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Azuelos C, Marquis MA, Laberge AM. A systematic review of the assessment of the clinical utility of genomic sequencing: Implications of the lack of standard definitions and measures of clinical utility. Eur J Med Genet 2024; 68:104925. [PMID: 38432472 DOI: 10.1016/j.ejmg.2024.104925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/31/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE Exome sequencing (ES) and genome sequencing (GS) are diagnostic tests for rare genetic diseases. Studies report clinical utility of ES/GS. The goal of this systematic review is to establish how clinical utility is defined and measured in studies evaluating the impacts of ES/GS results for pediatric patients. METHODS Relevant articles were identified in PubMed, Medline, Embase, and Web of Science. Eligible studies assessed clinical utility of ES/GS for pediatric patients published before 2021. Other relevant articles were added based on articles' references. Articles were coded to assess definitions and measures of clinical utility. RESULTS Of 1346 articles, 83 articles met eligibility criteria. Clinical utility was not clearly defined in 19% of studies and 92% did not use an explicit measure of clinical utility. When present, definitions of clinical utility diverged from recommended definitions and varied greatly, from narrow (diagnostic yield of ES/GS) to broad (including decisions about withdrawal of care/palliative care and/or impacts on other family members). CONCLUSION Clinical utility is used to guide policy and practice decisions about test use. The lack of a standard definition of clinical utility of ES/GS may lead to under- or overestimations of clinical utility, complicating policymaking and raising ethical issues.
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Affiliation(s)
- Claudia Azuelos
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
| | - Marc-Antoine Marquis
- Palliative Care, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Anne-Marie Laberge
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
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2
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Slavotinek A, Prasad H, Outram S, Scollon S, Rego S, Yip T, Hoban H, Foreman KM, Kelley W, Finnila C, Berg J, Murali P, Bonini KE, Martin LJ, Hott A. Information-seeking preferences in diverse patients receiving a genetic testing result in the Clinical Sequencing Evidence-Generating Research (CSER) study. Genet Med 2023; 25:100899. [PMID: 37212252 PMCID: PMC10524447 DOI: 10.1016/j.gim.2023.100899] [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: 07/19/2022] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 05/23/2023] Open
Abstract
PURPOSE Accurate and understandable information after genetic testing is critical for patients, family members, and professionals alike. METHODS As part of a cross-site study from the Clinical Sequencing Evidence-Generating Research consortium, we investigated the information-seeking practices among patients and family members at 5 to 7 months after genetic testing results disclosure, assessing the perceived utility of a variety of information sources, such as family and friends, health care providers, support groups, and the internet. RESULTS We found that individuals placed a high value on information obtained from genetics professionals and health care workers, independent of genetic testing result case classifications as positive, inconclusive, or negative. The internet was also highly utilized and ranked. Study participants rated some information sources as more useful for positive results compared with inconclusive or negative outcomes, emphasizing that it may be difficult to identify helpful information for individuals receiving an uncertain or negative result. There were few data from non-English speakers, highlighting the need to develop strategies to reach this population. CONCLUSION Our study emphasizes the need for clinicians to provide accurate and comprehensible information to individuals from diverse populations after genetic testing.
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Affiliation(s)
- Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA.
| | - Hannah Prasad
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Simon Outram
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Shannon Rego
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Tiffany Yip
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Hannah Hoban
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Kate M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Jonathan Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Priyanka Murali
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA
| | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lisa J Martin
- Division of Human Genetics Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Adam Hott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
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Shickh S, Mighton C, Uleryk E, Pechlivanoglou P, Bombard Y. The clinical utility of exome and genome sequencing across clinical indications: a systematic review. Hum Genet 2021; 140:1403-1416. [PMID: 34368901 DOI: 10.1007/s00439-021-02331-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022]
Abstract
Exome sequencing and genome sequencing have the potential to improve clinical utility for patients undergoing genetic investigations. However, evidence of clinical utility is limited to pediatric populations; we aimed to fill this gap by conducting a systematic review of the literature on the clinical utility of exome/genome sequencing across disease indications in pediatric and adult populations. MEDLINE, EMBASE and Cochrane Library were searched between 2016 and 2020. Quantitative studies evaluating diagnostic yield were included; other measures of clinical utility such as changes to clinical management were documented if reported. Two reviewers screened, extracted data, and appraised risk of bias. Fifty studies met our inclusion criteria. All studies reported diagnostic yield, which ranged from 3 to 70%, with higher range of yields reported for neurological indications and acute illness ranging from 22 to 68% and 37-70%, respectively. Diagnoses triggered a range of clinical management changes including surveillance, reproductive-risk counseling, and identifying at-risk relatives in 4-100% of patients, with higher frequencies reported for acute illness ranging from 67 to 95%. The frequency of variants of uncertain significance ranged from 5 to 85% across studies with a potential trend of decreasing frequency over time and higher rates identified in patients of non-European ancestry. This review provides evidence for a higher range of diagnostic yield of exome/genome sequencing compared to standard genetic tests, particularly in neurological and acute indications. However, we identified significant heterogeneity in study procedures and outcomes, precluding a meaningful meta-analysis and certainty in the evidence available for decision-making. Future research that incorporates a comprehensive and consistent approach in capturing clinical utility of exome/genome sequencing across broader ancestral groups is necessary to improve diagnostic accuracy and yield and allow for analysis of trends over time.Prospero registration CRD42019094101.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | | | - Petros Pechlivanoglou
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada. .,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada. .,Li Ka Shing Knowledge Institute of St. Michael's Hospital, University of Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
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Norouzi M, Shafiei M, Abdollahi Z, Miar P, Galehdari H, Emami MH, Zeinalian M, Tabatabaiefar MA. WRN Germline Mutation Is the Likely Inherited Etiology of Various Cancer Types in One Iranian Family. Front Oncol 2021; 11:648649. [PMID: 34164337 PMCID: PMC8215443 DOI: 10.3389/fonc.2021.648649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 05/05/2021] [Indexed: 11/15/2022] Open
Abstract
Background Familial cancers comprise a considerable distribution of colorectal cancers (CRCs), of which only about 5% occurs through well-established hereditary syndromes. It has been demonstrated that deleterious variants at the newly identified cancer-predisposing genes could describe the etiology of undefined familial cancers. Methods The present study aimed to identify the genetic etiology in a 32-year-old man with early onset familial CRC employing several molecular diagnostic techniques. DNA was extracted from tumoral and normal formalin-fixed-paraffin-embedded (FFPE) blocks, and microsatellite instability (MSI) was evaluated. Immunohistochemistry staining of MMR proteins was performed on tumoral FFPE blocks. Next-generation sequencing (NGS), multiplex ligation-dependent amplification (MLPA) assay, and Sanger sequencing were applied on the genomic DNA extracted from peripheral blood. Data analysis was performed using bioinformatics tools. Genetic variants interpretation was based on ACMG. Results MSI analysis indicated MSI-H phenotype, and IHC staining proved no expressions of MSH2 and MSH6 proteins. MLPA and NGS data showed no pathogenic variants in MMR genes. Further analysis of NGS data revealed a candidate WRN frameshift variant (p.R389Efs*3), which was validated with Sanger sequencing. The variant was interpreted as pathogenic since it met the criteria based on the ACMG guideline including very strong (PVS1), strong (PS3), and moderate (PM2). Conclusion WRN is a DNA helicase participating in DNA repair pathways to sustain genomic stability. WRN deficient function may contribute to CRC development that is valuable for further investigation as a candidate gene in hereditary cancer syndrome diagnosis.
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Affiliation(s)
- Mahnaz Norouzi
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Shafiei
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Zeinab Abdollahi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Paniz Miar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Hasan Emami
- Department of Gastroenterology, Poursina Hakim Digestive Disease Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehrdad Zeinalian
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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5
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Niu X, Amendola LM, Hart R, Bennette CS, Heagerty P, Horike-Pyne M, Trinidad SB, Rosenthal EA, Comstock B, Nefcy C, Hisama FM, Bennett RL, Grady WM, Gallego CJ, Tarczy-Hornoch P, Fullerton SM, Burke W, Regier DA, Dorschner MO, Shirts BH, Robertson PD, Nickerson DA, Patrick DL, Jarvik GP, Veenstra DL. Clinical exome sequencing vs. usual care for hereditary colorectal cancer diagnosis: A pilot comparative effectiveness study. Contemp Clin Trials 2019; 84:105820. [PMID: 31400517 PMCID: PMC6741782 DOI: 10.1016/j.cct.2019.105820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/26/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Clinical exome sequencing (CES) provides the advantage of assessing genetic variation across the human exome compared to a traditional stepwise diagnostic approach or multi-gene panels. Comparative effectiveness research methods offer an approach to better understand the patient-centered and economic outcomes of CES. PURPOSE To evaluate CES compared to usual care (UC) in the diagnostic work-up of inherited colorectal cancer/polyposis (CRCP) in a randomized controlled trial (RCT). METHODS The primary outcome was clinical sensitivity for the diagnosis of inherited CRCP; secondary outcomes included psychosocial outcomes, family communication, and healthcare resource utilization. Participants were surveyed 2 and 4 weeks after results return and at 3-month intervals up to 1 year. RESULTS Evolving outcome measures and standard of care presented critical challenges. The majority of participants in the UC arm received multi-gene panels [94.73%]. Rates of genetic findings supporting the diagnosis of hereditary CRCP were 7.5% [7/93] vs. 5.4% [5/93] in the CES and UC arms, respectively (P = 0.28). Differences in privacy concerns after receiving CRCP results were identified (0.88 in UC vs 0.38 in CES, P = 0.05); however, healthcare resource utilization, family communication and psychosocial outcomes were similar between the two arms. More participants with positive results (17.7%) intended to change their life insurance 1 month after the first return visit compared to participants returned a variant of uncertain significance (9.1%) or negative result (4.8%) (P = 0.09). CONCLUSION Our results suggest that CES provides similar clinical benefits to multi-gene panels in the diagnosis of hereditary CRCP.
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Affiliation(s)
- Xin Niu
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Laura M Amendola
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Ragan Hart
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | | | - Patrick Heagerty
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Martha Horike-Pyne
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Susan B Trinidad
- Department of Bioethics and Humanities, University of Washington, Seattle, WA 98195, USA
| | - Elisabeth A Rosenthal
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Bryan Comstock
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Chris Nefcy
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Fuki M Hisama
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Robin L Bennett
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98101, USA
| | - Carlos J Gallego
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; Comparative Health Outcomes, Economics and Policy Institute (CHOICE), University of Washington, Seattle, WA 98195, USA
| | - Peter Tarczy-Hornoch
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington, Seattle, WA 98195, USA
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA 98195, USA
| | - Dean A Regier
- Canadian Centre for Applied Research in Cancer Control, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Michael O Dorschner
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Peggy D Robertson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Donald L Patrick
- Department of Health Services, University of Washington, Seattle, WA 98195, USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - David L Veenstra
- Comparative Health Outcomes, Economics and Policy Institute (CHOICE), University of Washington, Seattle, WA 98195, USA.
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Ali M, Delozier CD, Chaudhary U. BRIP-1 germline mutation and its role in colon cancer: presentation of two case reports and review of literature. BMC MEDICAL GENETICS 2019; 20:75. [PMID: 31064327 PMCID: PMC6505212 DOI: 10.1186/s12881-019-0812-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/23/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Hereditary colon cancer is characterized by the inheritance of an abnormal gene mutation which predisposes to malignancy. Recent advances in genomic medicine have identified mutations in "novel" genes as conferring an increased risk of colorectal cancer. Mutations in the BRIP1 gene (BRCA1 Interacting Protein C- terminal helicase 1) are known to increase the risk of ovarian and breast cancers, but this genes association with colon cancer has not been previously reported. CASE PRESENTATION We describe two patients with colon cancer whose tumor tissue were found to harbor BRIP1 mutations on analysis by next-generation sequencing. These patients were confirmed by analysis of lymphocytes to carry the mutation in the germline as well. CONCLUSIONS These case reports highlight a previously unreported association of BRIP1 germline mutations with colon cancer predisposition.
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Affiliation(s)
- Mir Ali
- San Francisco-Fresno (UCSF Fresno), University of California, 155 N Fresno St, Fresno, CA, 93701, USA.
| | - Celia Dawn Delozier
- San Francisco-Fresno (UCSF Fresno), University of California, 155 N Fresno St, Fresno, CA, 93701, USA
| | - Uzair Chaudhary
- San Francisco-Fresno (UCSF Fresno), University of California, 155 N Fresno St, Fresno, CA, 93701, USA
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