Collapse
Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Jennifer L Kemppainen
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Carolyn R Rohrer Vitek
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Denise A Whalen
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kayla J Kolbert
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kaitlin J Sikkink
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Sarah A Kroc
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Teresa Kruisselbrink
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Gabrielle F Shupe
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Alyssa K Knudson
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Elizabeth M Burke
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Elle C Loftus
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Lorelei A Bandel
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Lindsay A Mulvihill
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Dale M Gable
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Courtney B Graddy
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | | | - Idara U Ekpoh
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | | | | | - Marie C Hogan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Mireille El Ters
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | - John M Davis
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | | | - Amir B Orandi
- Department of Pediatric Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Matthew L Basiaga
- Department of Pediatric Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Adrian Vella
- Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Seema Kumar
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ana L Creo
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Aida N Lteif
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Siobhan T Pittock
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Peter J Tebben
- Division of Pediatric Endocrinology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Avni Y Joshi
- Division of Pediatric Allergy and Immunology, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth H Ristagno
- Division of Pediatric Infectious Diseases, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Mrinal S Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Phoenix, AZ, USA
| | | | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA
| | - Mira T Keddis
- Division of Nephrology, Mayo Clinic, Scottsdale, AZ, USA
| | | | | | | | - Michael C Stephens
- Department of Pediatric Gastroenterology, Mayo Clinic, Rochester, MN, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sherilyn W Driscoll
- Division of Pediatric Rehabilitation Medicine, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | | | - Duygu Selcen
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | - Victor E Ortega
- Division of Respiratory Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Sarah A Anderson
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Tammy M McAllister
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
40
|
Subbiah V, Kurzrock R. Universal Germline and Tumor Genomic Testing Needed to Win the War Against Cancer: Genomics Is the Diagnosis. J Clin Oncol 2023; 41:3100-3103. [PMID: 36930859 PMCID: PMC10256401 DOI: 10.1200/jco.22.02833] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/08/2023] [Accepted: 02/13/2023] [Indexed: 03/19/2023] Open
Affiliation(s)
- Vivek Subbiah
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Razelle Kurzrock
- Department of Medicine, Medical College of Wisconsin Cancer Center and Genome Sciences and Precision Medicine Center, Milwaukee, WI
- WIN Consortium, Paris, France
| |
Collapse
|
41
|
Fife JD, Cassa CA. Estimating clinical risk in gene regions from population sequencing cohort data. Am J Hum Genet 2023; 110:940-949. [PMID: 37236177 PMCID: PMC10257006 DOI: 10.1016/j.ajhg.2023.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
While pathogenic variants can significantly increase disease risk, it is still challenging to estimate the clinical impact of rare missense variants more generally. Even in genes such as BRCA2 or PALB2, large cohort studies find no significant association between breast cancer and rare missense variants collectively. Here, we introduce REGatta, a method to estimate clinical risk from variants in smaller segments of individual genes. We first define these regions by using the density of pathogenic diagnostic reports and then calculate the relative risk in each region by using over 200,000 exome sequences in the UK Biobank. We apply this method in 13 genes with established roles across several monogenic disorders. In genes with no significant difference at the gene level, this approach significantly separates disease risk for individuals with rare missense variants at higher or lower risk (BRCA2 regional model OR = 1.46 [1.12, 1.79], p = 0.0036 vs. BRCA2 gene model OR = 0.96 [0.85, 1.07] p = 0.4171). We find high concordance between these regional risk estimates and high-throughput functional assays of variant impact. We compare our method with existing methods and the use of protein domains (Pfam) as regions and find REGatta better identifies individuals at elevated or reduced risk. These regions provide useful priors and are potentially useful for improving risk assessment for genes associated with monogenic diseases.
Collapse
Affiliation(s)
- James D Fife
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher A Cassa
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
42
|
Kral J, Jelinkova S, Zemankova P, Vocka M, Borecka M, Cerna L, Cerna M, Dostalek L, Duskova P, Foretova L, Havranek O, Horackova K, Hovhannisyan M, Chvojka S, Kalousova M, Kosarova M, Koudova M, Krutilkova V, Machackova E, Nehasil P, Novotny J, Otahalova B, Puchmajerova A, Safarikova M, Slama J, Stranecky V, Subrt I, Tavandzis S, Zikan M, Zima T, Soukupova J, Kleiblova P, Kleibl Z, Janatova M. Germline multigene panel testing of patients with endometrial cancer. Oncol Lett 2023; 25:216. [PMID: 37153042 PMCID: PMC10157349 DOI: 10.3892/ol.2023.13802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/03/2023] [Indexed: 05/09/2023] Open
Abstract
Endometrial cancer (EC) is the most common gynecological malignancy in developed countries. The present study aimed to determine the frequency of germline pathogenic variants (PV) in patients with EC. In this multicenter retrospective cohort study, germline genetic testing (GGT) was performed in 527 patients with EC using a next generation sequencing panel targeting 226 genes, including 5 Lynch syndrome (LS) and 14 hereditary breast and ovarian cancer (HBOC) predisposition genes, and 207 candidate predisposition genes. Gene-level risks were calculated using 1,662 population-matched controls (PMCs). Patients were sub-categorized to fulfill GGT criteria for LS, HBOC, both or none. A total of 60 patients (11.4%) carried PV in LS (5.1%) and HBOC (6.6%) predisposition genes, including two carriers of double PV. PV in LS genes conferred a significantly higher EC risk [odds ratio (OR), 22.4; 95% CI, 7.8-64.3; P=1.8×10-17] than the most frequently altered HBOC genes BRCA1 (OR, 3.9; 95% CI, 1.6-9.5; P=0.001), BRCA2 (OR, 7.4; 95% CI, 1.9-28.9; P=0.002) and CHEK2 (OR, 3.2; 95% CI, 1.0-9.9; P=0.04). Furthermore, >6% of patients with EC not fulfilling LS or HBOC GGT indication criteria carried a PV in a clinically relevant gene. Carriers of PV in LS genes had a significantly lower age of EC onset than non-carriers (P=0.01). Another 11.0% of patients carried PV in a candidate gene (the most frequent were FANCA and MUTYH); however, their individual frequencies did not differ from PMCs (except for aggregated frequency of loss-of-function variants in POLE/POLD1; OR, 10.44; 95% CI, 1.1-100.5; P=0.012). The present study demonstrated the importance of GGT in patients with EC. The increased risk of EC of PV carriers in HBOC genes suggests that the diagnosis of EC should be included in the HBOC GGT criteria.
Collapse
Affiliation(s)
- Jan Kral
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Sandra Jelinkova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Petra Zemankova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague 120 00, Czech Republic
| | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Marianna Borecka
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Leona Cerna
- Center for Medical Genetics and Reproductive Medicine, Gennet, Prague 170 00, Czech Republic
| | - Marta Cerna
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Lukas Dostalek
- Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Petra Duskova
- Laboratory of Molecular Genetics, Hospital Ceske Budejovice, Ceske Budejovice 370 00, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno 656 53, Czech Republic
| | - Ondrej Havranek
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
- BIOCEV (Biotechnology and Biomedicine Center of The Czech Academy of Sciences and Charles University), First Faculty of Medicine, Charles University, Prague 252 50, Czech Republic
| | - Klara Horackova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Milena Hovhannisyan
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Stepan Chvojka
- Center for Medical Genetics and Reproductive Medicine, Gennet, Prague 170 00, Czech Republic
| | - Marta Kalousova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Marcela Kosarova
- Department of Medical Genetics, Pronatal, Prague 140 00, Czech Republic
| | - Monika Koudova
- Center for Medical Genetics and Reproductive Medicine, Gennet, Prague 170 00, Czech Republic
| | - Vera Krutilkova
- Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, Novy Jicin 741 00, Czech Republic
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno 656 53, Czech Republic
| | - Petr Nehasil
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague 120 00, Czech Republic
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Jan Novotny
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Barbora Otahalova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague 120 00, Czech Republic
| | - Alena Puchmajerova
- Center for Medical Genetics and Reproductive Medicine, Gennet, Prague 170 00, Czech Republic
| | - Marketa Safarikova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Jiri Slama
- Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Viktor Stranecky
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Ivan Subrt
- Department of Medical Genetics, Faculty of Medicine in Pilsen, Charles University and University Hospital Pilsen, Pilsen 323 00, Czech Republic
| | - Spiros Tavandzis
- Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, Novy Jicin 741 00, Czech Republic
| | - Michal Zikan
- Department of Gynecology and Obstetrics, Bulovka University Hospital and First Faculty of Medicine, Charles University, Prague 180 00, Czech Republic
| | - Tomas Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague 120 00, Czech Republic
| | - Marketa Janatova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 120 00, Czech Republic
- Correspondence to: Dr Marketa Janatova, Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Katerinska 1660/32, Prague 120 00, Czech Republic, E-mail:
| |
Collapse
|
43
|
Liang H, Zhu Y, Wu YK. Ampulla of Vater carcinoma: advancement in the relationships between histological subtypes, molecular features, and clinical outcomes. Front Oncol 2023; 13:1135324. [PMID: 37274233 PMCID: PMC10233008 DOI: 10.3389/fonc.2023.1135324] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
The incidence of ampulla of Vater carcinoma, a type of periampullary cancer, has been increasing at an annual percentage rate of 0.9%. However, patients with ampulla of Vater carcinoma have quite different prognoses due to the heterogeneities of the tissue origin of this carcinoma. In addition to TNM staging, histological subtypes and molecular features of ampulla of Vater carcinoma are the key factors for predicting the clinical outcomes of patients. Fortunately, with the development of testing technology, information on the histological subtypes and molecular features of ampulla of Vater carcinoma is increasingly being analyzed in-depth. Patients with the pancreaticobiliary subtype have shorter survival times. In immunohistochemical examination, high cutoff values of positive MUC1 staining can be used to accurately predict the outcome of patients. Mutant KRAS, TP53, negative SMAD4 expression, and microsatellite stability are related to poor prognosis, while the clinical value of BRCA1/BRCA2 mutations is limited for prognosis. Testing the histological subtypes and molecular characteristics of ampulla of Vater carcinoma not only is the key to prognosis analysis but also provides extra information for targeted treatment to improve the clinical outcomes of patients.
Collapse
|
44
|
Kwong A, Ho CYS, Luk WP, Fung LH, Au CH, Ma ESK. Effect on Germline Mutation Rate in a High-Risk Chinese Breast Cancer Cohort after Compliance with The National Comprehensive Cancer Network (NCCN) 2023 v.1 Testing Criteria. Cancers (Basel) 2023; 15:cancers15092635. [PMID: 37174101 PMCID: PMC10177488 DOI: 10.3390/cancers15092635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND The National Comprehensive Cancer Network (NCCN) testing criteria for the high-penetrance breast cancer susceptibility genes, specifically BRCA1, BRCA2, CDH1, PALB2, PTEN, and TP53, have been recently modified in 2023 to 2023 v.1. The following criteria have been changed: (1) from a person diagnosed with breast cancer at ≤45 to ≤50; (2) from aged 45-50 of personal breast diagnosis to any age of diagnosis with multiple breast cancers; and (3) from aged ≥51 of personal breast diagnosis to any age of diagnosis with family history listed in NCCN 2022 v.2. METHODS High-risk breast cancer patients (n = 3797) were recruited from the Hong Kong Hereditary Breast Cancer Family Registry between 2007 and 2022. Patients were grouped according to NCCN testing criteria 2023 v.1 and 2022 v.2. A 30-gene panel for hereditary breast cancer was performed. The mutation rates on high-penetrance breast cancer susceptibility genes were compared. RESULTS About 91.2% of the patients met the 2022 v.2 criteria, while 97.5% of the patients met the 2023 v.1 criteria. An extra 6.4% of the patients were included after the revision of the criteria, and 2.5% of the patients did not meet both testing criteria. The germline BRCA1/2 mutation rates for patients meeting the 2022 v.2 and 2023 v.1 criteria were 10.1% and 9.6%, respectively. The germline mutation rates of all 6 high-penetrance genes in these two groups were 12.2% and 11.6%, respectively. Among the additional 242 patients who were included using the new selection criteria, the mutation rates were 2.1% and 2.5% for BRCA1/2 and all 6 high-penetrance genes, respectively. Patients who did not meet both testing criteria were those with multiple personal cancers, a strong family history of cancers not listed in the NCCN, unclear pathology information, or the patient's voluntary intention to be tested. The mutation rates of BRCA1/2 and the 6 high-penetrance genes in these patients were 5.3% and 6.4%, respectively. CONCLUSION This study provided a real-world application of the revision of NCCN guidelines and its effect on the germline mutation rate in the Chinese population. Applying the updated criteria for further genetic investigation would increase the positive detection rate, and potentially more patients would benefit. The balance between the resource and outcome requires careful consideration.
Collapse
Affiliation(s)
- Ava Kwong
- Division of Breast Surgery, Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Cecilia Y S Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Wing-Pan Luk
- Department of Research, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Ling-Hiu Fung
- Department of Research, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Chun-Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| |
Collapse
|
45
|
Al-Sukhun S, Masannat Y, Wegman-Ostrosky T, Shrikhande SV, Manirakiza A, Fadelu T, Rebbeck TR. Germline Testing Around the Globe: Challenges in Different Practice Settings. Am Soc Clin Oncol Educ Book 2023; 43:e390522. [PMID: 37220318 DOI: 10.1200/edbk_390522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Cancer is an increasing global public health burden. Lately, more emphasis has emerged on the importance of heredity in cancer, mostly driven by the introduction of germline genetic variants-directed therapeutics. It is true that 40% of cancer risk is attributed to modifiable environmental and lifestyle factors; still, 16% of cancers could be heritable, accounting for 2.9 of the 18.1 million cases diagnosed worldwide. At least two third of those will be diagnosed in countries with limited resources-low- and middle-income countries, especially where high rates of consanguine marriage and early age at diagnosis are already prevalent. Both are hallmarks of hereditary cancer. This creates a new opportunity for prevention, early detection, and recently therapeutic intervention. However, this opportunity is challenged by many obstacles along the path to addressing germline testing in patients with cancer in the clinic worldwide. Global collaboration and expertise exchange are important to bridge the knowledge gap and facilitate practical implementation. Adapting existing guidelines and prioritization according to local resources are essential to address the unique needs and overcome the unique barriers of each society.
Collapse
Affiliation(s)
| | - Yazan Masannat
- Aberdeen Royal Infirmary, Scotland, United Kingdom
- The University of Aberdeen, Scotland, United Kingdom
| | | | | | | | - Temidayo Fadelu
- Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA
| | - Timothy R Rebbeck
- Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA
- Harvard TH Chan School of Public Health, Boston, MA
| |
Collapse
|
46
|
Tricou EP, Morgan KM, Betts M, Sturm AC. Genetic Testing for Familial Hypercholesterolemia in Clinical Practice. Curr Atheroscler Rep 2023; 25:197-208. [PMID: 37060538 DOI: 10.1007/s11883-023-01094-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2023] [Indexed: 04/16/2023]
Abstract
PURPOSE OF REVIEW Genetic testing has proven utility in identifying and diagnosing individuals with FH. Here we outline the current landscape of genetic testing for FH, recommendations for testing practices and the efforts underway to improve access, availability, and uptake. RECENT FINDINGS Alternatives to the traditional genetic testing and counseling paradigm for FH are being explored including expanding screening programs, testing in primary care and/or cardiology clinics, leveraging electronic communication tools like chatbots, and implementing direct contact approaches to facilitate genetic testing of both probands and at-risk relatives. There is no consensus on if, when, and how genetic testing or accompanying genetic counseling should be provided for FH, though traditional genetic counseling and/or testing in specialty lipid clinics is often recommended in expert statements and professional guidelines. More evidence is needed to determine whether alternative approaches to the implementation of genetic testing for FH may be more effective.
Collapse
Affiliation(s)
| | - Kelly M Morgan
- Genomic Medicine Institute, Geisinger, Danville, PA, USA
| | - Megan Betts
- Genomic Medicine Institute, Geisinger, Danville, PA, USA
- Precision Medicine Center-Medical Group, WellSpan, York, PA, USA
| | | |
Collapse
|
47
|
Hoffman TL, Kershberg H, Goff J, Holmquist KJ, Haque R, Alvarado M. Next-generation universal hereditary cancer screening: implementation of an automated hereditary cancer screening program for patients with advanced cancer undergoing tumor sequencing in a large HMO. Fam Cancer 2023; 22:225-235. [PMID: 36261688 PMCID: PMC10020326 DOI: 10.1007/s10689-022-00317-w] [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: 01/14/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022]
Abstract
Variants in hereditary cancer risk genes are frequently identified following tumor-based DNA sequencing and represent an opportunity to diagnose hereditary cancer. We implemented an automated hereditary cancer screening program in a large HMO for all patients who underwent tumor-based DNA sequencing to identify patients with hereditary cancer and determine if this approach augmented existing genetic counseling approaches driven by personal/family history criteria. Regular automated searches of a centralized tumor DNA variant database were performed for ATM, BRCA1, BRCA2, MLH1, MSH2, MSH6, PALB2, and/or PMS2 variants, and germline hereditary cancer gene panel testing was offered to patients with tumor variants who had never undergone germline testing. Patients completing germline testing due to their tumor DNA test results were considered part of the tumor DNA safety net. Patients previously completing germline testing via traditional genetic counseling and tumor DNA safety net were compared for demographics, tumor type, presence of germline pathogenic/likely pathogenic (P/LP) variant, and whether NCCN criteria were met for hereditary cancer genetic testing. Germline P/LP variants were common in both groups. Patients who received germline testing through traditional genetic counseling were more likely to have cardinal hereditary tumors than the tumor DNA safety net group. Patients identified with hereditary cancer through traditional genetic counseling were more likely to meet NCCN personal/family history criteria for germline testing than the tumor DNA safety net group (99% versus 34%). A universal tumor DNA safety net screen is an important diagnostic strategy which augments traditional genetic counseling approaches based on personal/family history.
Collapse
Affiliation(s)
- Trevor L Hoffman
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA.
| | - Hilary Kershberg
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA
| | - John Goff
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA
| | - Kimberly J Holmquist
- Department of Research & Evaluation, Southern California Permanente Medical Group, Pasadena, CA, USA
| | - Reina Haque
- Department of Research & Evaluation, Southern California Permanente Medical Group, Pasadena, CA, USA
- Dept. of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, 91101, Pasadena, CA, USA
| | - Monica Alvarado
- Department of Regional Genetics, Southern California Permanente Medical Group, Pasadena, CA, USA
| |
Collapse
|
48
|
Huang E, Kalady MF. 45 is the New 50: Demographic Trends in Colorectal Cancer Drive Recent US Screening Guideline Changes. Ann Surg Oncol 2023; 30:1927-1929. [PMID: 36658246 DOI: 10.1245/s10434-022-12986-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/12/2022] [Indexed: 01/20/2023]
Affiliation(s)
- Emily Huang
- Division of Colon and Rectal Surgery, Department of Surgery, The Ohio State University, Columbus, OH, USA.
| | - Matthew F Kalady
- Division of Colon and Rectal Surgery, Department of Surgery, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
49
|
Jones JC, Golafshar MA, Coston TW, Rao R, Wysokinska E, Johnson E, Esplin ED, Nussbaum RL, Heald B, Klint M, Barrus K, Uson PL, Nguyen CC, Colon-Otero G, Bekaii-Saab TS, Dronca R, Kunze KL, Samadder NJ. Universal Genetic Testing vs. Guideline-Directed Testing for Hereditary Cancer Syndromes Among Traditionally Underrepresented Patients in a Community Oncology Program. Cureus 2023; 15:e37428. [PMID: 37181954 PMCID: PMC10173369 DOI: 10.7759/cureus.37428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Background Detection of pathogenic germline variants (PGVs) has implications for cancer screening, prognosis, treatment selection, clinical trial enrollment, and family testing. Published guidelines provide indications for PGV testing, determined by clinical and demographic factors, but their applicability in an ethnically and racially diverse community hospital population is unknown. This study describes the diagnostic and incremental yield of universal multi-gene panel testing in a diverse population in a community cancer practice. Methods We completed a prospective study of proactive germline genetic sequencing among patients with solid tumor malignancies at a community-based oncology practice in downtown Jacksonville, FL, between June 2020 and September 2021. The patients were unselected for cancer type, stage, family history, race/ethnicity, and age. PGVs identified using an 84-gene next-generation sequencing (NGS) tumor genomic testing platform were stratified by penetrance. National Comprehensive Cancer Networks (NCCN) guidelines determined incremental PGV rates. Results Two hundred twenty-three patients were enrolled, with a median age of 63 years, 78.5% female. 32.7% were Black/African American, and 5.4% were Hispanic. 39.9% of patients were commercially insured, Medicare/Medicaid insured 52.5%, and 2.7% were uninsured. The most common cancers in this cohort were breast (61.9%), lung (10.3%), and colorectal (7.2%). Twenty-three patients (10.3%) carried one or more PGVs, and 50.2% carried a variant of uncertain significance (VUS). Though there was no significant difference in the rate of PGVs based on race/ethnicity, African Americans were numerically more likely to have a VUS reported than whites (P=0.059). Eighteen (8.1%) patients had incremental clinically actionable findings that practice guidelines would not have detected, which was higher in non-whites. Conclusions In this racially/ethnically and socioeconomically diverse cohort, universal multi-gene panel testing (MGPT) increased diagnostic yield over targeted guideline-informed testing. Rates of VUS and incremental PGV were higher in non-white populations.
Collapse
Affiliation(s)
| | | | | | - Rohit Rao
- Hematology & Oncology, Mayo Clinic, Jacksonville, USA
| | | | | | | | | | - Brandie Heald
- Medical Affairs, Invitae Corporation, San Francisco, USA
| | | | | | - Pedro L Uson
- Hematology & Oncology, Mayo Clinic, Phoenix, USA
| | | | | | | | - Roxana Dronca
- Hematology & Oncology, Mayo Clinic, Jacksonville, USA
| | | | | |
Collapse
|
50
|
Clinical utility of liquid biopsy and integrative genomic profiling in early-stage and oligometastatic cancer patients treated with radiotherapy. Br J Cancer 2023; 128:857-876. [PMID: 36550207 PMCID: PMC9977775 DOI: 10.1038/s41416-022-02102-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Liquid biopsy and Integrative Genomic Profiling (IGP) are yet to be implemented into routine Radiation Oncology. Here we assess the utility of germline, tumour and circulating cell-free DNA-based genomic analyses for the clinical management of early-stage and oligometastatic cancer patients treated by precision radiotherapy. METHODS We performed germline, tissue- and liquid biopsy NGS panels on 50 early-stage/oligometastatic cancer patients undergoing radiotherapy. We also monitored ctDNA variants in serial liquid biopsies collected during radiotherapy and follow-up and evaluated the clinical utility of such comprehensive approach. RESULTS The integration of different genomic studies revealed that only 1/3 of the liquid biopsy variants are of tumour origin. Altogether, 55 tumour variants (affecting 3/4 of the patients) were considered potentially actionable (for treatment and prognosis), whereas potential follow-up biomarkers were identified in all cases. Germline cancer-predisposing variants were present in three patients, which would have not been eligible for hereditary cancer testing according to clinical guidelines. The presence of detectable ctDNA variants before radiotherapy was associated with progression-free survival both in oligometastatic patients and in those with early-stage. CONCLUSIONS IGP provides both valuable and actionable information for personalised decision-making in Radiation Oncology.
Collapse
|