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Ellard H, Clarke A, Wynn S, Pichini A, Lewis C. Written communication of whole genome sequencing results in the NHS Genomic Medicine Service: a multi-centre service evaluation. Eur J Hum Genet 2024:10.1038/s41431-024-01636-5. [PMID: 38806663 DOI: 10.1038/s41431-024-01636-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024] Open
Abstract
Whole genome sequencing (WGS) is being used in diagnostic testing for certain clinical indications within the NHS Genomic Medicine Service (GMS) in England. Letter writing is an integral part of delivering results. However, no national guidelines for writing results from WGS exist. This multi-centre service evaluation used mixed methods to understand the content and readability of letters returning diagnostic, variant of uncertain significance (VUS), and no-finding results to paediatric rare disease patients. Eight Regional Genetics Services (response rate 47%) in England provided a total of 37 letters returning diagnostic (n = 13), VUS (n = 10), and no-finding (n = 14) results. Diagnostic and VUS results were usually delivered during an appointment; no-finding results were typically delivered by letter only. Letters were diverse in which content topics they covered and level of detail. No-finding letters (14/14) explained the result but were less likely to cover other topics. Diagnostic letters discussed the result (13/13), the condition (13/13), clinical genetics follow-up (13/13), clinical management (10/13), and adapting to the result (9/13). VUS letters explained the result (10/10), diagnostic uncertainty (10/10), and clinical genetics follow-up (10/10). Uncertainty was a common component of letters (33/37), irrespective of the result. Reanalysis or review after one or more years was suggested in 6/13 diagnostic, 7/10 VUS, and 6/14 no-finding letters. The mean reading level of letters corresponded to 15-17 years. Understanding how WGS results are conveyed to families during appointments, as well as how families interpret that information, is needed to provide a more comprehensive overview of results communication and inform best practices.
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Affiliation(s)
- Holly Ellard
- School of Medicine, Cardiff University, Cardiff, Wales, UK.
- Population, Policy and Practice Department, UCL Great Ormond Street Institute of Child Health, London, UK.
| | - Angus Clarke
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, Wales, UK
| | - Sarah Wynn
- Unique, Rare Chromosome Support Group, Oxted, Surrey, UK
| | | | - Celine Lewis
- School of Medicine, Cardiff University, Cardiff, Wales, UK
- Population, Policy and Practice Department, UCL Great Ormond Street Institute of Child Health, London, UK
- NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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Goulão B, Morris TP, Blazeby J, Gamble C, Gillies K, Laidlaw L, Ramsay C, Soulsby I, Stewart D, Totton N. Involving patients and the public In sTatistIcal Analysis pLans (INITIAL): A delphi survey. PLoS One 2023; 18:e0292257. [PMID: 38096223 PMCID: PMC10721002 DOI: 10.1371/journal.pone.0292257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/17/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Patient and public involvement (PPI) in trials aims to enhance research by improving its relevance and transparency. Planning for statistical analysis begins at the design stage of a trial within the protocol and is refined and detailed in a Statistical Analysis Plan (SAP). While PPI is common in design and protocol development it is less common within SAPs. This study aimed to reach consensus on the most important and relevant statistical analysis items within an SAP to involve patients and the public. METHODS We developed a UK-based, two-round Delphi survey through an iterative consultation with public partners, statisticians, and trialists. The consultation process started with 55 items from international guidance for statistical analysis plans. We aimed to recruit at least 20 participants per key stakeholder group for inclusion in the final analysis of the Delphi survey. Participants were asked to vote on each item using a Likert scale from 1 to 9, where a rating of 1 to 3 was labelled as having 'limited importance'; 4 to 6 as 'important but not critical' and 7 to 9 as 'critical' to involve patients and the public. Results from the second round determined consensus on critical items for PPI. RESULTS The consultation exercise led to the inclusion of 15 statistical items in the Delphi survey. We recruited 179 participants, of whom 72% (129: 36 statisticians, 29 patients or public partners, 25 clinical researchers or methodologists, 27 trial managers, and 12 PPI coordinators) completed both rounds. Participants were on average 48 years old, 60% were female, 84% were White, 64% were based in England and 84% had at least five years' experience in trials. Four items reached consensus regarding critical importance for patient and public involvement: presentation of results to trial participants; summary and presentation of harms; interpretation and presentation of findings in an academic setting; factors impacting how well a treatment works. No consensus was reached for the remaining 11 items. In general, the results were consistent across stakeholder groups. DISCUSSION We identified four critical items to involve patients and the public in statistical analysis plans. The remaining 11 items did not reach consensus and need to be considered in a case-by-case basis with most responders considering patient and public involvement important (but not critical). Our research provides a platform to enable focused future efforts to improve patient and public involvement in trials and enhance the relevance of statistical analyses to patients and the public.
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Affiliation(s)
- Beatriz Goulão
- Health Services Research Unit, University of Aberdeen, Aberdeen, United Kingdom
| | - Tim P. Morris
- MRC Clinical Trials Unit at UCL, London, United Kingdom
| | - Jane Blazeby
- Bristol NIHR Biomedical Research Centre, Bristol Centre for Surgical Research, Population Health Sciences, Bristol Medical School, Bristol, United Kingdom
| | - Carrol Gamble
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, United Kingdom
| | - Katie Gillies
- Health Services Research Unit, University of Aberdeen, Aberdeen, United Kingdom
| | - Lynn Laidlaw
- Public Partner Co-author, INITIAL Advisory Group, University of Aberdeen, Aberdeen, United Kingdom
| | - Craig Ramsay
- Health Services Research Unit, University of Aberdeen, Aberdeen, United Kingdom
| | - Irene Soulsby
- Public Partner Co-author, INITIAL Advisory Group, University of Aberdeen, Aberdeen, United Kingdom
| | - Derek Stewart
- Public Partner Co-author, INITIAL Advisory Group, University of Aberdeen, Aberdeen, United Kingdom
- University of Galway, Galway, Ireland
| | - Nikki Totton
- School of Health and Related Research, University of Sheffield, Sheffield, United Kingdom
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Murphy R, Colclough K, Pollin TI, Ikle JM, Svalastoga P, Maloney KA, Saint-Martin C, Molnes J, Misra S, Aukrust I, de Franco E, Flanagan SE, Njølstad PR, Billings LK, Owen KR, Gloyn AL. The use of precision diagnostics for monogenic diabetes: a systematic review and expert opinion. COMMUNICATIONS MEDICINE 2023; 3:136. [PMID: 37794142 PMCID: PMC10550998 DOI: 10.1038/s43856-023-00369-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Monogenic diabetes presents opportunities for precision medicine but is underdiagnosed. This review systematically assessed the evidence for (1) clinical criteria and (2) methods for genetic testing for monogenic diabetes, summarized resources for (3) considering a gene or (4) variant as causal for monogenic diabetes, provided expert recommendations for (5) reporting of results; and reviewed (6) next steps after monogenic diabetes diagnosis and (7) challenges in precision medicine field. METHODS Pubmed and Embase databases were searched (1990-2022) using inclusion/exclusion criteria for studies that sequenced one or more monogenic diabetes genes in at least 100 probands (Question 1), evaluated a non-obsolete genetic testing method to diagnose monogenic diabetes (Question 2). The risk of bias was assessed using the revised QUADAS-2 tool. Existing guidelines were summarized for questions 3-5, and review of studies for questions 6-7, supplemented by expert recommendations. Results were summarized in tables and informed recommendations for clinical practice. RESULTS There are 100, 32, 36, and 14 studies included for questions 1, 2, 6, and 7 respectively. On this basis, four recommendations for who to test and five on how to test for monogenic diabetes are provided. Existing guidelines for variant curation and gene-disease validity curation are summarized. Reporting by gene names is recommended as an alternative to the term MODY. Key steps after making a genetic diagnosis and major gaps in our current knowledge are highlighted. CONCLUSIONS We provide a synthesis of current evidence and expert opinion on how to use precision diagnostics to identify individuals with monogenic diabetes.
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Affiliation(s)
- Rinki Murphy
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
- Auckland Diabetes Centre, Te Whatu Ora Health New Zealand, Te Tokai Tumai, Auckland, New Zealand.
| | - Kevin Colclough
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jennifer M Ikle
- Department of Pediatrics, Division of Endocrinology & Diabetes, Stanford School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA
| | - Pernille Svalastoga
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kristin A Maloney
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cécile Saint-Martin
- Department of Medical Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Janne Molnes
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Shivani Misra
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Diabetes and Endocrinology, Imperial College Healthcare NHS Trust, London, UK
| | - Ingvild Aukrust
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Elisa de Franco
- Department of Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Sarah E Flanagan
- Department of Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Pål R Njølstad
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Liana K Billings
- Division of Endocrinology, NorthShore University HealthSystem, Skokie, IL, USA
- Department of Medicine, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Katharine R Owen
- Oxford Center for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anna L Gloyn
- Department of Pediatrics, Division of Endocrinology & Diabetes, Stanford School of Medicine, Stanford, CA, USA.
- Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
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Su CC, Lin YP, Yen HK, Pan YT, Zijlstra H, Verlaan JJ, Schwab JH, Lai CY, Hu MH, Yang SH, Groot OQ. A Machine Learning Algorithm for Predicting 6-Week Survival in Spinal Metastasis: An External Validation Study Using 2,768 Taiwanese Patients. J Am Acad Orthop Surg 2023; 31:e645-e656. [PMID: 37192422 DOI: 10.5435/jaaos-d-23-00091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/11/2023] [Indexed: 05/18/2023] Open
Abstract
INTRODUCTION There are predictive algorithms for predicting 3-month and 1-year survival in patients with spinal metastasis. However, advance in surgical technique, immunotherapy, and advanced radiation therapy has enabled shortening of postoperative recovery, which returns dividends to the overall quality-adjusted life-year. As such, the Skeletal Oncology Research Group machine learning algorithm (SORG-MLA) was proposed to predict 6-week survival in patients with spinal metastasis, whereas its utility for patients treated with nonsurgical treatment was untested externally. This study aims to validate the survival prediction of the 6-week SORG-MLA for patients with spinal metastasis and provide the measurement of model consistency (MC). METHODS Discrimination using area under the receiver operating characteristic curve, calibration, Brier score, and decision curve analysis were conducted to assess the model's performance in the Taiwanese-based cohort. MC was also applied to detect the proportion of paradoxical predictions among 6-week, 3-month, and 1-year survival predictions. The long-term prognosis should not be better than the shorter-term prognosis in that of an individual. RESULTS The 6-week survival rate was 84.2%. The SORG-MLA retained good discrimination with an area under the receiver operating characteristic curve of 0.78 (95% confidence interval, 0.75 to 0.80) and good prediction accuracy with a Brier score of 0.11 (null model Brier score 0.13). There is an underestimation of the 6-week survival rate when the predicted survival rate is less than 50%. Decision curve analysis showed that the model was suitable for use over all threshold probabilities. MC showed suboptimal consistency between 6-week and 90-day survival prediction (78%). CONCLUSIONS The results of this study supported the utility of the algorithm. The online tool ( https://sorg-apps.shinyapps.io/spinemetssurvival/ ) can be used by both clinicians and patients in informative decision-making discussion before management of spinal metastasis.
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Affiliation(s)
- Chih-Chi Su
- From the Department of Orthopaedic Surgery, National Taiwan University Hospital, Taipei City, Taiwan (Su, Lin, Hu, and Yang), the Department of Medical Education, National Taiwan University Hospital, Taipei City, Taiwan (Su and Pan), the Department of Medical Education, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan (Yen), the Department of Orthopaedic Surgery, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan (Lai), the Department of Orthopaedic Surgery, Massachusetts General Hospital, Boston, MA (Zijlstra, Schwab, and Groot), and the Department of Orthopaedics, University Medical Center Utrecht, Utrecht, The Netherlands (Zijlstra, Verlaan, and Groot)
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Ellis SD, Brooks JV, Birken SA, Morrow E, Hilbig ZS, Wulff-Burchfield E, Kinney AY, Ellerbeck EF. Determinants of targeted cancer therapy use in community oncology practice: a qualitative study using the Theoretical Domains Framework and Rummler-Brache process mapping. Implement Sci Commun 2023; 4:66. [PMID: 37308981 PMCID: PMC10259814 DOI: 10.1186/s43058-023-00441-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/25/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Precision medicine holds enormous potential to improve outcomes for cancer patients, offering improved rates of cancer control and quality of life. Not all patients who could benefit from targeted cancer therapy receive it, and some who may not benefit do receive targeted therapy. We sought to comprehensively identify determinants of targeted therapy use among community oncology programs, where most cancer patients receive their care. METHODS Guided by the Theoretical Domains Framework, we conducted semi-structured interviews with 24 community cancer care providers and mapped targeted therapy delivery across 11 cancer care delivery teams using a Rummler-Brache diagram. Transcripts were coded to the framework using template analysis, and inductive coding was used to identify key behaviors. Coding was revised until a consensus was reached. RESULTS Intention to deliver precision medicine was high across all participants interviewed, who also reported untenable knowledge demands. We identified distinctly different teams, processes, and determinants for (1) genomic test ordering and (2) delivery of targeted therapies. A key determinant of molecular testing was role alignment. The dominant expectation for oncologists to order and interpret genomic tests is at odds with their role as treatment decision-makers' and pathologists' typical role to stage tumors. Programs in which pathologists considered genomic test ordering as part of their staging responsibilities reported high and timely testing rates. Determinants of treatment delivery were contingent on resources and ability to offset delivery costs, which low- volume programs could not do. Rural programs faced additional treatment delivery challenges. CONCLUSIONS We identified novel determinants of targeted therapy delivery that potentially could be addressed through role re-alignment. Standardized, pathology-initiated genomic testing may prove fruitful in ensuring patients eligible for targeted therapy are identified, even if the care they need cannot be delivered at small and rural sites which may have distinct challenges in treatment delivery. Incorporating behavior specification and Rummler-Brache process mapping with determinant analysis may extend its usefulness beyond the identification of the need for contextual adaptation.
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Affiliation(s)
- Shellie D. Ellis
- University of Kansas School of Medicine, 3901 Rainbow Blvd., Kansas City, KS 66610 USA
| | - Joanna Veazey Brooks
- University of Kansas School of Medicine, 3901 Rainbow Blvd., Kansas City, KS 66610 USA
| | - Sarah A. Birken
- Wake Forest University School of Medicine, 525 Vine Street, Winston-Salem, NC 27101 USA
| | - Emily Morrow
- Kansas City Kansas Community College, 7250 State Ave., Kansas City, KS 66112 USA
| | - Zachary S. Hilbig
- University of Kansas School of Medicine, 3901 Rainbow Blvd., Kansas City, KS 66610 USA
| | | | - Anita Y. Kinney
- Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany St., New Brunswick, NJ 08901 USA
| | - Edward F. Ellerbeck
- University of Kansas School of Medicine, 3901 Rainbow Blvd., Kansas City, KS 66610 USA
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Fellner A, Goldberg Y, Basel-Salmon L. Ordering genetic testing by neurologists: points to consider. J Neurol 2023:10.1007/s00415-023-11758-3. [PMID: 37154893 DOI: 10.1007/s00415-023-11758-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/10/2023]
Abstract
A significant challenge limiting the comprehensive utilization of genomic medicine is the lack of timely access to genetics specialists. Although neurologists see patients for whom genetic testing should be considered, the knowledge regarding the choice of the optimal genetic test for each case and the management of the test results are out of the scope of their everyday practice. In this review, we provide a step-by-step guide for non-geneticist physicians through the decision-making process when ordering diagnostic genetic testing for monogenic neurological diseases and when dealing with their results.
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Affiliation(s)
- Avi Fellner
- The Neurogenetics Clinic, Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel.
| | - Yael Goldberg
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Lina Basel-Salmon
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Felsenstein Medical Research Center, Tel-Aviv University, Tel-Aviv, Israel
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Murphy R, Colclough K, Pollin TI, Ikle JM, Svalastoga P, Maloney KA, Saint-Martin C, Molnes J, Misra S, Aukrust I, de Franco A, Flanagan SE, Njølstad PR, Billings LK, Owen KR, Gloyn AL. A Systematic Review of the use of Precision Diagnostics in Monogenic Diabetes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.15.23288269. [PMID: 37131594 PMCID: PMC10153302 DOI: 10.1101/2023.04.15.23288269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Monogenic forms of diabetes present opportunities for precision medicine as identification of the underlying genetic cause has implications for treatment and prognosis. However, genetic testing remains inconsistent across countries and health providers, often resulting in both missed diagnosis and misclassification of diabetes type. One of the barriers to deploying genetic testing is uncertainty over whom to test as the clinical features for monogenic diabetes overlap with those for both type 1 and type 2 diabetes. In this review, we perform a systematic evaluation of the evidence for the clinical and biochemical criteria used to guide selection of individuals with diabetes for genetic testing and review the evidence for the optimal methods for variant detection in genes involved in monogenic diabetes. In parallel we revisit the current clinical guidelines for genetic testing for monogenic diabetes and provide expert opinion on the interpretation and reporting of genetic tests. We provide a series of recommendations for the field informed by our systematic review, synthesizing evidence, and expert opinion. Finally, we identify major challenges for the field and highlight areas for future research and investment to support wider implementation of precision diagnostics for monogenic diabetes.
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Affiliation(s)
- Rinki Murphy
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Auckland Diabetes Centre, Te Whatu Ora Health New Zealand, Te Tokai Tumai, Auckland, New Zealand
| | - Kevin Colclough
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jennifer M Ikle
- Department of Pediatrics, Division of Endocrinology & Diabetes, Stanford School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA
| | - Pernille Svalastoga
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kristin A Maloney
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cécile Saint-Martin
- Department of Medical Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Janne Molnes
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Shivani Misra
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Diabetes and Endocrinology, Imperial College Healthcare NHS Trust, London, UK
| | - Ingvild Aukrust
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - aiElisa de Franco
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Sarah E Flanagan
- Department of Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, UK
| | - Pål R Njølstad
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Liana K Billings
- Division of Endocrinology, NorthShore University HealthSystem, Skokie, IL, USA; Department of Medicine, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Katharine R Owen
- Oxford Center for Diabetes, Endocrinology & Metabolism, University of Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anna L Gloyn
- Department of Pediatrics, Division of Endocrinology & Diabetes, Stanford School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
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Handra J, Guimond C, Jordan I, Lenahan B, Ohs K, Beauchesne R, Adam S, Friedman JM, Birch P. A personalized genomic results e-booklet, co-designed and pilot-tested by families. PEC INNOVATION 2022; 1:100039. [PMID: 37213729 PMCID: PMC10194288 DOI: 10.1016/j.pecinn.2022.100039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/19/2022] [Accepted: 04/12/2022] [Indexed: 05/23/2023]
Abstract
Objective To develop and evaluate a personalizable genomic results e-booklet that helps families understand their genomic testing results and navigate available resources. Methods The need for the Genomics Results e-Booklet was identified by families, after which this tool was developed by a team of clinical researchers and three parent-advisors. We customized the genomic results e-booklet for 50 families participating in a genomic sequencing research study. We conducted an assessment using a 19-question survey and semi-structured interviews to elicit feedback and iteratively improve the tool. Results 25 users provided feedback via questionnaires and seven respondents were interviewed. Genomic Results e-Booklet recipients responded favorably: 96% of participants stated that it helped them remember information shared during their results appointment, 80% said it had or would help them communicate their results with other healthcare providers, 68% felt that it helped to identify and guide their next steps, and 72% anticipated that the e-booklet would have future utility. Conclusion The Genomic Results e-Booklet is a patient and family-oriented resource that complements post-test genetic counselling. Innovation Compared to traditional laboratory reports and clinical letters, the Genomics Results e-Booklet is patient-conceived and patient-centered, and allows clinicians to efficiently personalize content and prioritize patient understanding and support.
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Affiliation(s)
- Julia Handra
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- Corresponding author.
| | - Colleen Guimond
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | | | | | - Kelsey Ohs
- Parent Research Advisor, British Columbia, Canada
| | - Rhea Beauchesne
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Shelin Adam
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Jan M. Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Patricia Birch
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, C201 - 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
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Recchia G, Lawrence AC, Freeman AL. Investigating the presentation of uncertainty in an icon array: A randomized trial. PEC INNOVATION 2022; 1:None. [PMID: 36518604 PMCID: PMC9731905 DOI: 10.1016/j.pecinn.2021.100003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 06/17/2023]
Abstract
BACKGROUND Clinicians are often advised to use pictographs to communicate risk, but whether they offer benefits when communicating risk imprecision (e.g., 65%-79%) is unknown. PURPOSE To test whether any of three approaches to visualizing imprecision would more effectively communicate breast and ovarian cancer risk for BRCA1 pathogenic variant carriers. METHODS 1,300 UK residents were presented with a genetic report with information about BRCA1-related risks, with random assignment to one of four formats: no visualization (text alone), or a pictograph using shaded icons, a gradient, or arrows marking range endpoints. We also tested pictographs in two layouts. Analysis of variance (ANOVA) and regression was employed. RESULTS There was no effect of format. Participants shown pictographs vs. text alone had better uptake of breast cancer risk messages (p < .05, η 2 = 0.003). Pictographs facilitated memory for the specific amount of risk (p < 0.001, η 2 = 0.019), as did the tabular layout. Individuals not having completed upper secondary education may benefit most. CONCLUSIONS We found weak evidence in favor of using simple pictographs with ranges to communicate BRCA risk (versus text alone), and of the tabular layout. INNOVATION Testing different ways of communicating imprecision within pictographs is a novel and promising line of research.
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Affiliation(s)
- Gabriel Recchia
- Corresponding author at: Centre for Mathematical Sciences, Wilberforce Rd, Cambridge CB3 0WA, UK.
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Brett GR, Ward A, Bouffler SE, Palmer EE, Boggs K, Lynch F, Springer A, Nisselle A, Stark Z. Co-design, implementation, and evaluation of plain language genomic test reports. NPJ Genom Med 2022; 7:61. [PMID: 36272999 PMCID: PMC9588009 DOI: 10.1038/s41525-022-00332-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022] Open
Abstract
Understanding and communicating genomic results can be challenging for families and health professionals without genetic specialty training. Unlike modifying existing laboratory reports, plain language genomic test reports provide an opportunity for patient/family-centered approaches. However, emerging examples generally lack co-design and/or evaluation in real-world settings. Through co-design involving patient groups, plain language experts, educators, and genetic health professionals, plain language genomic test report templates were produced for common test outcomes in rare diseases. Eight plain language genomic test report templates were developed. These reports were piloted and evaluated as part of a national pediatric ultra-rapid genomic testing program. Family and genetic health professional experiences with report layout, content, and use were explored using surveys. Of 154 families and 107 genetic health professionals issued with reports, 51 families and 57 clinicians responded (RR = 33% and 53%, respectively). Most families (82%) found their report helpful in understanding the result. Reports were shared by 63% of families, predominantly with family members (72%), or health professionals (68%). Clinicians (15%) adapted the reports for other settings. Through co-design, plain language genomic test reports implemented in a real-world setting can facilitate patient/family and caregiver understanding and communication of genomic test purpose, outcome, and potential clinical implications.
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Affiliation(s)
- Gemma R Brett
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia. .,The University of Melbourne, Melbourne, VIC, Australia.
| | - Aisha Ward
- The University of Melbourne, Melbourne, VIC, Australia
| | | | - Elizabeth E Palmer
- Sydney Children's Hospitals Network, Sydney, NSW, Australia.,The University of New South Wales, Sydney, NSW, Australia
| | - Kirsten Boggs
- Australian Genomics, Melbourne, VIC, Australia.,Sydney Children's Hospitals Network, Sydney, NSW, Australia
| | - Fiona Lynch
- The University of Melbourne, Melbourne, VIC, Australia.,Australian Genomics, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Amanda Springer
- Monash Genetics, Monash Health, Melbourne, VIC, Australia.,Monash University, Melbourne, VIC, Australia
| | - Amy Nisselle
- The University of Melbourne, Melbourne, VIC, Australia.,Australian Genomics, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,The University of Melbourne, Melbourne, VIC, Australia.,Australian Genomics, Melbourne, VIC, Australia
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11
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Krey I, Platzer K, Esterhuizen A, Berkovic SF, Helbig I, Hildebrand MS, Lerche H, Lowenstein D, Møller RS, Poduri A, Sadleir L, Sisodiya SM, Weckhuysen S, Wilmshurst JM, Weber Y, Lemke JR. Current practice in diagnostic genetic testing of the epilepsies. Epileptic Disord 2022; 24:765-786. [PMID: 35830287 PMCID: PMC10752379 DOI: 10.1684/epd.2022.1448] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/10/2022] [Indexed: 01/19/2023]
Abstract
Epilepsy genetics is a rapidly developing field, in which novel disease-associated genes, novel mechanisms associated with epilepsy, and precision medicine approaches are continuously being identified. In the past decade, advances in genomic knowledge and analysis platforms have begun to make clinical genetic testing accessible for, in principle, people of all ages with epilepsy. For this reason, the Genetics Commission of the International League Against Epilepsy (ILAE) presents this update on clinical genetic testing practice, including current techniques, indications, yield of genetic testing, recommendations for pre- and post-test counseling, and follow-up after genetic testing is completed. We acknowledge that the resources vary across different settings but highlight that genetic diagnostic testing for epilepsy should be prioritized when the likelihood of an informative finding is high. Results of genetic testing, in particular the identification of causative genetic variants, are likely to improve individual care. We emphasize the importance of genetic testing for individuals with epilepsy as we enter the era of precision therapy.
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Affiliation(s)
- Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Alina Esterhuizen
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Samuel F. Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne (Austin Health), Heidelberg, VIC, Australia
| | - Ingo Helbig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts-University, Building C, Arnold-Heller-Straße 3, 24105 Kiel, Germany
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104 USA
| | - Michael S. Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg and Murdoch Children’s Research Institute, Royal Children’s Hospital, Victoria, Australia
| | - Holger Lerche
- Department of Epileptology and Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany
| | - Daniel Lowenstein
- Department of Neurology, University of California, San Francisco, USA
| | - Rikke S. Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Annapurna Poduri
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynette Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, New Zealand
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology London, UK and Chalfont Centre for Epilepsy, Buckinghamshire, UK
| | - Sarah Weckhuysen
- Center for Molecular Neurology, VIB-University of Antwerp, VIB, Antwerp, Belgium; Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Jo M. Wilmshurst
- Department of Paediatric Neurology, Paediatric and Child Health, Red Cross War Memorial Children’s Hospital, Neuroscience Institute, University of Cape Town, South Africa
| | - Yvonne Weber
- Department of Epileptology and Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany
- Department of Epileptology and Neurology, University of Aachen, Germany
| | - Johannes R. Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
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12
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Krauss E, Macher J, Capasso J, Bernhardt B, Ali-KhanCatts Z, Levin A, Brandt R. Experiences of genetic testing among individuals with retinitis pigmentosa. Ophthalmic Genet 2022; 43:633-640. [PMID: 35796432 DOI: 10.1080/13816810.2022.2096243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND Retinitis pigmentosa (RP) is a genetically heterogeneous retinal dystrophy which results in progressive vision loss. There is scant literature on the experiences of genetic testing in patients with RP. MATERIALS AND METHODS Patients with a clinical diagnosis of RP who received genetic testing at the Wills Eye Ocular Genetics clinic between 2016 and 2020 were recruited. Telephone interviews were conducted using a semi-structured guide designed to elicit participant experiences with genetic testing. A thematic analysis was performed to describe patterns in participant responses. RESULTS Twelve patients participated. Seven participants identified as female and five as male, with ages ranging from 22 to 70. Ten patients had positive genetic test results, while two had negative genetic testing. Reported motivations for genetic testing included qualification for clinical trials (58% of total participants), determination of etiology or usal gene (50%), reproductive concerns (50%), and prognostic outlook (50%). Most participants (75%) expressed satisfaction about their decision to pursue genetic testing. Participants with both positive and negative genetic testing reported persistent uncertainty regarding their prognosis for visual decline (50%). Genetic confirmation of disease leads to initiation of safety and vision-protecting health behaviors (42%). CONCLUSION Patients with RP are generally satisfied with their testing experience, despite approaching testing with a wide range of motivations and expectations. Future research can leverage this methodology to identify targets for improvement in pre- and post-test education and counselling.
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Affiliation(s)
- Emily Krauss
- Duke Eye Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jared Macher
- University of Rochester School of Medicine, Rochester, New York, USA
| | - Jenina Capasso
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Rochester, New York, USA.,Pediatric Genetics, Golisano Children's Hospital, Rochester, New York, USA
| | - Barbara Bernhardt
- Human Genetics and Genetic Counseling, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Zohra Ali-KhanCatts
- Human Genetics and Genetic Counseling, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Alex Levin
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Rochester, New York, USA.,Pediatric Genetics, Golisano Children's Hospital, Rochester, New York, USA
| | - Rachael Brandt
- Human Genetics and Genetic Counseling, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Lankenau Medical Center, Main Line Health Hospitals, Wynnewood, Pennsylvania, USA.,Lankenau Institute for Medical Research, Wynnewood, Pennsylvania, USA
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13
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Recchia G, Lawrence ACE, Capacchione L, Freeman ALJ. Making BRCA1 genetic test reports easier to understand through user-centered design: A randomized trial. Genet Med 2022; 24:1684-1696. [PMID: 35522238 DOI: 10.1016/j.gim.2022.04.016] [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: 12/14/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE Our objective was to apply a user-centered design process to identify phrases, graphics, and ways of communicating numerical risks that could be used to help patients understand their cancer risk and next steps on receiving BRCA1 genetic test results (positive, negative, and variants of uncertain significance). METHODS The first phase of the study, a user-centered design process, consisted of 4 rounds of interviews (N = 42, including 13 health care professionals and 16 patients having undergone BRCA testing). The second was a randomized, between-participants experimental study of 456 United Kingdom residents that compared the resulting reports to reports used in a United Kingdom national genomic laboratory hub. Outcomes were subjective and objective comprehension, communication efficacy, actionability, and perceived risk. RESULTS Subjective comprehension, communication efficacy, and actionability were all higher for the user-centered reports, with no difference in perceived risk. Comprehension of participants viewing user-centered reports was significantly better on 2 items, directionally (but not significantly) better on 6 items, and directionally (but not significantly) worse on 2 items. CONCLUSION Our results imply that user-centered design is a promising approach for developing materials about complex genetic risks. We suggest wordings that are likely to lead to improved comprehension when communicating BRCA-associated risks.
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Affiliation(s)
- Gabriel Recchia
- Winton Centre for Risk and Evidence Communication, Department of Pure Mathematics and Mathematical Statistics, University of Cambridge, Cambridge, United Kingdom.
| | - Alice C E Lawrence
- Winton Centre for Risk and Evidence Communication, Department of Pure Mathematics and Mathematical Statistics, University of Cambridge, Cambridge, United Kingdom
| | | | - Alexandra L J Freeman
- Winton Centre for Risk and Evidence Communication, Department of Pure Mathematics and Mathematical Statistics, University of Cambridge, Cambridge, United Kingdom
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14
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Hao L, Kraft P, Berriz GF, Hynes ED, Koch C, Korategere V Kumar P, Parpattedar SS, Steeves M, Yu W, Antwi AA, Brunette CA, Danowski M, Gala MK, Green RC, Jones NE, Lewis ACF, Lubitz SA, Natarajan P, Vassy JL, Lebo MS. Development of a clinical polygenic risk score assay and reporting workflow. Nat Med 2022; 28:1006-1013. [PMID: 35437332 PMCID: PMC9117136 DOI: 10.1038/s41591-022-01767-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/02/2022] [Indexed: 12/31/2022]
Abstract
Implementation of polygenic risk scores (PRS) may improve disease prevention and management but poses several challenges: the construction of clinically valid assays, interpretation for individual patients, and the development of clinical workflows and resources to support their use in patient care. For the ongoing Veterans Affairs Genomic Medicine at Veterans Affairs (GenoVA) Study we developed a clinical genotype array-based assay for six published PRS. We used data from 36,423 Mass General Brigham Biobank participants and adjustment for population structure to replicate known PRS-disease associations and published PRS thresholds for a disease odds ratio (OR) of 2 (ranging from 1.75 (95% CI: 1.57-1.95) for type 2 diabetes to 2.38 (95% CI: 2.07-2.73) for breast cancer). After confirming the high performance and robustness of the pipeline for use as a clinical assay for individual patients, we analyzed the first 227 prospective samples from the GenoVA Study and found that the frequency of PRS corresponding to published OR > 2 ranged from 13/227 (5.7%) for colorectal cancer to 23/150 (15.3%) for prostate cancer. In addition to the PRS laboratory report, we developed physician- and patient-oriented informational materials to support decision-making about PRS results. Our work illustrates the generalizable development of a clinical PRS assay for multiple conditions and the technical, reporting and clinical workflow challenges for implementing PRS information in the clinic.
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Affiliation(s)
- Limin Hao
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Gabriel F Berriz
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | - Elizabeth D Hynes
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | - Christopher Koch
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | | | - Shruti S Parpattedar
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | - Marcie Steeves
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
- Medical Genetics, Massachusetts General Hospital, Boston, MA, USA
| | - Wanfeng Yu
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | - Ashley A Antwi
- Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | | | | | - Manish K Gala
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Robert C Green
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Precision Population Health, Ariadne Labs, Boston, MA, USA
| | - Natalie E Jones
- Veterans Affairs Boston Healthcare System, Boston, MA, USA
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna C F Lewis
- E J Safra Center for Ethics, Harvard University, Cambridge, MA, USA
| | - Steven A Lubitz
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Pradeep Natarajan
- Harvard Medical School, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jason L Vassy
- Veterans Affairs Boston Healthcare System, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Precision Population Health, Ariadne Labs, Boston, MA, USA.
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
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15
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French CE, Dolling H, Mégy K, Sanchis-Juan A, Kumar A, Delon I, Wakeling M, Mallin L, Agrawal S, Austin T, Walston F, Park SM, Parker A, Piyasena C, Bradbury K, Ellard S, Rowitch DH, Raymond FL. Refinements and considerations for trio whole genome sequence analysis when investigating Mendelian Diseases presenting in early childhood. HGG ADVANCES 2022; 3:100113. [PMID: 35586607 PMCID: PMC9108978 DOI: 10.1016/j.xhgg.2022.100113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022] Open
Abstract
To facilitate early deployment of whole-genome sequencing (WGS) for severely ill children, a standardized pipeline for WGS analysis with timely turnaround and primary care pediatric uptake is needed. We developed a bioinformatics pipeline for comprehensive gene-agnostic trio WGS analysis of children suspected of having an undiagnosed monogenic disease that included detection and interpretation of primary genetic mechanisms of disease, including SNVs/indels, CNVs/SVs, uniparental disomy (UPD), imprinted genes, short tandem repeat expansions, mobile element insertions, SMN1/2 copy number calling, and mitochondrial genome variants. We assessed primary care practitioner experience and competence in a large cohort of 521 families (comprising 90% WGS trios). Children were identified by primary practitioners for recruitment, and we used the UK index of multiple deprivation to confirm lack of patient socio-economic status ascertainment bias. Of the 521 children sequenced, 176 (34%) received molecular diagnoses, with rates as high as 45% for neurology clinics. Twenty-three of the diagnosed cases (13%) required bespoke methods beyond routine SNV/CNV analysis. In our multidisciplinary clinician user experience assessment, both pediatricians and clinical geneticists expressed strong support for rapid WGS early in the care pathway, but requested further training in determining patient selection, consenting, and variant interpretation. Rapid trio WGS provides an efficacious single-pass screening test for children when deployed by primary practitioners in clinical settings that carry high a priori risk for rare pediatric disease presentations.
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Affiliation(s)
- Courtney E. French
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Boston Children’s Hospital, Boston, MA 02115, USA
| | - Helen Dolling
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Centre for Family Research, Department of Psychology, University of Cambridge, Cambridge CB2 3RQ, UK
| | - Karyn Mégy
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alba Sanchis-Juan
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Ajay Kumar
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
| | - Isabelle Delon
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Matthew Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX4 4PY, UK
| | - Lucy Mallin
- Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Shruti Agrawal
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Topun Austin
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Florence Walston
- Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich NR4 7UY, UK
| | - Soo-Mi Park
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alasdair Parker
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | | | | | | | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter EX4 4PY, UK
- Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - David H. Rowitch
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - F. Lucy Raymond
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- NIHR Bioresource, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Corresponding author
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16
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Parry CM, Seddon G, Rogers N, Sinha IP, Bracken L, King C, Peak M, Hawcutt DB. Pharmacogenomics and asthma treatment: acceptability to children, families and healthcare professionals. Arch Dis Child 2022; 107:394-399. [PMID: 35074833 DOI: 10.1136/archdischild-2021-322396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 12/30/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Evidence supporting personalised treatment for asthma based on an individual's genetics is mounting. The views of children and young people (CYP), parents and healthcare professionals (HCPs) about this evolution of clinical care are not known. METHODS A pilot prospective questionnaire-based study was undertaken of CYP with asthma, their parents and HCPs at a secondary/tertiary children's hospital in the UK. RESULTS Fifty-nine questionnaires were distributed and 50 returned (response rate 84.7%), comprising 26 CYP (10 were 5-11 years, 11 were 12-15 years and 5 were 16-18 years old), 13 parents and 11 HCPs. For all types of data, personal information was ranked as the 'most important' (n=19, 47.5%) and 'most private' (n=16, 40%), but with considerable variation across groups. Within health data, allergies were rated as 'most important' (n=12, 30.8%), and mental health records the 'most private' (n=21, 53.8%), again with variation across groups. A 'personalised genetic asthma plan' was acceptable to the majority overall (n=40, 80.0%). With regard to sharing CYP's genetic data, 23 (46%) of participants were happy for unconditional sharing between HCPs, and 23 (46%) agreed to sharing solely in relation to the CYP's asthma management. Forty-two (84.0%) of participants felt CYP should be informed about genetic data being shared, and the majority felt this should commence by 12 years of age. CONCLUSION The use of genetic information to guide management of asthma in CYP is largely acceptable to CYP, parents/guardians and HCPs. However, there are key differences between the opinions of CYP, parents and HCPs.
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Affiliation(s)
- Christopher Mark Parry
- Department of Research, NIHR Alder Hey Clinical Research Facility, Liverpool, UK.,Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - Gabrielle Seddon
- Paediatric Medicines Research Unit, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Naomi Rogers
- Paediatric Medicines Research Unit, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Ian P Sinha
- Department of Respiratory Medicine, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Louise Bracken
- Paediatric Medicines Research Unit, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Charlotte King
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - Matthew Peak
- Paediatric Medicines Research Unit, Alder Hey Children's NHS Foundation Trust, Liverpool, UK.,Research and Development, NIHR Alder Hey Clinical Research Facility, Liverpool, UK
| | - Daniel B Hawcutt
- Department of Research, NIHR Alder Hey Clinical Research Facility, Liverpool, UK .,Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
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17
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Laforet PE, Yalamanchili B, Hillyer GC, Basch CH. YouTube as an information source on BRCA mutations: implications for patients and professionals. J Community Genet 2022; 13:257-262. [PMID: 35023041 DOI: 10.1007/s12687-022-00576-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/05/2022] [Indexed: 10/19/2022] Open
Abstract
Genetic testing for BRCA1/2 mutations in early breast cancer has been shown to be beneficial, and an increase in surveillance using these genetic markers is recommended. Given this recommendation, it is likely that individuals gather information about such testing. Social media is increasingly becoming a common source of health information. One such platform known for sharing health information is YouTube. The purpose of this study was to describe content related to BRCA1/2 mutations on YouTube. The sample included 100 English language videos, which were coded for content related to BRCA1/2 mutations. The 100 videos evaluated in this study were viewed 5.5 million times. In general, the BRCA1 and BRCA2 gene mutations were mentioned simultaneously, with only 15% of videos explaining the difference in prevalence or implication of the variants individually. A great number of videos (85.0%) discussed having genetic testing to determine the presence of BRCA mutations, but only 16.0% discussed the potential harms of BRCA mutation testing and 42.0% mentioned seeking genetic counseling to determine the need for testing and interpretation of the test results. Comparing the characteristics and content of videos created by healthcare professionals (n = 71) to those created by consumers and the media (n = 29), we found that consumer/media videos were viewed twice as many times as professional videos (3,704,351 vs. 1,851,825, p = 0.04). Videos from medical professionals should include consistent information on the recommendations for individuals who test positive for a BRCA mutation. Such content should include education about BRCA mutations, testing, implications of those results and ways to reduce risk, and recommendations for increased surveillance and enhanced screening for individuals positive for BRCA mutations.
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Affiliation(s)
- Priscila E Laforet
- Department of Epidemiology, Mailman School of Public Health, Columbia University NY, New York, NY, 10032, USA
| | - Bhavya Yalamanchili
- Department of Public Health, William Paterson University, University Hall, Wayne, NJ, 07470, USA
| | - Grace C Hillyer
- Department of Epidemiology, Mailman School of Public Health, Columbia University NY, New York, NY, 10032, USA
| | - Corey H Basch
- Department of Public Health, William Paterson University, University Hall, Wayne, NJ, 07470, USA.
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18
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A Next Generation Sequencing-Based Protocol for Screening of Variants of Concern in Autism Spectrum Disorder. Cells 2021; 11:cells11010010. [PMID: 35011571 PMCID: PMC8750892 DOI: 10.3390/cells11010010] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 01/11/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with strong genetic influences. There is an increasing demand for ASD genetic testing beyond the traditionally recommended microarray and syndromic autism testing; however, the current whole genome sequencing (WGS) and whole exome sequencing (WES) methods are lacking an academic standard for WGS variant annotation, reporting, and interpretation, tailored towards patients with ASD and offer very limited interpretation for clinical significance. Using WGS data from six family trios, we demonstrate the clinical feasibility and technical implementation of an evidence-based, fully transparent bioinformatics pipeline and report framework for an ASD-focused WGS genetic report. We confirmed a portion of the key variants with Sanger sequencing and provided interpretation with consideration of patients’ clinical symptoms and detailed literature review. Furthermore, we showed that identification of the genetic contributions of ASD core symptoms and comorbidities may promote a better understanding of the ASD pathophysiology, lead to early detection of associated comorbidities, and facilitate pharmacologic intervention based on pathological pathways inferred from the genetic information. We will make the bioinformatics pipeline and interpretation framework publicly available, in an easily accessible format, after validation with a larger cohort. We hope that the present proposed protocol can serve as a starting point to invite discourse and debate to further improve approaches in WGS-based genetic consultation for patients with ASD.
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19
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Challenges and practical solutions for managing secondary genomic findings in primary care. Eur J Med Genet 2021; 65:104384. [PMID: 34768014 DOI: 10.1016/j.ejmg.2021.104384] [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: 04/22/2021] [Revised: 07/25/2021] [Accepted: 11/07/2021] [Indexed: 11/22/2022]
Abstract
Primary care providers will increasingly be tasked with managing most secondary findings from genomic sequencing, but literature exploring their capacity to manage findings beyond conventional genetic testing is limited. This study aimed to explore primary care providers' challenges and potential solutions for managing secondary findings. Providers were recruited in two groups. Group 1 providers had a patient in their practice who received secondary findings and all potential group 1 providers were invited to participate. Group 2 providers were provided with the secondary findings of a hypothetical patient and were purposefully sampled for maximal variation in sex, practice setting, and geographic location. Providers were interviewed about their challenges and solutions managing secondary findings from a patient in their practice or a hypothetical patient. Using interpretive description methodology, transcripts were analysed thematically complemented by constant comparison. Out of the fifty-five providers invited, 15 family physicians participated across community and academic settings in Ontario, Canada (range 6-40 years in practice; 10/15 female). Providers described a responsibility to manage secondary findings, but limited capacity for this, describing practice, knowledge, and technical challenges. Providers expressed concern that compared to other incidental findings, secondary genomic findings might be reported directly to patients and result in longer-term anxiety. Potential solutions were a structured letter with categorized results and summary tables highlighting key secondary findings with follow-up recommendations and resources, as well as electronic medical records (EMRs) that store and integrate genomic information for prescribing or referrals. These solutions were deemed essential to address knowledge and technical challenges faced by primary care physicians and ultimately promote clinical utility of secondary findings.
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20
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Carter AB, Abruzzo LV, Hirschhorn JW, Jones D, Jordan DC, Nassiri M, Ogino S, Patel NR, Suciu CG, Temple-Smolkin RL, Zehir A, Roy S. Electronic Health Records and Genomics: Perspectives from the Association for Molecular Pathology Electronic Health Record (EHR) Interoperability for Clinical Genomics Data Working Group. J Mol Diagn 2021; 24:1-17. [PMID: 34656760 DOI: 10.1016/j.jmoldx.2021.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/14/2021] [Accepted: 09/28/2021] [Indexed: 02/09/2023] Open
Abstract
The use of genomics in medicine is expanding rapidly, but information systems are lagging in their ability to support genomic workflows both from the laboratory and patient-facing provider perspective. The complexity of genomic data, the lack of needed data standards, and lack of genomic fluency and functionality as well as several other factors have contributed to the gaps between genomic data generation, interoperability, and utilization. These gaps are posing significant challenges to laboratory and pathology professionals, clinicians, and patients in the ability to generate, communicate, consume, and use genomic test results. The Association for Molecular Pathology Electronic Health Record Working Group was convened to assess the challenges and opportunities and to recommend solutions on ways to resolve current problems associated with the display and use of genomic data in electronic health records.
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Affiliation(s)
- Alexis B Carter
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Children's Healthcare of Atlanta, Atlanta, Georgia.
| | - Lynne V Abruzzo
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, Ohio
| | - Julie W Hirschhorn
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Medical University of South Carolina, Charleston, South Carolina
| | - Dan Jones
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; The Ohio State University Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, Columbus, Ohio
| | | | - Mehdi Nassiri
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Shuji Ogino
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Brigham & Women's Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts; Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Nimesh R Patel
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Rhode Island Hospital and Alpert Medical School of Brown University, Providence, Rhode Island
| | - Christopher G Suciu
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri; Institute for Informatics, Washington University School of Medicine, St. Louis, Missouri
| | | | - Ahmet Zehir
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Somak Roy
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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21
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Brockman DG, Petronio L, Dron JS, Kwon BC, Vosburg T, Nip L, Tang A, O'Reilly M, Lennon N, Wong B, Ng K, Huang KH, Fahed AC, Khera AV. Design and user experience testing of a polygenic score report: a qualitative study of prospective users. BMC Med Genomics 2021; 14:238. [PMID: 34598685 PMCID: PMC8485114 DOI: 10.1186/s12920-021-01056-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
Background Polygenic scores—which quantify inherited risk by integrating information from many common sites of DNA variation—may enable a tailored approach to clinical medicine. However, alongside considerable enthusiasm, we and others have highlighted a lack of standardized approaches for score disclosure. Here, we review the landscape of polygenic score reporting and describe a generalizable approach for development of a polygenic score disclosure tool for coronary artery disease. Methods We assembled a working group of clinicians, geneticists, data visualization specialists, and software developers. The group reviewed existing polygenic score reports and then designed a two-page mock report for coronary artery disease. We then conducted a qualitative user-experience study with this report using an interview guide focused on comprehension, experience, and attitudes. Interviews were transcribed and analyzed for themes identification to inform report revision. Results Review of nine existing polygenic score reports from commercial and academic groups demonstrated significant heterogeneity, reinforcing the need for additional efforts to study and standardize score disclosure. Using a newly developed mock score report, we conducted interviews with ten adult individuals (50% females, 70% without prior genetic testing experience, age range 20–70 years) recruited via an online platform. We identified three themes from interviews: (1) visual elements, such as color and simple graphics, enable participants to interpret, relate to, and contextualize their polygenic score, (2) word-based descriptions of risk and polygenic scores presented as percentiles were the best recognized and understood, (3) participants had varying levels of interest in understanding complex genomic information and therefore would benefit from additional resources that can adapt to their individual needs in real time. In response to user feedback, colors used for communicating risk were modified to minimize unintended color associations and odds ratios were removed. All 10 participants expressed interest in receiving a polygenic score report based on their personal genomic information. Conclusions Our findings describe a generalizable approach to develop a polygenic score report understandable by potential patients. Although additional studies are needed across a wider spectrum of patient populations, these results are likely to inform ongoing efforts related to polygenic score disclosure within clinical practice. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01056-0.
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Affiliation(s)
- Deanna G Brockman
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building
- CPZN 6.256, Boston, MA, 02114, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lia Petronio
- Pattern Visualization Team, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacqueline S Dron
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bum Chul Kwon
- Center for Computational Health, IBM Research, Cambridge, MA, USA
| | - Trish Vosburg
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lisa Nip
- Pattern Visualization Team, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew Tang
- Pattern Visualization Team, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mary O'Reilly
- Pattern Visualization Team, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Niall Lennon
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bang Wong
- Pattern Visualization Team, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenney Ng
- Center for Computational Health, IBM Research, Cambridge, MA, USA
| | - Katherine H Huang
- Pattern Visualization Team, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Akl C Fahed
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building
- CPZN 6.256, Boston, MA, 02114, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Amit V Khera
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building
- CPZN 6.256, Boston, MA, 02114, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
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22
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Farmer GD, Pearson M, Skylark WJ, Freeman ALJ, Spiegelhalter DJ. Redevelopment of the Predict: Breast Cancer website and recommendations for developing interfaces to support decision-making. Cancer Med 2021; 10:5141-5153. [PMID: 34152085 PMCID: PMC8335820 DOI: 10.1002/cam4.4072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 12/24/2022] Open
Abstract
Objectives To develop a new interface for the widely used prognostic breast cancer tool: Predict: Breast Cancer. To facilitate decision‐making around post‐surgery breast cancer treatments. To derive recommendations for communicating the outputs of prognostic models to patients and their clinicians. Method We employed a user‐centred design process comprised of background research and iterative testing of prototypes with clinicians and patients. Methods included surveys, focus groups and usability testing. Results The updated interface now caters to the needs of a wider audience through the addition of new visualisations, instantaneous updating of results, enhanced explanatory information and the addition of new predictors and outputs. A programme of future research was identified and is now underway, including the provision of quantitative data on the adverse effects of adjuvant breast cancer treatments. Based on our user‐centred design process, we identify six recommendations for communicating the outputs of prognostic models including the need to contextualise statistics, identify and address gaps in knowledge, and the critical importance of engaging with prospective users when designing communications. Conclusions For prognostic algorithms to fulfil their potential to assist with decision‐making they need carefully designed interfaces. User‐centred design puts patients and clinicians needs at the forefront, allowing them to derive the maximum benefit from prognostic models.
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Affiliation(s)
- George D Farmer
- Winton Centre for Risk and Evidence Communication, University of Cambridge, Cambridge, UK.,Division of Neuroscience and Experimental Psychology, University of Manchester, Manchester, UK
| | - Mike Pearson
- Winton Centre for Risk and Evidence Communication, University of Cambridge, Cambridge, UK
| | | | - Alexandra L J Freeman
- Winton Centre for Risk and Evidence Communication, University of Cambridge, Cambridge, UK
| | - David J Spiegelhalter
- Winton Centre for Risk and Evidence Communication, University of Cambridge, Cambridge, UK
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23
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Uhlig HH, Charbit-Henrion F, Kotlarz D, Shouval DS, Schwerd T, Strisciuglio C, de Ridder L, van Limbergen J, Macchi M, Snapper SB, Ruemmele FM, Wilson DC, Travis SP, Griffiths AM, Turner D, Klein C, Muise AM, Russell RK. Clinical Genomics for the Diagnosis of Monogenic Forms of Inflammatory Bowel Disease: A Position Paper From the Paediatric IBD Porto Group of European Society of Paediatric Gastroenterology, Hepatology and Nutrition. J Pediatr Gastroenterol Nutr 2021; 72:456-473. [PMID: 33346580 PMCID: PMC8221730 DOI: 10.1097/mpg.0000000000003017] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND It is important to identify patients with monogenic IBD as management may differ from classical IBD. In this position statement we formulate recommendations for the use of genomics in evaluating potential monogenic causes of IBD across age groups. METHODS The consensus included paediatric IBD specialists from the Paediatric IBD Porto group of the European Society of Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) and specialists from several monogenic IBD research consortia. We defined key topics and performed a systematic literature review to cover indications, technologies (targeted panel, exome and genome sequencing), gene panel setup, cost-effectiveness of genetic screening, and requirements for the clinical care setting. We developed recommendations that were voted upon by all authors and Porto group members (32 voting specialists). RESULTS We recommend next-generation DNA-sequencing technologies to diagnose monogenic causes of IBD in routine clinical practice embedded in a setting of multidisciplinary patient care. Routine genetic screening is not recommended for all IBD patients. Genetic testing should be considered depending on age of IBD-onset (infantile IBD, very early-onset IBD, paediatric or young adult IBD), and further criteria, such as family history, relevant comorbidities, and extraintestinal manifestations. Genetic testing is also recommended in advance of hematopoietic stem cell transplantation. We developed a diagnostic algorithm that includes a gene panel of 75 monogenic IBD genes. Considerations are provided also for low resource countries. CONCLUSIONS Genomic technologies should be considered an integral part of patient care to investigate patients at risk for monogenic forms of IBD.
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Affiliation(s)
- Holm H. Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- Department of Pediatrics, University of Oxford, Oxford, United Kingdom
- Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Fabienne Charbit-Henrion
- Université de Paris, INSERM UMR 1163 Immunité Intestinale, APHP, Hôpital Necker Enfants Malades, Service de Génétique moléculaire, Paris, France
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Dror S. Shouval
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Tobias Schwerd
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | | | - Lissy de Ridder
- Department of Paediatric Gastroenterology, Erasmus University Medical Center Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Johan van Limbergen
- Amsterdam University Medical Centres, Emma Children’s Hospital, The Netherlands and Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Marina Macchi
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
| | - Scott B. Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Frank M. Ruemmele
- Université de Paris, APHP, Hôpital Necker Enfants Malades, Service de Gastroentérologie pédiatrique, Paris, France
| | - David C. Wilson
- Child Life and Health, University of Edinburgh, Department of Paediatric Gastroenterology, The Royal Hospital for Sick Children, Edinburgh
| | - Simon P.L. Travis
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Anne M. Griffiths
- The Hospital for Sick Children, University of Toronto
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, The Hospital for Sick Children
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Toronto, Ontario, Canada
| | - Dan Turner
- Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Aleixo M. Muise
- The Hospital for Sick Children, University of Toronto
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, The Hospital for Sick Children
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Toronto, Ontario, Canada
| | - Richard K. Russell
- Child Life and Health, University of Edinburgh, Department of Paediatric Gastroenterology, The Royal Hospital for Sick Children, Edinburgh
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