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Majeed S, Johnston C, Saeedi S, Mighton C, Rokoszak V, Abbasi I, Grewal S, Aguda V, Kissoondoyal A, Malkin D, Bombard Y. International policies guiding the selection, analysis, and clinical management of secondary findings from genomic sequencing: A systematic review. Am J Hum Genet 2024; 111:2079-2093. [PMID: 39299240 DOI: 10.1016/j.ajhg.2024.08.012] [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: 01/25/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024] Open
Abstract
Secondary findings (SFs) from genomic sequencing can have significant impacts on patient health, yet existing practices guiding their clinical investigation are inconsistent. We systematically reviewed existing SFs policies to identify variations and gaps in guidance. We cataloged and appraised international policies from academic databases (n = 5, inception-02/2022) and international human genetic societies (n = 64; inception-05/2022), across the continuum of SFs selection, analysis, and clinical management. We assessed quality using AGREE-II and interpreted results using qualitative description. Of the 63 SFs policies identified, most pertained to clinical management of SFs (98%; n = 62; primarily consent and disclosure), some guided SFs analysis (60%; n = 38), while fewer mentioned SFs selection (48%; n = 30). Overall, policies recommend (1) identifying clinically actionable, pathogenic variants with high positive predictive values for disease (selection), (2) bioinformatically filtering variants using evidence-informed gene lists (analysis), and (3) discussing with affected individuals the SFs identified, their penetrance, expressivity, medical implications, and management (clinical management). Best practices for SFs variant analysis, clinical validation, and follow-up (i.e., surveillance, treatment, etc.) were minimally described. Upon quality assessment, policies were highly rated for scope and clarity (median score, 69) but were limited by their rigor and applicability (median scores, 27 and 25). Our review represents a comprehensive international synthesis of policy guiding SFs across the continuum of selection, analysis, and clinical management. Our synthesis will help providers navigate critical decision points in SFs investigation, although significant work is needed to address gaps in SFs analysis, clinical validation, and follow-up processes and to support evidence-based practice.
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Affiliation(s)
- Safa Majeed
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christine Johnston
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Saumeh Saeedi
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, 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, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Vanessa Rokoszak
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Ilham Abbasi
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Sonya Grewal
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, ON, Canada; Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Vernie Aguda
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Ashby Kissoondoyal
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - David Malkin
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Pediatrics, Temerty Faculty of Medicine, University of Toronto, 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, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada; Genetics Adviser, Toronto, ON, Canada.
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Flaharty KA, Hu P, Hanchard SL, Ripper ME, Duong D, Waikel RL, Solomon BD. Evaluating large language models on medical, lay-language, and self-reported descriptions of genetic conditions. Am J Hum Genet 2024; 111:1819-1833. [PMID: 39146935 PMCID: PMC11393706 DOI: 10.1016/j.ajhg.2024.07.011] [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: 04/03/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 08/17/2024] Open
Abstract
Large language models (LLMs) are generating interest in medical settings. For example, LLMs can respond coherently to medical queries by providing plausible differential diagnoses based on clinical notes. However, there are many questions to explore, such as evaluating differences between open- and closed-source LLMs as well as LLM performance on queries from both medical and non-medical users. In this study, we assessed multiple LLMs, including Llama-2-chat, Vicuna, Medllama2, Bard/Gemini, Claude, ChatGPT3.5, and ChatGPT-4, as well as non-LLM approaches (Google search and Phenomizer) regarding their ability to identify genetic conditions from textbook-like clinician questions and their corresponding layperson translations related to 63 genetic conditions. For open-source LLMs, larger models were more accurate than smaller LLMs: 7b, 13b, and larger than 33b parameter models obtained accuracy ranges from 21%-49%, 41%-51%, and 54%-68%, respectively. Closed-source LLMs outperformed open-source LLMs, with ChatGPT-4 performing best (89%-90%). Three of 11 LLMs and Google search had significant performance gaps between clinician and layperson prompts. We also evaluated how in-context prompting and keyword removal affected open-source LLM performance. Models were provided with 2 types of in-context prompts: list-type prompts, which improved LLM performance, and definition-type prompts, which did not. We further analyzed removal of rare terms from descriptions, which decreased accuracy for 5 of 7 evaluated LLMs. Finally, we observed much lower performance with real individuals' descriptions; LLMs answered these questions with a maximum 21% accuracy.
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Affiliation(s)
- Kendall A Flaharty
- Medical Genomics Unit, National Human Genome Research Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD 20892, USA.
| | - Ping Hu
- Medical Genomics Unit, National Human Genome Research Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD 20892, USA
| | - Suzanna Ledgister Hanchard
- Medical Genomics Unit, National Human Genome Research Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD 20892, USA
| | - Molly E Ripper
- Medical Genomics Unit, National Human Genome Research Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD 20892, USA
| | - Dat Duong
- Medical Genomics Unit, National Human Genome Research Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD 20892, USA
| | - Rebekah L Waikel
- Medical Genomics Unit, National Human Genome Research Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD 20892, USA
| | - Benjamin D Solomon
- Medical Genomics Unit, National Human Genome Research Institute, National Institutes of Health, 10 Center Dr, Bethesda, MD 20892, USA.
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Shi F, Liu Y, Chen Z, Li D, Yao Y, Zhou M, Zhuo Y, Ma X, Cao D. An integrated approach for improving clinical management of non-obstructive azoospermia. Andrology 2024; 12:1312-1323. [PMID: 38221731 DOI: 10.1111/andr.13587] [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: 05/10/2023] [Revised: 11/06/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND Non-obstructive azoospermia is the most severe form of male infertility. A testicular biopsy is required for the diagnosis of non-obstructive azoospermia, and the causal factors for non-obstructive azoospermia remain unknown. OBJECTIVES To reduce the risk of multiple biopsies and identify factors that contribute to non-obstructive azoospermia, we proposed an integrated approach for the preoperative diagnosis and clinical management of non-obstructive azoospermia by applying the chromosome-spreading technique and whole-exome sequencing. MATERIALS AND METHODS Between July 2020 and December 2022, after ruling out definitive obstructive azoospermia and non-obstructive azoospermia patients with testicular volume < 6 mL, 20 patients with non-obstructive azoospermia who underwent preoperative testicular diagnostic biopsy using testicular sperm aspiration were subjected to retrospective analysis. RESULTS Microscopic examination identified four patients with sperm cells, and 16 without sperm cells. Routine pathological analysis classified one patient as normal spermatogenesis, three as hypospermatogenesis, five as maturation arrest, nine as Sertoli cell-only, and two as unable to judge. With chromosome-spreading technology using routine cell suspension samples for microscopic examination, 18 patient diagnoses were validated, and two patients without a definitive diagnosis were supplemented. Detection of the Y chromosome and a well-organized whole-exome sequencing analysis revealed potential genetic factors. DISCUSSION AND CONCLUSION The full use of testicular biopsy is beneficial for the diagnosis of azoospermia, as it avoids the risk of multiple biopsies. Moreover, in combination with whole-exome sequencing, clinicians can obtain more information regarding the pathogenesis of non-obstructive azoospermia, which may guide treatment.
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Affiliation(s)
- Fu Shi
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong Shenzhen Hospital, Shenzhen, China
| | - Ye Liu
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong Shenzhen Hospital, Shenzhen, China
| | - Zheng Chen
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Dongliang Li
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuanqing Yao
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong Shenzhen Hospital, Shenzhen, China
| | - Meixun Zhou
- Department of Pathology, The University of Hong Kong Shenzhen Hospital, Shenzhen, China
| | - Yumin Zhuo
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xin Ma
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
- Senior Department of Urology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Dandan Cao
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong Shenzhen Hospital, Shenzhen, China
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Furley K, Hunter MF, Fahey M, Williams K. Diagnostic findings and yield of investigations for children with developmental regression. Am J Med Genet A 2024; 194:e63607. [PMID: 38536866 DOI: 10.1002/ajmg.a.63607] [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: 02/28/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 07/05/2024]
Abstract
Childhood conditions that feature developmental regression are poorly understood. Phenotype-genotype characterization and diagnostic yield data are needed to inform clinical decision-making. The aim of this study was to report the conditions featuring developmental regression and assess diagnostic yields of investigations. A retrospective chart review of children presenting with developmental regression to a tertiary pediatric genetic clinic between 2018 and 2021 was performed. Of 99 children, 30% (n = 30) had intellectual disability (ID), 21% (n = 21) were autistic, 39% (n = 39) were autistic with ID, and 9% (n = 9) did not have ID or autism. Thirty-two percent (n = 32) of children received a new diagnosis, including eight molecular findings not previously reported to feature developmental regression. Of the children investigated, exome sequencing (ES) provided the highest diagnostic yield (51.1%, n = 24/47), highest (63.6%, n = 14/22) for children with ID, 50% for autistic children with ID (n = 6/12) and children without autism or ID (n = 3/6), and 14.3% (n = 1/7) for autistic children without ID. We highlight the conditions that feature developmental regression and report on novel phenotypic expansions. The high diagnostic yield of ES, regardless of autism or ID diagnosis, indicates the presence of developmental regression as an opportunity to identify the cause, including for genetic differences not previously reported to include regression.
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Affiliation(s)
- Kirsten Furley
- Department of Paediatrics, Monash University, Melbourne, Australia
- Monash Children's Hospital, Melbourne, Australia
| | - Matthew F Hunter
- Department of Paediatrics, Monash University, Melbourne, Australia
- Monash Genetics, Monash Health, Melbourne, Australia
| | - Michael Fahey
- Department of Paediatrics, Monash University, Melbourne, Australia
- Monash Children's Hospital, Melbourne, Australia
- Neurology, Monash Health, Melbourne, Australia
| | - Katrina Williams
- Department of Paediatrics, Monash University, Melbourne, Australia
- Monash Children's Hospital, Melbourne, Australia
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Hammer-Hansen S, Stoltze U, Bartels E, Hansen TVO, Byrjalsen A, Tybjærg-Hansen A, Juul K, Schmiegelow K, Tfelt J, Bundgaard H, Wadt K, Diness BR. Actionability and familial uptake following opportunistic genomic screening in a pediatric cancer cohort. Eur J Hum Genet 2024; 32:846-857. [PMID: 38740897 PMCID: PMC11220050 DOI: 10.1038/s41431-024-01618-7] [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: 07/04/2023] [Revised: 04/02/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024] Open
Abstract
The care for patients with serious conditions is increasingly guided by genomic medicine, and genomic medicine may equally transform care for healthy individual if genomic population screening is implemented. This study examines the medical impact of opportunistic genomic screening (OGS) in a cohort of patients undergoing comprehensive genomic germline DNA testing for childhood cancer, including the impact on their relatives. Medical actionability and uptake after cascade testing in the period following disclosure of OGS results was quantified. A secondary finding was reported to 19/595 (3.2%) probands primarily in genes related to cardiovascular and lipid disorders. After a mean follow up time of 1.6 years (Interquartile range (IQR): 0.57-1.92 yrs.) only 12 (63%) of these variants were found to be medically actionable. Clinical follow up or treatment was planned in 16 relatives, and as in the probands, the prescribed treatment was primarily betablockers or cholesterol lowering therapy. No invasive procedures or implantation of medical devices were performed in probands or relatives, and no reproductive counseling was requested. After an average of 1.6 years of follow-up 2.25 relatives per family with an actionable finding had been tested. This real-world experience of OGS grants new insight into the practical implementation effects and derived health care demands of genotype-first screening. The resulting health care effect and impact on demand for genetic counseling and workup in relatives extends beyond the effect in the probands.
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Affiliation(s)
- Sophia Hammer-Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Ulrik Stoltze
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Emil Bartels
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Biochemistry, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anna Byrjalsen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anne Tybjærg-Hansen
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Biochemistry, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Klaus Juul
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Jacob Tfelt
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Forensic Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Henning Bundgaard
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Birgitte Rode Diness
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.
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Rastogi R, Chung R, Li S, Li C, Lee K, Woo J, Kim DW, Keum C, Babbi G, Martelli PL, Savojardo C, Casadio R, Chennen K, Weber T, Poch O, Ancien F, Cia G, Pucci F, Raimondi D, Vranken W, Rooman M, Marquet C, Olenyi T, Rost B, Andreoletti G, Kamandula A, Peng Y, Bakolitsa C, Mort M, Cooper DN, Bergquist T, Pejaver V, Liu X, Radivojac P, Brenner SE, Ioannidis NM. Critical assessment of missense variant effect predictors on disease-relevant variant data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597828. [PMID: 38895200 PMCID: PMC11185644 DOI: 10.1101/2024.06.06.597828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Regular, systematic, and independent assessment of computational tools used to predict the pathogenicity of missense variants is necessary to evaluate their clinical and research utility and suggest directions for future improvement. Here, as part of the sixth edition of the Critical Assessment of Genome Interpretation (CAGI) challenge, we assess missense variant effect predictors (or variant impact predictors) on an evaluation dataset of rare missense variants from disease-relevant databases. Our assessment evaluates predictors submitted to the CAGI6 Annotate-All-Missense challenge, predictors commonly used by the clinical genetics community, and recently developed deep learning methods for variant effect prediction. To explore a variety of settings that are relevant for different clinical and research applications, we assess performance within different subsets of the evaluation data and within high-specificity and high-sensitivity regimes. We find strong performance of many predictors across multiple settings. Meta-predictors tend to outperform their constituent individual predictors; however, several individual predictors have performance similar to that of commonly used meta-predictors. The relative performance of predictors differs in high-specificity and high-sensitivity regimes, suggesting that different methods may be best suited to different use cases. We also characterize two potential sources of bias. Predictors that incorporate allele frequency as a predictive feature tend to have reduced performance when distinguishing pathogenic variants from very rare benign variants, and predictors supervised on pathogenicity labels from curated variant databases often learn label imbalances within genes. Overall, we find notable advances over the oldest and most cited missense variant effect predictors and continued improvements among the most recently developed tools, and the CAGI Annotate-All-Missense challenge (also termed the Missense Marathon) will continue to assess state-of-the-art methods as the field progresses. Together, our results help illuminate the current clinical and research utility of missense variant effect predictors and identify potential areas for future development.
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Oladayo AM, Prochaska S, Busch T, Adeyemo WL, Gowans LJ, Eshete M, Awotoye W, Sule V, Alade A, Adeyemo AA, Mossey PA, Prince A, Murray JC, Butali A. Parents and Provider Perspectives on the Return of Genomic Findings for Cleft Families in Africa. AJOB Empir Bioeth 2024; 15:133-146. [PMID: 38236653 PMCID: PMC11153024 DOI: 10.1080/23294515.2024.2302993] [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] [Indexed: 04/21/2024]
Abstract
BACKGROUND Inadequate knowledge among health care providers (HCPs) and parents of affected children limits the understanding and utility of secondary genetic findings (SFs) in under-represented populations in genomics research. SFs arise from deep DNA sequencing done for research or diagnostic purposes and may burden patients and their families despite their potential health importance. This study aims to evaluate the perspective of both groups regarding SFs and their choices in the return of results from genetic testing in the context of orofacial clefts. METHODS Using an online survey, we evaluated the experiences of 252 HCPs and 197 parents across participating cleft clinics in Ghana and Nigeria toward the return of SFs across several domains. RESULTS Only 1.6% of the HCPs felt they had an expert understanding of when and how to incorporate genomic medicine into practice, while 50.0% agreed that all SFs should be returned to patients. About 95.4% of parents were willing to receive all the information from genetic testing (including SFs), while the majority cited physicians as their primary information source (64%). CONCLUSIONS Overall, parents and providers were aware that genetic testing could help in the clinical management of diseases. However, they cited a lack of knowledge about genomic medicine, uncertain clinical utility, and lack of available learning resources as barriers. The knowledge gained from this study will assist with developing guidelines and policies to guide providers on the return of SFs in sub-Saharan Africa and across the continent.
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Affiliation(s)
- Abimbola M Oladayo
- Department Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Sydney Prochaska
- Department of Global Health, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Tamara Busch
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos
| | - Lord J.J. Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen Eshete
- Addis Ababa University, School of Medicine, Department of Surgery, Addis Ababa, Ethiopia
| | - Waheed Awotoye
- Department Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Veronica Sule
- Department of Operative Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Azeez Alade
- Department Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | | | - Peter A. Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | | | | | - Azeez Butali
- Department Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
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Schwartz MLB, McDonald WS, Hallquist MLG, Hu Y, McCormick CZ, Walters NL, Tsun J, Zimmerman K, Decker A, Gray C, Malinowski J, Sturm AC, Buchanan AH. Genetics Visit Uptake Among Individuals Receiving Clinically Actionable Genomic Screening Results. JAMA Netw Open 2024; 7:e242388. [PMID: 38488794 PMCID: PMC10943406 DOI: 10.1001/jamanetworkopen.2024.2388] [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: 09/25/2023] [Accepted: 01/23/2024] [Indexed: 03/18/2024] Open
Abstract
Importance Screening unselected populations for clinically actionable genetic disease risk can improve ascertainment and facilitate risk management. Genetics visits may encourage at-risk individuals to perform recommended management, but little has been reported on genetics visit completion or factors associated with completion in genomic screening programs. Objective To identify factors associated with postdisclosure genetics visits in a genomic screening cohort. Design, Setting, and Participants This was a cohort study of biobank data in a health care system in central Pennsylvania. Participants' exome sequence data were reviewed for pathogenic or likely pathogenic (P/LP) results in all genes on the American College of Medical Genetics and Genomics Secondary Findings list. Clinically confirmed results were disclosed by phone and letter. Participants included adult MyCode biobank participants who received P/LP results between July 2015 and November 2019. Data were analyzed from May 2021 to March 2022. Exposure Clinically confirmed P/LP result disclosed by phone or letter. Main Outcomes and Measures Completion of genetics visit in which the result was discussed and variables associated with completion were assessed by electronic health record (EHR) review. Results Among a total of 1160 participants (703 [60.6%] female; median [IQR] age, 57.0 [42.1-68.5] years), fewer than half of participants (551 of 1160 [47.5%]) completed a genetics visit. Younger age (odds ratio [OR] for age 18-40 years, 2.98; 95% CI, 1.40-6.53; OR for age 41-65 years, 2.36; 95% CI, 1.22-4.74; OR for age 66-80 years, 2.60; 95% CI, 1.41-4.98 vs age ≥81 years); female sex (OR, 1.49; 95% CI, 1.14-1.96); being married (OR, 1.74; 95% CI, 1.23-2.47) or divorced (OR, 1.80; 95% CI, 1.11-2.91); lower Charlson comorbidity index (OR for score of 0-2, 1.76; 95% CI, 1.16-2.68; OR for score of 3-4, 1.73; 95% CI, 1.18-2.54 vs score of ≥5); EHR patient portal use (OR, 1.42; 95% CI, 1.06-1.89); living closer to a genetics clinic (OR, 1.64; 95% CI, 1.14-2.36 for <8.9 miles vs >20.1 miles); successful results disclosure (OR for disclosure by genetic counselor, 16.32; 95% CI, 8.16-37.45; OR for disclosure by research assistant, 20.30; 95% CI, 10.25-46.31 vs unsuccessful phone disclosure); and having a hereditary cancer result (OR, 2.13; 95% CI, 1.28-3.58 vs other disease risk) were significantly associated with higher rates of genetics visit completion. Preference to follow up with primary care was the most common reported reason for declining a genetics visit (68 of 152 patients [44.7%]). Conclusions and Relevance This cohort study of a biobank-based population genomic screening program suggests that targeted patient engagement, improving multidisciplinary coordination, and reducing barriers to follow-up care may be necessary for enhancing genetics visit uptake.
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Affiliation(s)
- Marci L. B. Schwartz
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Yirui Hu
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania
| | | | | | - Jessica Tsun
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
| | | | - Amie Decker
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
- University of Arkansas Medical Sciences, Little Rock
| | - Celia Gray
- Phenomics and Clinical Data Core, Geisinger, Danville, Pennsylvania
| | | | - Amy C. Sturm
- Department of Genomic Health, Geisinger, Danville, Pennsylvania
- 23andMe, Sunnyvale, California
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9
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Nolan J, Buchanan J, Taylor J, Almeida J, Bedenham T, Blair E, Broadgate S, Butler S, Cazeaux A, Craft J, Cranston T, Crawford G, Forrest J, Gabriel J, George E, Gillen D, Haeger A, Hastings Ward J, Hawkes L, Hodgkiss C, Hoffman J, Jones A, Karpe F, Kasperaviciute D, Kovacs E, Leigh S, Limb E, Lloyd-Jani A, Lopez J, Lucassen A, McFarlane C, O'Rourke AW, Pond E, Sherman C, Stewart H, Thomas E, Thomas S, Thomas T, Thomson K, Wakelin H, Walker S, Watson M, Williams E, Ormondroyd E. Secondary (additional) findings from the 100,000 Genomes Project: Disease manifestation, health care outcomes, and costs of disclosure. Genet Med 2024; 26:101051. [PMID: 38131308 DOI: 10.1016/j.gim.2023.101051] [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: 07/13/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE The UK 100,000 Genomes Project offered participants screening for additional findings (AFs) in genes associated with familial hypercholesterolemia (FH) or hereditary cancer syndromes including breast/ovarian cancer (HBOC), Lynch, familial adenomatous polyposis, MYH-associated polyposis, multiple endocrine neoplasia (MEN), and von Hippel-Lindau. Here, we report disclosure processes, manifestation of AF-related disease, outcomes, and costs. METHODS An observational study in an area representing one-fifth of England. RESULTS Data were collected from 89 adult AF recipients. At disclosure, among 57 recipients of a cancer-predisposition-associated AF and 32 recipients of an FH-associated AF, 35% and 88%, respectively, had personal and/or family history evidence of AF-related disease. During post-disclosure investigations, 4 cancer-AF recipients had evidence of disease, including 1 medullary thyroid cancer. Six women with an HBOC AF, 3 women with a Lynch syndrome AF, and 2 individuals with a MEN AF elected for risk-reducing surgery. New hyperlipidemia diagnoses were made in 6 FH-AF recipients and treatment (re-)initiated for 7 with prior hyperlipidemia. Generating and disclosing AFs in this region cost £1.4m; £8680 per clinically significant AF. CONCLUSION Generation and disclosure of AFs identifies individuals with and without personal or familial evidence of disease and prompts appropriate clinical interventions. Results can inform policy toward secondary findings.
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Affiliation(s)
- Joshua Nolan
- Radcliffe Department of Medicine, University of Oxford, United Kingdom
| | - James Buchanan
- Health Economics Research Centre, University of Oxford, United Kingdom
| | - John Taylor
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joao Almeida
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Tina Bedenham
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Suzanne Broadgate
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Samantha Butler
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Angela Cazeaux
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Judith Craft
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Treena Cranston
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Gillian Crawford
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Jamie Forrest
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; University of Manchester, Manchester, United Kingdom
| | - Jessica Gabriel
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Elaine George
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Donna Gillen
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Ash Haeger
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | | | - Lara Hawkes
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Claire Hodgkiss
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Jonathan Hoffman
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Alan Jones
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Fredrik Karpe
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Dalia Kasperaviciute
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Erika Kovacs
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Sarah Leigh
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Limb
- Population Health Research Institute, St George's University of London, London, United Kingdom
| | - Anjali Lloyd-Jani
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Javier Lopez
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Anneke Lucassen
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Centre for Personalised Medicine, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Carlos McFarlane
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Anthony W O'Rourke
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Emily Pond
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Catherine Sherman
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Ellen Thomas
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Simon Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Tessy Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Kate Thomson
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Hannah Wakelin
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Susan Walker
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Melanie Watson
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Eleanor Williams
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Ormondroyd
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
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10
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Mitchell LA, Jivani K, Young MA, Jacobs C, Willis AM. Systematic review of the uptake and outcomes from returning secondary findings to adult participants in research genomic testing. J Genet Couns 2024. [PMID: 38197527 DOI: 10.1002/jgc4.1865] [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: 06/19/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 01/11/2024]
Abstract
The increasing use of genomic sequencing in research means secondary findings (SF) is more frequently detected and becoming a more pressing issue for researchers. This is reflected by the recent publication of multiple guidelines on this issue, calling for researchers to have a plan for managing SF prior to commencing their research. A deeper understanding of participants' experiences and outcomes from receiving SF is needed to ensure that the return of SF is conducted ethically and with adequate support. This review focuses on the uptake and outcomes of receiving actionable SF for research participants. This review included studies from January 2010 to January 2023. Databases searched included Medline, Embase, PsycINFO, and Scopus. Of the 3903 studies identified, 29 were included in the analysis. The uptake of SF ranged between 20% and 97%, and outcomes were categorized into psychological, clinical, lifestyle and behavioral, and family outcomes. The results indicate there is minimal psychological impact from receiving SF. Almost all participants greatly valued receiving SF. These findings highlight considerations for researchers when returning results, including the importance of involving genetic health professionals in consenting, results return process, and ensuring continuity of care by engaging healthcare providers.
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Affiliation(s)
- Lucas A Mitchell
- Clinical Translation and Engagement Platform, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Karishma Jivani
- Graduate School of Health, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Mary-Anne Young
- Clinical Translation and Engagement Platform, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Chris Jacobs
- Graduate School of Health, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Amanda M Willis
- Clinical Translation and Engagement Platform, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
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11
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Solomon BD. The future of commercial genetic testing. Curr Opin Pediatr 2023; 35:615-619. [PMID: 37218641 PMCID: PMC10667560 DOI: 10.1097/mop.0000000000001260] [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] [Indexed: 05/24/2023]
Abstract
PURPOSE OF REVIEW There are thousands of different clinical genetic tests currently available. Genetic testing and its applications continue to change rapidly for multiple reasons. These reasons include technological advances, accruing evidence about the impact and effects of testing, and many complex financial and regulatory factors. RECENT FINDINGS This article considers a number of key issues and axes related to the current and future state of clinical genetic testing, including targeted versus broad testing, simple/Mendelian versus polygenic and multifactorial testing models, genetic testing for individuals with high suspicion of genetic conditions versus ascertainment through population screening, the rise of artificial intelligence in multiple aspects of the genetic testing process, and how developments such as rapid genetic testing and the growing availability of new therapies for genetic conditions may affect the field. SUMMARY Genetic testing is expanding and evolving, including into new clinical applications. Developments in the field of genetics will likely result in genetic testing becoming increasingly in the purview of a very broad range of clinicians, including general paediatricians as well as paediatric subspecialists.
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Affiliation(s)
- Benjamin D. Solomon
- Medical Genetics Branch, National Human Genome Research Institute, United States of America
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12
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Schwiter R, Rocha H, Johns A, Savatt JM, Diehl DL, Kelly MA, Williams MS, Buchanan AH. Low adenoma burden in unselected patients with a pathogenic APC variant. Genet Med 2023; 25:100949. [PMID: 37542411 DOI: 10.1016/j.gim.2023.100949] [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: 12/20/2022] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/06/2023] Open
Abstract
PURPOSE Genomic screening can improve clinical outcomes, but presentation of individuals with risk for polyposis identified via genomic screening is unknown. To inform assessment of clinical utility of genomic screening for polyposis risk, clinical presentation of individuals in an unselected health care system cohort with an APC pathogenic or likely pathogenic (P/LP) variant causative of familial adenomatous polyposis are described. METHODS Electronic health records of individuals with an APC P/LP variant identified via the MyCode program (MyCode APC+) were reviewed to assess adenoma burden and compare it among individuals with a clinical diagnosis of familial adenomatous polyposis and matched variant-negative controls. RESULTS The prevalence of APC P/LP variants in this health care cohort is estimated to be 1 in 2800. Twenty-four MyCode APC+ individuals were identified during the study period. Median age at result disclosure was 53 years. Rate of clinical polyposis was 8%. Two of six participants with a classic region variant and none of those with an attenuated region variant had polyposis. MyCode APC+ participants did not differ from controls in cumulative adenoma count. CONCLUSION APC P/LP variant prevalence estimate in the MyCode cohort is higher than prior published prevalence rates. Individuals with APC P/LP variants identified via genomic screening had a low adenoma burden.
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Affiliation(s)
| | - Heather Rocha
- Department of Genomic Health, Geisinger, Danville, PA
| | - Alicia Johns
- Department of Population Health Sciences, Geisinger, Danville, PA
| | | | - David L Diehl
- Department of Medicine, Division of Gastroenterology and Hepatology, Geisinger, Danville, PA
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13
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Washington AM, Foss K, Krause JH, Davis AM, Kuczynski KJ, Milko LV, Berg JS, Roberts MC. Consideration of the Beneficiary Inducement Statute on Access to Health Care Systems' Population Genetic Screening Programs. Public Health Genomics 2023; 26:183-187. [PMID: 37778346 PMCID: PMC10619584 DOI: 10.1159/000534365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Affiliation(s)
- Aurora M. Washington
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kimberly Foss
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joan H. Krause
- School of Law, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Arlene M. Davis
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kristine J. Kuczynski
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura V. Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Megan C. Roberts
- School of Pharmacy – Division of Pharmaceutical Outcomes and Policy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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14
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Solomon BD, Chung WK. Artificial intelligence and the impact on medical genetics. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2023; 193:e32060. [PMID: 37565625 DOI: 10.1002/ajmg.c.32060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/12/2023]
Abstract
Virtually all areas of biomedicine will be increasingly affected by applications of artificial intelligence (AI). We discuss how AI may affect fields of medical genetics, including both clinicians and laboratorians. In addition to reviewing the anticipated impact, we provide recommendations for ways in which these groups may want to evolve in light of the influence of AI. We also briefly discuss how educational and training programs can play a key role in preparing the future workforce given these anticipated changes.
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Affiliation(s)
- Benjamin D Solomon
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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15
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Kodida R, Reble E, Clausen M, Shickh S, Mighton C, Sam J, Forster N, Panchal S, Aronson M, Semotiuk K, Graham T, Silberman Y, Randall Armel S, McCuaig JM, Cohn I, Morel CF, Elser C, Eisen A, Carroll JC, Glogowski E, Schrader KA, Di Gioacchino V, Lerner-Ellis J, Kim RH, Bombard Y. A model for the return and referral of all clinically significant secondary findings of genomic sequencing. J Med Genet 2023; 60:733-739. [PMID: 37217257 DOI: 10.1136/jmg-2022-109091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/19/2023] [Indexed: 05/24/2023]
Abstract
Secondary findings (SFs) identified through genomic sequencing (GS) can offer a wide range of health benefits to patients. Resource and capacity constraints pose a challenge to their clinical management; therefore, clinical workflows are needed to optimise the health benefits of SFs. In this paper, we describe a model we created for the return and referral of all clinically significant SFs, beyond medically actionable results, from GS. As part of a randomised controlled trial evaluating the outcomes and costs of disclosing all clinically significant SFs from GS, we consulted genetics and primary care experts to determine a feasible workflow to manage SFs. Consensus was sought to determine appropriate clinical recommendations for each category of SF and which clinician specialist would provide follow-up care. We developed a communication and referral plan for each category of SFs. This involved referrals to specialised clinics, such as an Adult Genetics clinic, for highly penetrant medically actionable findings. Common and non-urgent SFs, such as pharmacogenomics and carrier status results for non-family planning participants, were directed back to the family physician (FP). SF results and recommendations were communicated directly to participants to respect autonomy and to their FPs to support follow-up of SFs. We describe a model for the return and referral of all clinically significant SFs to facilitate the utility of GS and promote the health benefits of SFs. This may serve as a model for others returning GS results transitioning participants from research to clinical settings.
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Affiliation(s)
- Rita Kodida
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Emma Reble
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Marc Clausen
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Salma Shickh
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management & Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management & Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Sam
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Nicole Forster
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Seema Panchal
- The Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Kara Semotiuk
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Tracy Graham
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yael Silberman
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Susan Randall Armel
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology & Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Jeanna M McCuaig
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology & Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Iris Cohn
- Division of Clinical Pharmacology & Toxicology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chantal F Morel
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Christine Elser
- The Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Eisen
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - June C Carroll
- Department of Family & Community Medicine, University of Toronto, Toronto, Ontario, Canada
- Granovsky Gluskin Family Medicine Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | | | - Kasmintan A Schrader
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Vanessa Di Gioacchino
- The Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Pathology & Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Pathology & Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Raymond H Kim
- Division of Medical Oncology & Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management & Evaluation, University of Toronto, Toronto, Ontario, Canada
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16
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Kurzlechner LM, Kishnani S, Chowdhury S, Atkins SL, Moya-Mendez ME, Parker LE, Rosamilia MB, Tadros HJ, Pace LA, Patel V, Chahal CAA, Landstrom AP. DiscoVari: A Web-Based Precision Medicine Tool for Predicting Variant Pathogenicity in Cardiomyopathy- and Channelopathy-Associated Genes. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:317-327. [PMID: 37409478 PMCID: PMC10527712 DOI: 10.1161/circgen.122.003911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/30/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND With genetic testing advancements, the burden of incidentally identified cardiac disease-associated gene variants is rising. These variants may carry a risk of sudden cardiac death, highlighting the need for accurate diagnostic interpretation. We sought to identify pathogenic hotspots in sudden cardiac death-associated genes using amino acid-level signal-to-noise (S:N) analysis and develop a web-based precision medicine tool, DiscoVari, to improve variant evaluation. METHODS The minor allele frequency of putatively pathogenic variants was derived from cohort-based cardiomyopathy and channelopathy studies in the literature. We normalized disease-associated minor allele frequencies to rare variants in an ostensibly healthy population (Genome Aggregation Database) to calculate amino acid-level S:N. Amino acids with S:N above the gene-specific threshold were defined as hotspots. DiscoVari was built using JavaScript ES6 and using open-source JavaScript library ReactJS, web development framework Next.js, and JavaScript runtime NodeJS. We validated the ability of DiscoVari to identify pathogenic variants using variants from ClinVar and individuals clinically evaluated at the Duke University Hospitals with cardiac genetic testing. RESULTS We developed DiscoVari as an internet-based tool for S:N-based variant hotspots. Upon validation, a higher proportion of ClinVar likely pathogenic/pathogenic variants localized to DiscoVari hotspots (43.1%) than likely benign/benign variants (17.8%; P<0.0001). Further, 75.3% of ClinVar variants reclassified to likely pathogenic/pathogenic were in hotspots, compared with 41.3% of those reclassified as variants of uncertain significance (P<0.0001) and 23.4% of those reclassified as likely benign/benign (P<0.0001). Of the clinical cohort variants, 73.1% of likely pathogenic/pathogenic were in hotspots, compared with 0.0% of likely benign/benign (P<0.01). CONCLUSIONS DiscoVari reliably identifies disease-susceptible amino acid residues to evaluate variants by searching amino acid-specific S:N ratios.
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Affiliation(s)
| | - Sujata Kishnani
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | - Shawon Chowdhury
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | - Sage L. Atkins
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | | | - Lauren E. Parker
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | | | - Hanna J. Tadros
- Dept of Pediatrics, Section of Pediatric Cardiology, Baylor College of Medicine, Houston, TX
| | - Leslie A. Pace
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | - Viraj Patel
- North West Thames Regional Genetics Service, St Mark’s Hospital, London, United Kingdom
| | - C. Anwar A. Chahal
- Center for Inherited Cardiovascular Diseases, WellSpan Health, Lancaster, PA
- Barts Heart Centre, St Bartholomew’s Hospital, Barts Health NHS Trust, London, United Kingdom
- Cardiac Electrophysiology, Cardiovascular Division, Hospital of the Univ of Pennsylvania, Philadelphia, PA
- Dept of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Andrew P. Landstrom
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
- Dept of Cell Biology, Duke Univ School of Medicine, Durham, NC
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17
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Martone S, Buonagura AT, Marra R, Rosato BE, Del Giudice F, Bonfiglio F, Capasso M, Iolascon A, Andolfo I, Russo R. Clinical exome-based panel testing for medically actionable secondary findings in a cohort of 383 Italian participants. Front Genet 2022; 13:956723. [DOI: 10.3389/fgene.2022.956723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Background: Next-generation sequencing-based genetic testing represents a great opportunity to identify hereditary predispositions to specific pathological conditions and to promptly implement health surveillance or therapeutic protocols in case of disease. The term secondary finding refers to the active search for causative variants in genes associated with medically actionable conditions.Methods: We evaluated 59 medically actionable ACMG genes using a targeted in silico analysis of clinical exome sequencing performed in 383 consecutive individuals referred to our Medical Genetics Unit. A three-tier classification system of SFs for assessing their clinical impact and supporting a decision-making process for reporting was established.Results: We identified SFs with high/moderate evidence of pathogenicity in 7.0% (27/383) of analyzed subjects. Among these, 12/27 (44.4%) were carriers of a high-risk recessive disease allele. The most represented disease domains were cancer predisposition (33.3%), cardiac disorders (16.7%), and familial hypercholesterolemia (12.5%).Conclusion: Although still debated, ensuring during NGS-based genetic testing an opportunistic screening might be valuable for personal and familial early management and surveillance of medically actionable disorders, the individual’s reproductive choices, and the prevalence assessment of underestimated hereditary genetic diseases.
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18
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Ledgister Hanchard SE, Dwyer MC, Liu S, Hu P, Tekendo-Ngongang C, Waikel RL, Duong D, Solomon BD. Scoping review and classification of deep learning in medical genetics. Genet Med 2022; 24:1593-1603. [PMID: 35612590 PMCID: PMC11056027 DOI: 10.1016/j.gim.2022.04.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022] Open
Abstract
Deep learning (DL) is applied in many biomedical areas. We performed a scoping review on DL in medical genetics. We first assessed 14,002 articles, of which 133 involved DL in medical genetics. DL in medical genetics increased rapidly during the studied period. In medical genetics, DL has largely been applied to small data sets of affected individuals (mean = 95, median = 29) with genetic conditions (71 different genetic conditions were studied; 24 articles studied multiple conditions). A variety of data types have been used in medical genetics, including radiologic (20%), ophthalmologic (14%), microscopy (8%), and text-based data (4%); the most common data type was patient facial photographs (46%). DL authors and research subjects overrepresent certain geographic areas (United States, Asia, and Europe). Convolutional neural networks (89%) were the most common method. Results were compared with human performance in 31% of studies. In total, 51% of articles provided data access; 16% released source code. To further explore DL in genomics, we conducted an additional analysis, the results of which highlight future opportunities for DL in medical genetics. Finally, we expect DL applications to increase in the future. To aid data curation, we evaluated a DL, random forest, and rule-based classifier at categorizing article abstracts.
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Affiliation(s)
| | - Michelle C Dwyer
- Medical Genomics Unit, National Human Genome Research Institute, Bethesda, MD
| | - Simon Liu
- Medical Genomics Unit, National Human Genome Research Institute, Bethesda, MD
| | - Ping Hu
- Medical Genomics Unit, National Human Genome Research Institute, Bethesda, MD
| | | | - Rebekah L Waikel
- Medical Genomics Unit, National Human Genome Research Institute, Bethesda, MD
| | - Dat Duong
- Medical Genomics Unit, National Human Genome Research Institute, Bethesda, MD
| | - Benjamin D Solomon
- Medical Genomics Unit, National Human Genome Research Institute, Bethesda, MD.
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19
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Menko FH, Monkhorst K, Hogervorst FB, Rosenberg EH, Adank M, Ruijs MW, Bleiker EM, Sonke GS, Russell NS, Oldenburg HS, van der Kolk LE. Challenges in breast cancer genetic testing. A call for novel forms of multidisciplinary care and long-term evaluation. Crit Rev Oncol Hematol 2022; 176:103642. [DOI: 10.1016/j.critrevonc.2022.103642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 02/04/2022] [Accepted: 02/16/2022] [Indexed: 11/25/2022] Open
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20
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Johnston JJ, Brennan ML, Radenbaugh B, Yoo SJ, Hernandez SM, Lewis KL, Katz AE, Manolio TA, Biesecker LG. The ACMG SF v3.0 gene list increases returnable variant detection by 22% when compared with v2.0 in the ClinSeq cohort. Genet Med 2021; 24:736-743. [PMID: 34906458 PMCID: PMC10120277 DOI: 10.1016/j.gim.2021.11.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 01/17/2023] Open
Abstract
PURPOSE The American College of Medical Genetics and Genomics (ACMG) recommends the return of pathogenic and likely pathogenic (P/LP) secondary findings from exome and genome sequencing. The latest version (ACMG secondary finding [SF] v3.0) includes 14 additional genes. We interrogated the ClinSeq cohort for variants in these genes to determine the additional yield in unselected individuals. METHODS Exome data from 1473 individuals (60% White, 34% African American or Black, 6% other) were analyzed. We restricted our analyses to coding variants; +1,+2,-1, and -2 splice site variants; and the pathogenic GAA variant, NM_000152.5:c.-32-13T>G. Variants were assessed with slightly modified ACMG/Association of Molecular Pathology guidelines. RESULTS A total of 25 P/LP variants were identified. In total, 7 individuals had P/LP variants in genes recommended for return of heterozygous variants, namely HNF1A (1), PALB2 (3), TMEM127 (1), and TTN (2). In total, 4 individuals had a homozygous variant in a gene recommended for biallelic variant return, namely HFE, NM_000410.3(HFE):c.845G>A p.Cys282Tyr. A total of 17 P/LP variants were identified in the heterozygous state in genes recommended only for biallelic variant reporting and were not returned. The frequency of returnable P/LP variants did not significantly differ by race. CONCLUSION Using the ACMG SF v3.0, the returnable P/LP variant frequency increased in the ClinSeq cohort by 22%, from 3.4% (n = 50, ACMG SF v2.0) to 4.1% (n = 61, ACMG SF v3.0).
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Affiliation(s)
- Jennifer J Johnston
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD.
| | - Marie-Luise Brennan
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD; American College of Medical Genetics and Genomics, Bethesda, MD
| | - Bailey Radenbaugh
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Seeley J Yoo
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Sophia M Hernandez
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
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- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Katie L Lewis
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Alexander E Katz
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Teri A Manolio
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD; Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
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21
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Landstrom AP, Kim JJ, Gelb BD, Helm BM, Kannankeril PJ, Semsarian C, Sturm AC, Tristani-Firouzi M, Ware SM. Genetic Testing for Heritable Cardiovascular Diseases in Pediatric Patients: A Scientific Statement From the American Heart Association. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2021; 14:e000086. [PMID: 34412507 PMCID: PMC8546375 DOI: 10.1161/hcg.0000000000000086] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genetic diseases that affect the cardiovascular system are relatively common and include cardiac channelopathies, cardiomyopathies, aortopathies, hypercholesterolemias, and structural diseases of the heart and great vessels. The rapidly expanding availability of clinical genetic testing leverages decades of research into the genetic origins of these diseases, helping inform diagnosis, clinical management, and prognosis. Although a number of guidelines and statements detail best practices for cardiovascular genetic testing, there is a paucity of pediatric-focused statements addressing the unique challenges in testing in this vulnerable population. In this scientific statement, we seek to coalesce the existing literature around the use of genetic testing for cardiovascular disease in infants, children, and adolescents.
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22
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Sapp JC, Facio FM, Cooper D, Lewis KL, Modlin E, van der Wees P, Biesecker LG. A systematic literature review of disclosure practices and reported outcomes for medically actionable genomic secondary findings. Genet Med 2021; 23:2260-2269. [PMID: 34433902 PMCID: PMC9017985 DOI: 10.1038/s41436-021-01295-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 01/14/2023] Open
Abstract
Purpose: Secondary findings (SF) are present in 1–4% of individuals undergoing genome/exome sequencing. A review of how SF are disclosed and what outcomes result from their receipt is urgent and timely. Methods: We conducted a systematic literature review of SF disclosure practices and outcomes after receipt including cascade testing, family and provider communication, and healthcare actions. Of the 1,184 non-duplicate records screened we summarize findings from 27 included research articles describing SF disclosure practices, outcomes after receipt, or both. Results: The included articles reported 709 unique SF index recipients/families. Referrals and/or recommendations were provided 647 SF recipients and outcome data were available for 236. At least one recommended evaluation was reported for 146 SF recipients; 16 reports of treatment or prophylactic surgery were identified. We found substantial variations in how the constructs of interest were defined and described. Conclusion: Variation in how SF disclosure and outcomes were described limited our ability to compare findings. We conclude the literature provided limited insight into how the ACMG guidelines have been translated into precision health outcomes for SF recipients. Robust studies of SF recipients are needed and should be prioritized for future research.
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Affiliation(s)
- Julie C Sapp
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA. .,Translational Health Sciences, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
| | - Flavia M Facio
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - Diane Cooper
- National Institutes of Health Library, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Katie L Lewis
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - Emily Modlin
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - Philip van der Wees
- Translational Health Sciences, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Radboud University Medical Center, IQ Healthcare and Rehabilitation, Nijmegen, Netherlands
| | - Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
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23
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Ezekian JE, Rehder C, Kishnani PS, Landstrom AP. Interpretation of Incidental Genetic Findings Localizing to Genes Associated With Cardiac Channelopathies and Cardiomyopathies. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e003200. [PMID: 34384235 DOI: 10.1161/circgen.120.003200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent advances in next-genetic sequencing technology have facilitated an expansion in the use of exome and genome sequencing in the research and clinical settings. While this has aided in the genetic diagnosis of individuals with atypical clinical presentations, there has been a marked increase in the number of incidentally identified variants of uncertain diagnostic significance in genes identified as clinically actionable by the American College of Medical Genetics guidelines. Approximately 20 of these genes are associated with cardiac diseases, which carry a significant risk of sudden cardiac death. While identification of at-risk individuals is paramount, increased discovery of incidental variants of uncertain diagnostic significance has placed a burden on the clinician tasked with determining the diagnostic significance of these findings. Herein, we describe the scope of this emerging problem using cardiovascular genetics to illustrate the challenges associated with variants of uncertain diagnostic significance interpretation. We review the evidence for diagnostic weight of these variants, discuss the role of clinical genetics providers in patient care, and put forward general recommendations about the interpretation of incidentally identified variants found with clinical genetic testing.
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Affiliation(s)
- Jordan E Ezekian
- Division of Cardiology, Department of Pediatrics (J.E.E., A.P.L.), Duke University School of Medicine, Durham, NC
| | - Catherine Rehder
- Department of Pathology (C.R.), Duke University School of Medicine, Durham, NC
| | - Priya S Kishnani
- Division of Medical Genetics, Department of Pediatrics (P.S.K.), Duke University School of Medicine, Durham, NC
| | - Andrew P Landstrom
- Division of Cardiology, Department of Pediatrics (J.E.E., A.P.L.), Duke University School of Medicine, Durham, NC.,Department of Cell Biology (A.P.L.), Duke University School of Medicine, Durham, NC
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24
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Schoot VVD, Viellevoije SJ, Tammer F, Brunner HG, Arens Y, Yntema HG, Oerlemans AJM. The impact of unsolicited findings in clinical exome sequencing, a qualitative interview study. Eur J Hum Genet 2021; 29:930-939. [PMID: 33637888 PMCID: PMC8187681 DOI: 10.1038/s41431-021-00834-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/10/2021] [Indexed: 12/14/2022] Open
Abstract
Unsolicited findings (UFs) in clinical exome sequencing are variants that are unrelated to the initial clinical question the DNA test was performed for, but that may nonetheless be of medical relevance to patients and/or their families. There is limited knowledge about the impact of UFs on patients' lives. In order to characterise patient perceptions of the impact of an UF, we conducted 20 semi-structured face-to-face interviews with patients and/or their relatives to whom an UF predisposing to oncological disease (n = 10) or predisposing to a cardiac condition (n = 10) had been disclosed. We have identified a psychological, physical and financial aspect of the perceived impact of UF disclosure in exome sequencing. Actionability, understanding, patients' pre-test health and social context were influencing factors, according to our participants. Although most expressed considerable psychological impact initially, all but one participant would choose to undergo genetic testing again, knowing what they know now. These novel findings provide insight in patients' perspectives on the impact of UF disclosure. Our study highlights the value of incorporating patients' perceptions in UF disclosure policy.
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Affiliation(s)
- Vyne van der Schoot
- Department of Clinical Genetics, Maastricht University Medical Centre, PO Box 5800, 6202 AZ, Maastricht, The Netherlands.
| | - Simone J Viellevoije
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- IQ healthcare, Radboud Institute for Health Sciences, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Femke Tammer
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre, PO Box 5800, 6202 AZ, Maastricht, The Netherlands
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Yvonne Arens
- Department of Clinical Genetics, Maastricht University Medical Centre, PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Anke J M Oerlemans
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
- IQ healthcare, Radboud Institute for Health Sciences, Radboud university medical center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
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25
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Schwartz MLB, Buchanan AH, Hallquist MLG, Haggerty CM, Sturm AC. Genetic counseling for patients with positive genomic screening results: Considerations for when the genetic test comes first. J Genet Couns 2021; 30:634-644. [PMID: 33786929 DOI: 10.1002/jgc4.1386] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/18/2020] [Accepted: 12/31/2020] [Indexed: 01/06/2023]
Abstract
Emerging genetic testing delivery models have enabled individuals to receive testing without a medical indication. This article will highlight key considerations for patient care in the setting of adult patients with positive results for monogenic disease identified through genomic screening. Suggestions for how to adapt genetic counseling to a genomic screening population will encompass topics such as phenotyping, risk assessments, and the use of existing guidelines and resources. Case examples will demonstrate principles of genotype-first patient care.
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Affiliation(s)
| | | | | | - Christopher M Haggerty
- The Heart Institute, Geisinger, Danville, PA, USA.,Department of Translational Data Science and Informatics, Geisinger, Danville, PA, USA
| | - Amy C Sturm
- Genomic Medicine Institute, Geisinger, Danville, PA, USA
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26
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Vu M, Degeling K, Martyn M, Lynch E, Chong B, Gaff C, IJzerman MJ. Evaluating the resource implications of different service delivery models for offering additional genomic findings. Genet Med 2020; 23:606-613. [PMID: 33214711 DOI: 10.1038/s41436-020-01030-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To evaluate the resource implications of different delivery models for the provision of additional findings (AF) in genomics from a health-care purchaser perspective. METHODS Data from the Additional Findings study were used to develop and validate a discrete event simulation model that represented the pathway of delivering AF. Resource implications were estimated by microcosting the consultations, sample verifications, bioinformatics, curation, and multidisciplinary case review meetings. A proof-of-concept model was used to generate costing, and then the simulation model was varied to assess the impact of an automated analysis pipeline, use of telehealth consultation, full automation with electronic decision support, and prioritizing case review for cases with pathogenic variants. RESULTS For the proof-of-concept delivery model, the average total cost to report AF was US$430 per patient irrespective of result pathogenicity (95% confidence interval [CI] US$375-US$489). However, the cost of per AF diagnosis was US$4349 (95% CI US$3794-US$4953). Alternative approaches to genetic counseling (telehealth, decision support materials) and to multidisciplinary case review (pathogenic AF cases only) lowered the total per patient cost of AF analysis and reporting by 41-51%. CONCLUSION Resources required to provide AF can be reduced substantially by implementing alternative approaches to counseling and multidisciplinary case review.
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Affiliation(s)
- Martin Vu
- Centre for Cancer Research and Centre for Health Policy, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia.,Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Koen Degeling
- Centre for Cancer Research and Centre for Health Policy, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia.,Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Melissa Martyn
- Murdoch Children's Research Institute, Melbourne, Australia.,Melbourne Genomics Health Alliance, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Elly Lynch
- Murdoch Children's Research Institute, Melbourne, Australia.,Melbourne Genomics Health Alliance, Melbourne, Australia.,Victorian Clinical Genetics Services, Melbourne, Australia
| | - Belinda Chong
- Murdoch Children's Research Institute, Melbourne, Australia.,Victorian Clinical Genetics Services, Melbourne, Australia
| | - Clara Gaff
- Murdoch Children's Research Institute, Melbourne, Australia.,Melbourne Genomics Health Alliance, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Maarten J IJzerman
- Centre for Cancer Research and Centre for Health Policy, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia. .,Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia. .,Department of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia.
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