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Hahn E, Mighton C, Fisher Y, Wong A, Di Gioacchino V, Watkins N, Mayers J, Bombard Y, Charames GS, Lerner-Ellis J. Variant classification changes over time in the clinical molecular diagnostic laboratory setting. J Med Genet 2024:jmg-2023-109772. [PMID: 38806232 DOI: 10.1136/jmg-2023-109772] [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: 11/20/2023] [Accepted: 05/12/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND Variant classification in the setting of germline genetic testing is necessary for patients and their families to receive proper care. Variants are classified as pathogenic (P), likely pathogenic (LP), uncertain significance (VUS), likely benign (LB) and benign (B) using the standards and guidelines recommended by the American College of Medical Genetics and the Association for Molecular Pathology, with modifications for specific genes. As the literature continues to rapidly expand, and evidence continues to accumulate, prior classifications can be updated accordingly. In this study, we aim to characterise variant reclassifications in Ontario. METHODS DNA samples from patients seen at hereditary cancer clinics in Ontario from January 2012 to April 2022 were submitted for testing. Patients met provincial eligibility criteria for testing for hereditary cancer syndromes or polycystic kidney disease. Reclassification events were determined to be within their broader category of significance (B to LB or vice versa, or P to LP or vice versa) or outside of their broader category as significance (ie, significant reclassifications from B/LB or VUS or P/LP, from P/LP to VUS or B/LB, or from VUS to any other category). RESULTS Of the 8075 unique variants included in this study, 23.7% (1912) of variants were reassessed, and 7.2% (578) of variants were reclassified. Of these, 351 (60.7%) variants were reclassified outside of their broader category of significance. Overall, the final classification was significantly different for 336 (58.1%) variants. Importantly, most reclassified variants were downgraded to a more benign classification (n=245; 72.9%). Of note, most reclassified VUS was downgraded to B/LB (n=233; 84.7%). CONCLUSIONS The likelihood for reclassification of variants on reassessment is high. Most reclassified variants were downgraded to a more benign classification. Our findings highlight the importance of periodic variant reassessment to ensure timely and appropriate care for patients and their families.
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Affiliation(s)
- Elan Hahn
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Genomics Health Services Research Program, St Michael's Hospital Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Yael Fisher
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Andrew Wong
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Vanessa Di Gioacchino
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Watkins
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Justin Mayers
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, St Michael's Hospital Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - George S Charames
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
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Matoy EJ, Plowman JN, Watson CJ, Belshan MA, Blue EE, Huff CD, Stessman HAF. In vitro data suggest a role for PMS2 Kozak sequence mutations in Lynch syndrome risk. HGG ADVANCES 2024; 5:100298. [PMID: 38654521 PMCID: PMC11087717 DOI: 10.1016/j.xhgg.2024.100298] [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: 04/10/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024] Open
Abstract
Lynch syndrome (LS) is the most common hereditary cancer syndrome. Heterozygous loss-of-function variants in PMS2 are linked to LS. While these variants are not directly cancer causing, reduced PMS2 function results in the accumulation of somatic variants and increased cancer risk over time due to DNA mismatch repair dysfunction. It is reasonable that other types of genetic variation that impact the expression of PMS2 may also contribute to cancer risk. The Kozak sequence is a highly conserved translation initiation motif among higher eukaryotes and is defined as the nine base pairs upstream of the translation start codon through the first four bases of the translated sequence (5'-[GTT]GCATCCATGG-3'; human PMS2: NM_000535.7). While Kozak sequence variants in PMS2 have been reported in ClinVar in patients with suspected hereditary cancer, all variants upstream of the translation start site are currently classified as variants of undetermined significance (VUSs). We hypothesized that variants significantly disrupting the Kozak sequence of PMS2 would decrease PMS2 protein expression, contributing to increased cancer risk over time. Using a dual-luciferase reporter plasmid and site-directed mutagenesis, we generated the wild-type human PMS2 and the ClinVar VUSs within the PMS2 Kozak sequence. Besides the c.1A>C variant, which is already known to be pathogenic, we implicate six additional variants as American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) pathogenic supporting (PP) variants and classify ten as benign supporting (BP). In summary, we present a method developed for the classification of human PMS2 Kozak sequence variants that can contribute to the re-classification of VUSs identified in patients.
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Affiliation(s)
- Evanjalina J Matoy
- Department of Pharmacology and Neuroscience, Creighton University, Omaha, NE 68178, USA
| | - Jocelyn N Plowman
- Department of Pharmacology and Neuroscience, Creighton University, Omaha, NE 68178, USA
| | - Cynthia J Watson
- Creighton University Core Facilities, Creighton University, Omaha, NE 68178, USA
| | - Michael A Belshan
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178, USA
| | - Elizabeth E Blue
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA; Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute, Seattle, WA 98195, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Holly A F Stessman
- Department of Pharmacology and Neuroscience, Creighton University, Omaha, NE 68178, USA; Creighton University Core Facilities, Creighton University, Omaha, NE 68178, USA.
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3
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Chow RD, Parikh RB, Nathanson KL. Real-world evaluation of deep learning algorithms to classify functional pathogenic germline variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24305402. [PMID: 38633773 PMCID: PMC11023677 DOI: 10.1101/2024.04.05.24305402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Deep learning models for variant pathogenicity prediction can recapitulate expert-curated annotations, but their performance remains unexplored on actual disease phenotypes in a real-world setting. Here, we apply three state-of-the-art pathogenicity prediction models to classify hereditary breast cancer gene variants in the UK Biobank. Predicted pathogenic variants in BRCA1, BRCA2 and PALB2, but not ATM and CHEK2, were associated with increased breast cancer risk. We explored gene-specific score thresholds for variant pathogenicity, finding that they could improve model performance. However, when specifically tasked with classifying variants of uncertain significance, the deep learning models were generally of limited clinical utility.
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Affiliation(s)
- Ryan D Chow
- Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Ravi B Parikh
- Division of Health Policy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Philadelphia, PA, USA
- Division of Hematology and Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Katherine L Nathanson
- Basser Center for BRCA, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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4
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Agaoglu NB, Unal B, Hayes CP, Walker M, Ng OH, Doganay L, Can ND, Rana HQ, Ghazani AA. Genomic disparity impacts variant classification of cancer susceptibility genes in Turkish breast cancer patients. Cancer Med 2024; 13:e6852. [PMID: 38308423 PMCID: PMC10905328 DOI: 10.1002/cam4.6852] [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: 05/20/2023] [Revised: 11/23/2023] [Accepted: 12/10/2023] [Indexed: 02/04/2024] Open
Abstract
OBJECTIVE Turkish genome is underrepresented in large genomic databases. This study aims to evaluate the effect of allele frequency in the Turkish population in determining the clinical utility of germline findings in breast cancer, including invasive lobular carcinoma (ILC), mixed invasive ductal and lobular carcinoma (IDC-L), and ductal carcinoma (DC). METHODS Two clinic-based cohorts from the Umraniye Research and Training Hospital (URTH) were used in this study: a cohort consisting of 132 women with breast cancer and a non-cancer cohort consisting of 492 participants. The evaluation of the germline landscape was performed by analysis of 27 cancer genes. The frequency and type of variants in the breast cancer cohort were compared to those in the non-cancer cohort to investigate the effect of population genetics. The variant allele frequencies in Turkish Variome and gnomAD were statistically evaluated. RESULTS The genetic analysis identified 121 variants in the breast cancer cohort (actionable = 32, VUS = 89) and 223 variants in the non-cancer cohort (actionable = 25, VUS = 188). The occurrence of 21 variants in both suggested a possible genetic population effect. Evaluation of allele frequency of 121 variants from the breast cancer cohort showed 22% had a significantly higher value in Turkish Variome compared to gnomAD (p < 0.0001, 95% CI) with a mean difference of 60 times (ranging from 1.37-354.4). After adjusting for variant allele frequency using the ancestry-appropriate database, 6.7% (5/75) of VUS was reclassified to likely benign. CONCLUSION To our knowledge, this is the first study of population genetic effects in breast cancer subtypes in Turkish women. Our findings underscore the need for a large genomic database representing Turkish population-specific variants. It further highlights the significance of the ancestry-appropriate population database for accurate variant assessment in clinical settings.
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Affiliation(s)
- Nihat B. Agaoglu
- Department of Medical Genetics, Division of Cancer GeneticsUmraniye Training and Research HospitalIstanbulTurkey
| | - Busra Unal
- Department of Medical Genetics, Division of Cancer GeneticsUmraniye Training and Research HospitalIstanbulTurkey
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
| | - Connor P. Hayes
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
| | - McKenzie Walker
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
| | - Ozden Hatirnaz Ng
- Department of Medical Biology, School of MedicineAcibadem UniversityIstanbulTurkey
| | - Levent Doganay
- Department of Medical Genetics, Division of Cancer GeneticsUmraniye Training and Research HospitalIstanbulTurkey
| | - Nisan D. Can
- Department of Molecular Biology Genetics and BiotechnologyIstanbul Technical UniversityIstanbulTurkey
| | - Huma Q. Rana
- Division of Cancer Genetics and PreventionDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of MedicineBrigham and Women's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Arezou A. Ghazani
- Division of GeneticsBrigham and Women's HospitalBostonMassachusettsUSA
- Department of MedicineBrigham and Women's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
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5
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Knerr S, Guo B, Wernli KJ, Mittendorf KF, Feigelson HS, Gilmore MJ, Jarvik GP, Kauffman TL, Keast E, Liles EG, Lynch FL, Muessig KR, Okuyama S, Veenstra DL, Zepp JM, Wilfond BS, Devine B, Goddard KAB. Longitudinal adherence to breast cancer surveillance following cancer genetic testing in an integrated health care system. Breast Cancer Res Treat 2023; 201:461-470. [PMID: 37470892 PMCID: PMC10503958 DOI: 10.1007/s10549-023-07007-w] [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: 04/20/2023] [Accepted: 05/31/2023] [Indexed: 07/21/2023]
Abstract
PURPOSE Screening with mammography and breast magnetic resonance imaging (MRI) is an important risk management strategy for individuals with inherited pathogenic variants (PVs) in genes associated with increased breast cancer risk. We describe longitudinal screening adherence in individuals who underwent cancer genetic testing as part of usual care in a vertically integrated health system. METHODS We determined the proportion time covered (PTC) by annual mammography and breast MRI for individuals with PVs in TP53, BRCA1, BRCA2, PALB2, NF1, CHEK2, and ATM. We determined time covered by biennial mammography beginning at age 50 years for individuals who received negative results, uncertain results, or with PVs in genes without specific breast cancer screening recommendations. RESULTS One hundred and forty individuals had PVs in TP53, BRCA1, BRCA2, PALB2, NF1, CHEK2, or ATM. Among these individuals, average PTC was 48% (range 0-99%) for annual screening mammography and 34% (range 0-100%) for annual breast MRI. Average PTC was highest for individuals with PVs in CHEK2 (N = 14) and lowest for individuals with PVs in TP53 (N = 3). Average PTC for biennial mammography (N = 1,027) was 49% (0-100%). CONCLUSION Longitudinal screening adherence in individuals with PVs in breast cancer associated genes, as measured by the proportion of time covered, is low; adherence to annual breast MRI falls below that of annual mammography. Additional research should examine screening behavior in individuals with PVs in breast cancer associated genes with a goal of developing interventions to improve adherence to recommended risk management.
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Affiliation(s)
- Sarah Knerr
- Department of Health Systems and Population Health, School of Public Health, University of Washington, Box 351621, Seattle, WA, 98195, USA.
| | - Boya Guo
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Karen J Wernli
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Kathleen F Mittendorf
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Marian J Gilmore
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Gail P Jarvik
- Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Tia L Kauffman
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Erin Keast
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | | | - Frances L Lynch
- Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Kristin R Muessig
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Sonia Okuyama
- Denver Health and Hospital Authority, Denver, CO, USA
| | - David L Veenstra
- Department of Pharmacy, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Jamilyn M Zepp
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
| | - Benjamin S Wilfond
- Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Beth Devine
- Department of Health Systems and Population Health, School of Public Health, University of Washington, Box 351621, Seattle, WA, 98195, USA
- Department of Pharmacy, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Katrina A B Goddard
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR, USA
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, USA
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6
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Guo B, Knerr S, Kauffman TL, Mittendorf KF, Keast E, Gilmore MJ, Feigelson HS, Lynch FL, Muessig KR, Okuyama S, Zepp JM, Veenstra DL, Hsu L, Phipps AI, Lindström S, Leo MC, Goddard KAB, Wilfond BS, Devine B. Risk management actions following genetic testing in the Cancer Health Assessments Reaching Many (CHARM) Study: A prospective cohort study. Cancer Med 2023; 12:19112-19125. [PMID: 37644850 PMCID: PMC10557878 DOI: 10.1002/cam4.6485] [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: 06/20/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Genetic testing can identify cancer risk early, enabling prevention and early detection. We describe use of risk management interventions following genetic testing in the Cancer Health Assessment Reaching Many (CHARM) study. CHARM assessed risk and provided genetic testing to low income, low literacy, and other underserved populations that historically face barriers to accessing cancer genetic services. METHODS CHARM was implemented in Kaiser Permanente Northwest (KPNW) and Denver Health (DH) between 2018 and 2020. We identified post-testing screening (mammography, breast MRI, colonoscopy) and surgical (mastectomy, oophorectomy) procedures using electronic health records. We examined utilization in participants who did and did not receive actionable risk management recommendations from study genetic counselors following national guidelines. RESULTS CHARM participants were followed for an average of 15.4 months (range: 0.4-27.8 months) after results disclosure. Less than 2% (11/680) received actionable risk management recommendations (i.e., could be completed in the initial years following testing) based on their test result. Among those who received actionable recommendations, risk management utilization was moderate (54.5%, 6/11 completed any procedure) and varied by procedure (mammogram: 0/3; MRI: 2/4; colonoscopy: 4/5; mastectomy: 1/5; oophorectomy: 0/3). Cancer screening and surgery procedures were rare in participants without actionable recommendations. CONCLUSION Though the number of participants who received actionable risk management recommendations was small, our results suggest that implementing CHARM's risk assessment and testing model increased access to evidence-based genetic services and provided opportunities for patients to engage in recommended preventive care, without encouraging risk management overuse.
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Affiliation(s)
- Boya Guo
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
| | - Sarah Knerr
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
| | - Tia L. Kauffman
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Kathleen F. Mittendorf
- Vanderbilt‐Ingram Cancer CenterVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Erin Keast
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Marian J. Gilmore
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | | | - Frances L. Lynch
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Kristin R. Muessig
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | - Sonia Okuyama
- Division of Oncology, Denver Health and Hospital AuthorityDenverColoradoUSA
| | - Jamilyn M. Zepp
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | - David L. Veenstra
- The Comparative Health Outcomes, Policy, and Economics (CHOICE) Institute, School of PharmacyUniversity of WashingtonSeattleWashingtonUSA
| | - Li Hsu
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- Division of Public Health SciencesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Amanda I. Phipps
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- Division of Public Health SciencesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Sara Lindström
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- Division of Public Health SciencesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Michael C. Leo
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Katrina A. B. Goddard
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | - Benjamin S. Wilfond
- Treuman Katz Center for Pediatric BioethicsSeattle Children's Research InstituteSeattleWashingtonUSA
- Department of Pediatrics, Division of Bioethics and Palliative CareUniversity of WashingtonSeattleWashingtonUSA
| | - Beth Devine
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- The Comparative Health Outcomes, Policy, and Economics (CHOICE) Institute, School of PharmacyUniversity of WashingtonSeattleWashingtonUSA
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7
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Makhnoon S, Davidson E, Shirts B, Arun B, Shete S. Practices and Views of US Oncologists and Genetic Counselors Regarding Patient Recontact After Variant Reclassification: Results of a Nationwide Survey. JCO Precis Oncol 2023; 7:e2300079. [PMID: 37384863 PMCID: PMC10581618 DOI: 10.1200/po.23.00079] [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: 02/16/2023] [Revised: 04/26/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
PURPOSE Over a 5-year or 10-year period, between 6% and 15% of germline cancer genetic variants undergo reclassification. Up-to-date interpretation can clarify a variant's clinical significance and guide patient management. As the frequency of reclassifications increase, the issue of whether, how, when, and which providers should recontact patients with information about reclassification becomes important. However, the field lacks research evidence and definitive guidance from professional organizations about how providers should recontact patients. We compared the perspectives of US oncologists and cancer genetic counselors (GCs) to describe their practices and views regarding recontact. MATERIALS AND METHODS We developed a survey using themes identified from semistructured interviews with oncologists and GCs and administered it in a national sample of oncologists and GCs between July and September 2022. RESULTS In total, 634 respondents completed the survey including 349 oncologists and 285 GCs. On frequency of recontacting patients with reclassified results, 40% of GCs reported recontacting often compared with 12.5% of oncologists. Neither group reported recording patient preference for recontact on electronic medical record (EMR). Both groups agreed that all reclassified variants, even those that do not affect clinical management, should be returned to patients. They also reported that recontact via EMR messages, mailed letters, and phone calls from GC assistants were more suitable for downgrades. By contrast, face-to-face meetings and phone calls were preferred for upgrades. Remarkably, oncologists were more likely to endorse face-to-face return of results and were more likely to endorse return through a nongenetics provider compared to GCs. CONCLUSION These data on current recontact practices and opinions provide a foundation for developing guidelines with explicit recommendations on patient recontact that can help maximize clinical effect while considering provider preferences for recontact within resource-constrained genomic practice settings.
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Affiliation(s)
- Sukh Makhnoon
- Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX
| | - Elenita Davidson
- Department of Behavioral Science, UT MD Anderson Cancer Center, Houston, TTX
| | - Brian Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Banu Arun
- Clinical Cancer Genetics, UT MD Anderson Cancer Center, Houston, TX
| | - Sanjay Shete
- Department of Epidemiology, UT MD Anderson Cancer Center, Houston, TX
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8
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Schick S, Manghelli J, Ludwig KK. The Role of the Surgeon in the Germline Testing of the Newly Diagnosed Breast Cancer Patient. Curr Oncol 2023; 30:4677-4687. [PMID: 37232811 DOI: 10.3390/curroncol30050353] [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: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 05/27/2023] Open
Abstract
For patients with newly diagnosed breast cancer, information regarding hereditary predisposition can influence treatment decisions. From a surgical standpoint, patients with known germline mutations may alter decisions of local therapy to reduce the risk of second breast primaries. This information may also be considered in the choice of adjuvant therapies or eligibility for clinical trials. In recent years, the criteria for the consideration of germline testing in patients with breast cancer has expanded. Additionally, studies have shown a similar prevalence of pathogenic mutations in those patients outside of these traditional criteria, prompting calls for genetic testing for all patients with a history of breast cancer. While data confirms the benefit of counseling by certified genetics professionals, the capacity of genetic counselors may no longer meet the needs of these growing numbers of patients. National societies assert that counseling and testing can be performed by providers with training and experience in genetics. Breast surgeons are well positioned to offer this service, as they receive formal genetics training during their fellowship, manage these patients daily in their practices, and are often the first providers to see patients after their cancer diagnosis.
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Affiliation(s)
- Stephanie Schick
- Department of Surgery, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Joshua Manghelli
- Department of Surgery, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Kandice K Ludwig
- Department of Surgery, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
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9
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Bhat V, Adzhubei IA, Fife JD, Lebo M, Cassa CA. Informing variant assessment using structured evidence from prior classifications (PS1, PM5, and PVS1 sequence variant interpretation criteria). Genet Med 2023; 25:16-26. [PMID: 36305854 DOI: 10.1016/j.gim.2022.09.009] [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: 05/07/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/06/2022] Open
Abstract
PURPOSE This study aimed to explore whether evidence of pathogenicity from prior variant classifications in ClinVar could be used to inform variant interpretation using the American College of Medical Genetics and Genomics/Association for Molecular Pathology clinical guidelines. METHODS We identified distinct single-nucleotide variants (SNVs) that are either similar in location or in functional consequence to pathogenic variants in ClinVar and analyzed evidence in support of pathogenicity using 3 interpretation criteria. RESULTS Thousands of variants, including many in clinically actionable disease genes (American College of Medical Genetics and Genomics secondary findings v3.0), have evidence of pathogenicity from existing variant classifications, accounting for 2.5% of nonsynonymous SNVs within ClinVar. Notably, there are many variants with uncertain or conflicting classifications that cause the same amino acid substitution as other pathogenic variants (PS1, N = 323), variants that are predicted to cause different amino acid substitutions in the same codon as pathogenic variants (PM5, N = 7692), and loss-of-function variants that are present in genes in which many loss-of-function variants are classified as pathogenic (PVS1, N = 3635). Most of these variants have similar computational predictions of pathogenicity and splicing effect as their associated pathogenic variants. CONCLUSION Broadly, for >1.4 million SNVs exome wide, information from previously classified variants could be used to provide evidence of pathogenicity. We have developed a pipeline to identify variants meeting these criteria that may inform interpretation efforts.
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Affiliation(s)
- Vineel Bhat
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ivan A Adzhubei
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - James D Fife
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Matthew Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Boston, MA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Christopher A Cassa
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
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10
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Makhnoon S, Chen M, Levin B, Ensinger M, Mattie KD, Grana G, Shete S, Arun BK, Peterson SK. Use of breast surveillance between women with pathogenic variants and variants of uncertain significance in breast cancer susceptibility genes. Cancer 2022; 128:3709-3717. [PMID: 35996941 PMCID: PMC11160485 DOI: 10.1002/cncr.34429] [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: 05/06/2022] [Revised: 06/22/2022] [Accepted: 07/05/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Use of surveillance mammography and magnetic resonance imaging (MRI) has been understudied among women with variant of uncertain significance (VUS) compared to pathogenic and likely pathogenic variants (P/LP). METHODS Using data from two cancer settings, we calculated use of risk-reducing mastectomy (RRM) and surveillance during each 13-month span after genetic testing up to 6 years afterwards for a cohort of genetically elevated risk women. RESULTS Of 889 women, VUS carriers were less likely to undergo RRM compared to those with P/LP (hazard ratio [HR], 0.17; p = <.001) and high-risk women were more likely to undergo RRM than average-risk women (HR, 3.91; p = .005). Longitudinally, surveillance use among unaffected women decreased from 49.8% in the first year to 31.2% in the sixth year after genetic testing. In comparison, a greater proportion of women with a personal history of breast cancer underwent surveillance, which increased from 59.3% in the first year to 63.6% in the sixth year after genetic testing. Mammography rates did not differ between women with P/LP and VUS within the first 13 months after genetic testing and up to 4 years afterward. Over the first 4 years after genetic testing, women with VUS were less likely to undergo annual MRIs compared to P/LP. CONCLUSION The authors found that VUS, whether in high or moderate penetrance breast cancer susceptibility genes, was associated with lower use of annual breast MRI compared to P/LP variants and equivalent use of annual mammography. These results add important evidence regarding VUS-related breast surveillance.
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Affiliation(s)
- Sukh Makhnoon
- Department of Behavioral Science, UT MD Anderson Cancer Center, Houston, TX
| | - Minxing Chen
- Department of Biostatistics, UT MD Anderson Cancer Center, Houston TX
| | - Brooke Levin
- William G. Rohrer Cancer Genetics Program, Division of Hematology and Medical Oncology, MD Anderson Cancer Center at Cooper University Health Care, Camden, NJ
| | - Megan Ensinger
- OhioHealth Cancer Genetics Program, OhioHealth, Columbus, OH
| | - Kristin D Mattie
- William G. Rohrer Cancer Genetics Program, Division of Hematology and Medical Oncology, MD Anderson Cancer Center at Cooper University Health Care, Camden, NJ
| | - Generosa Grana
- William G. Rohrer Cancer Genetics Program, Division of Hematology and Medical Oncology, MD Anderson Cancer Center at Cooper University Health Care, Camden, NJ
| | - Sanjay Shete
- Division of Cancer Prevention and Population Sciences, UT MD Anderson Cancer Center, Houston TX
| | - Banu K Arun
- Breast Medical Oncology, UT MD Anderson Cancer Center, Houston, TX
| | - Susan K Peterson
- Department of Behavioral Science, UT MD Anderson Cancer Center, Houston, TX
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Vargason AB, Turner CE, Shriver CD, Ellsworth RE. Influence of germline test results on surgical decision making in women with invasive breast cancer. Cancer Genet 2022; 266-267:81-85. [PMID: 35868102 DOI: 10.1016/j.cancergen.2022.07.003] [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: 04/05/2022] [Revised: 06/10/2022] [Accepted: 07/10/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND While therapeutic mastectomy with contralateral prophylactic mastectomy (TM+CPM) and/or bilateral salpingo-oophorectomy (BSO) are recommended for women with pathogenic variants (PV) in some cancer predisposition genes, evidence for the utility of these surgeries for women with PV in other genes currently is insufficient. In conjunction, current guidelines recommend that clinical management should not be influenced by a return of a variant of uncertain significance (VUS). Return of germline test results may, however, influence surgical decision making regardless of current guidelines. We thus evaluated surgical choices amongst a cohort of women with invasive breast cancer who underwent clinical genetic testing. METHODS Germline test results and all surgical procedures were extracted for women who had unilateral invasive breast cancer and had clinical testing before definitive surgery (n = 591). Results were classified as pathogenic/likely pathogenic (PV, 17.1%), VUS (19.5%) or benign/likely benign (63.4%). Data were analyzed using chi-square tests with p<0.05 defining significance. RESULTS Rates of TM+CPM and BSO were not significantly different for women with VUS compared to those with benign findings. Rates of TM+CPM were significantly higher for women with PV in BRCA1 and BRCA2, PALB2, PTEN and TP53, as well in genes with insufficient data to recommend risk-reducing mastectomy. Rates of BSO were significantly higher in women with PV in BRCA1 and BRCA2, PALB2, PTEN and TP53 and BRIP1, RAD51C and RAD51D compared to those with benign findings. CONCLUSION Overall, surgical choices for women with a VUS were more similar to those from women with benign variants than to those with PV, however, in the group with PV in genes for which insufficient evidence exists for the benefit of risk-reducing mastectomy, rates of TM+CPM were high. Thus, while the management of women with VUS is in agreement with ACMG guidelines, patients with mutations in other cancer genes demonstrate a preference for more aggressive breast surgeries.
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Affiliation(s)
- Ashlee B Vargason
- Breast Care Clinic, Department of Surgery, Walter Reed National Military Medical Center, 8901 Rockville Pike, Bethesda, MD 20889, USA.
| | - Clesson E Turner
- National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | - Craig D Shriver
- Murtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, 8901 Rockville Pike, Bethesda, MD 20889, USA; Department of Surgery, Uniformed Services University of the Health Sciences, 8901 Rockville Pike, Bethesda, MD 20889, USA.
| | - Rachel E Ellsworth
- Murtha Cancer Center/Research Program, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, 8901 Rockville Pike, Bethesda, MD 20889, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Dr., Bethesda, MD 20817, USA.
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12
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Burke W, Parens E, Chung WK, Berger SM, Appelbaum PS. The Challenge of Genetic Variants of Uncertain Clinical Significance : A Narrative Review. Ann Intern Med 2022; 175:994-1000. [PMID: 35436152 PMCID: PMC10555957 DOI: 10.7326/m21-4109] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genomic tests expand diagnostic and screening opportunities but also identify genetic variants of uncertain clinical significance (VUSs). Only a minority of VUSs are likely to prove pathogenic when later reassessed, but resolution of the uncertainty is rarely timely. That uncertainty adds complexity to clinical decision making and can result in harms and costs to patients and the health care system, including the time-consuming analysis required to interpret a VUS and the potential for unnecessary treatment and adverse psychological effects. Current efforts to improve variant interpretation will help reduce the scope of the problem, but the high prevalence of rare and novel variants in the human genome points to VUSs as an ongoing challenge. Additional strategies can help mitigate the potential harms of VUSs, including testing protocols that limit identification or reporting of VUSs, subclassification of VUSs according to the likelihood of pathogenicity, routine family-based evaluation of variants, and enhanced counseling efforts. All involve tradeoffs, and the appropriate balance of measures is likely to vary for different test uses and clinical settings. Cross-specialty deliberation and public input could contribute to systematic and broadly supported policies for managing VUSs.
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Affiliation(s)
- Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA, USA
| | | | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sara M. Berger
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul S. Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
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Lou J, Chen H, Huang S, Chen P, Yu Y, Chen F. Update on risk factors and biomarkers of sudden unexplained cardiac death. J Forensic Leg Med 2022; 87:102332. [DOI: 10.1016/j.jflm.2022.102332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/21/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023]
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