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Carrasco E, López-Fernández A, Codina-Sola M, Valenzuela I, Cueto-González AM, Villacampa G, Navarro V, Torres-Esquius S, Palau D, Cruellas M, Torres M, Perez-Dueñas B, Abulí A, Diez O, Sábado-Álvarez C, García-Arumí E, Tizzano EF, Moreno L, Balmaña J. Clinical and psychological implications of secondary and incidental findings in cancer susceptibility genes after exome sequencing in patients with rare disorders. J Med Genet 2022:jmg-2022-108929. [DOI: 10.1136/jmg-2022-108929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022]
Abstract
Background/ObjectivesExome sequencing may identify pathogenic variants unrelated with the purpose of the analysis. We investigated the frequency of secondary and incidental findings (SF/IF) in cancer susceptibility genes (CSG), their clinical actionability and the psychological impact in individuals with an SF/IF (cases) compared with individuals tested due to their cancer history (controls).MethodsThis study analysed 533 exomes ordered for non-cancer conditions. Medical records were reviewed for clinical actionability of SF/IF. Psychological impact was analysed using the Multidimensional Impact of Cancer Risk Assessment (MICRA) scale and compared between cases and controls with a propensity score weighting method.ResultsThe frequency of SF/IF in CSG was 2.1% (95% CI 1.1% to 3.8%): threeBRCA2, threePMS2, twoSDHB, and one each inBRCA1,MLH1andRAD51C. Among the relatives, 18 were carriers. Twenty enrolled for surveillance, and a neoplasm was diagnosed in 20%: three paragangliomas and one breast cancer. Cases presented higher MICRA mean scores than controls (21.3 vs 16.2 in MICRA total score, 6.3 vs 4.2 in the distress subscale, and 8.3 vs 6.6 in the uncertainty subscale; all p<0.001).ConclusionSF/IF in CSG were identified in 2.1% of patients. Despite a numerically higher psychological impact, the identification of SF/IF allowed early detection and cancer prevention in families without cancer history.
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McCormick CZ, Yu KD, Johns A, Campbell-Salome G, Hallquist MLG, Sturm AC, Buchanan AH. Investigating Psychological Impact after Receiving Genetic Risk Results-A Survey of Participants in a Population Genomic Screening Program. J Pers Med 2022; 12:1943. [PMID: 36556164 PMCID: PMC9781266 DOI: 10.3390/jpm12121943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
Genomic screening programs have potential to benefit individuals who may not be clinically ascertained, but little is known about the psychological impact of receiving genetic results in this setting. The current study sought to further the understanding of individuals’ psychological response to receiving an actionable genetic test result from genomic screening. Telephone surveys were conducted with patient-participants at 6 weeks and 6 months post genetic result disclosure between September 2019 and May 2021 and assessed emotional response to receiving results via the FACToR, PANAS, and decision regret scales. Overall, 354 (29.4%) study participants completed both surveys. Participants reported moderate positive emotions and low levels of negative emotions, uncertainty, privacy concern, and decision regret over time. There were significant decreases in negative emotions (p = 0.0004) and uncertainty (p = 0.0126) between time points on the FACToR scale. “Interested” was the highest scoring discrete emotion (T1 3.6, T2 3.3, scale 0−5) but was significantly lower at 6 months (<0.0001). Coupled with other benefits of genomic screening, these results of modest psychological impact waning over time adds support to clinical utility of population genomic screening programs. However, questions remain regarding how to elicit an emotional response that motivates behavior change without causing psychological harm.
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Affiliation(s)
| | | | - Alicia Johns
- Department of Population Health Sciences, Geisinger, Danville, PA 17822, USA
| | - Gemme Campbell-Salome
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
- Department of Population Health Sciences, Geisinger, Danville, PA 17822, USA
| | | | - Amy C. Sturm
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
- 23andMe, Sunnyvale, CA 94086, USA
| | - Adam H. Buchanan
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
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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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Rodríguez-Salgado LE, Silva-Aldana CT, Medina-Méndez E, Bareño-Silva J, Arcos-Burgos M, Silgado-Guzmán DF, Restrepo CM. Frequency of actionable Exomic secondary findings in 160 Colombian patients: Impact in the healthcare system. Gene 2022; 838:146699. [PMID: 35803546 DOI: 10.1016/j.gene.2022.146699] [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: 10/05/2021] [Revised: 06/11/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION By 2021, the American College of Medical Genetics and Genomics (ACMG) published the last version of their secondary findings (SF) reporting recommendations for cases in which a person receives a genetic test. OBJECTIVE To determine in a sample of the Colombian population the prevalence of SF for the 59 genes on the ACMG SF v2.0 list associated with 27 genetic diseases. MATERIALS AND METHODS An analytical cross-sectional study was developed by examining the sequences of 160 exomes. Based on the ACMG guidelines, a variant classification algorithm was designed to filter and select reportable SF. RESULTS Eleven pathogenic variants were identified in 13/160 (8.13%) patients in genes APOB, BRCA2, CACNA1S, COL3A1, LDLR, MYBPC3, PCSK9, PKP2, PMS2 and RYR2. No association was found between the sociodemographic variables and the SF to report (P > 0,05). CONCLUSION We reported the first approach of actionable pathogenic variants spectrum in the Colombian population. Given the frequency found in this study and the clinical impact of genomic variants on health, it is essential to actively search for SF having the opportunity to receive genetic counselling, prevention and clinical management.
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Affiliation(s)
| | | | | | - José Bareño-Silva
- School of Medicine, Mental Health Research Group, CES University, Medellin, Colombia
| | - Mauricio Arcos-Burgos
- Research Group on Psychiatric Disorders (GIPSI), Department of Psychiatry, Institute of Medical Research, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | - Carlos M Restrepo
- Center for Research in Genetics and Genomics (CIGGUR), GeniURos Research Group, School of Medicine and Health Sciences, University of Rosario, Bogotá, Colombia.
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Elander J, Ullmark T, Ehrencrona H, Jonson T, Piccinelli P, Samuelsson S, Löwgren K, Falkenius-Schmidt K, Ehinger J, Stenfeldt K, Värendh M. Extended genetic diagnostics for children with profound sensorineural hearing loss by implementing massive parallel sequencing. Diagnostic outcome, family experience and clinical implementation. Int J Pediatr Otorhinolaryngol 2022; 159:111218. [PMID: 35779349 DOI: 10.1016/j.ijporl.2022.111218] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/12/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022]
Abstract
OBJECTIVES The aim of this study was to investigate genetic outcomes, analyze the family experience, and describe the process of implementing genetic sequencing for children with profound sensorineural hearing loss (SNHL) at a tertial audiological center in southern Sweden. DESIGN This is a prospective pilot study including eleven children with profound bilateral SNHL who underwent cochlear implant surgery. Genetic diagnostic investigation was performed with whole exome sequencing (WES) complemented with XON-array to identify copy number variants, using a manually curated gene panel incorporating 179 genes associated with non-syndromic and syndromic SNHL. Mitochondrial DNA (mtDNA) from blood was examined separately. A patient reported experience measures (PREM) questionnaire was used to evaluate parental experience. We also describe here the process of implementing WES in an audiology department. RESULTS Six female and five male children (mean 3.4 years, SD 3.5 years), with profound bilateral SNHL were included. Genetic variants of interest were found in six subjects (55%), where three (27%) could be classified as pathogenic or likely pathogenic. Among the six cases, one child was found to have a homozygous pathogenic variant in MYO7A and two children had homozygous likely pathogenic variants in SLC26A4 and PCDH15, respectively. One was carrying a compound heterozygote frameshift variant of uncertain significance (VUS) on one allele and in trans, a likely pathogenic deletion on the other allele in PCDH15. Two subjects had homozygous VUS in PCDH15 and ADGRV1, respectively. In five of the cases the variants were in genes associated with Usher syndrome. For one of the likely pathogenic variants, the finding was related to Pendred syndrome. No mtDNA variants related to SNHL were found. The PREM questionnaire revealed that the families had difficulty in fully understanding the results of the genetic analysis. However, the parents of all eleven (100%) subjects still recommended that other families with children with SNHL should undergo genetic testing. Specifically addressed referrals for prompt complementary clinical examination and more individualized care were possible, based on the genetic results. Close clinical collaboration between different specialists, including physicians of audiology, audiologists, clinical geneticists, ophthalmologists, pediatricians, otoneurologists, physiotherapists and hearing habilitation teams was initiated during the implementation of the new regime. For all professionals involved, a better knowledge of the diversity of the genetic background of hearing loss was achieved. CONCLUSIONS Whole exome sequencing and XON-array using a panel of genes associated with SNHL had a high diagnostic yield, added value to the families, and provided guidance for further examinations and habilitation for the child. Great care should be taken to thoroughly inform parents about the genetic test result. Collaborations between departments were intensified and knowledge of hearing genomics was increased among the staff.
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Affiliation(s)
- Johanna Elander
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden.
| | - Tove Ullmark
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Hans Ehrencrona
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 85, Lund, Sweden
| | - Tord Jonson
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Paul Piccinelli
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Sofie Samuelsson
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Karolina Löwgren
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
| | - Karolina Falkenius-Schmidt
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
| | - Johannes Ehinger
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
| | - Karin Stenfeldt
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden; Lund University, Department of Clinical Sciences Lund, Logopedics, Phoniatrics and Audiology, 221 84, Lund, Sweden
| | - Maria Värendh
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
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Rahimzadeh V, Friedman JM, de Wert G, Knoppers BM. Exome/Genome-Wide Testing in Newborn Screening: A Proportionate Path Forward. Front Genet 2022; 13:865400. [PMID: 35860465 PMCID: PMC9289115 DOI: 10.3389/fgene.2022.865400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/27/2022] [Indexed: 11/20/2022] Open
Abstract
Population-based newborn screening (NBS) is among the most effective public health programs ever launched, improving health outcomes for newborns who screen positive worldwide through early detection and clinical intervention for genetic disorders discovered in the earliest hours of life. Key to the success of newborn screening programs has been near universal accessibility and participation. Interest has been building to expand newborn screening programs to also include many rare genetic diseases that can now be identified by exome or genome sequencing (ES/GS). Significant declines in sequencing costs as well as improvements to sequencing technologies have enabled researchers to elucidate novel gene-disease associations that motivate possible expansion of newborn screening programs. In this paper we consider recommendations from professional genetic societies in Europe and North America in light of scientific advances in ES/GS and our current understanding of the limitations of ES/GS approaches in the NBS context. We invoke the principle of proportionality-that benefits clearly outweigh associated risks-and the human right to benefit from science to argue that rigorous evidence is still needed for ES/GS that demonstrates clinical utility, accurate genomic variant interpretation, cost effectiveness and universal accessibility of testing and necessary follow-up care and treatment. Confirmatory or second-tier testing using ES/GS may be appropriate as an adjunct to conventional newborn screening in some circumstances. Such cases could serve as important testbeds from which to gather data on relevant programmatic barriers and facilitators to wider ES/GS implementation.
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Affiliation(s)
- Vasiliki Rahimzadeh
- Stanford Center for Biomedical Ethics, Stanford University, Stanford, CA, United States
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Guido de Wert
- Department of Health, Ethics and Society, Maastricht University, Maastricht, Netherlands
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Buchanan J, Hill M, Vass CM, Hammond J, Riedijk S, Klapwijk JE, Harding E, Lou S, Vogel I, Hui L, Ingvoldstad-Malmgren C, Soller MJ, Ormond KE, Choolani M, Zheng Q, Chitty LS, Lewis C. Factor's that impact on women's decision-making around prenatal genomic tests: An international discrete choice survey. Prenat Diagn 2022; 42:934-946. [PMID: 35476801 PMCID: PMC9325352 DOI: 10.1002/pd.6159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/12/2022]
Abstract
OBJECTIVE We conducted a survey-based discrete-choice experiment (DCE) to understand the test features that drive women's preferences for prenatal genomic testing, and explore variation across countries. METHODS Five test attributes were identified as being important for decision-making through a literature review, qualitative interviews and quantitative scoring exercise. Twelve scenarios were constructed in which respondents choose between two invasive tests or no test. Women from eight countries who delivered a baby in the previous 24 months completed a DCE presenting these scenarios. Choices were modeled using conditional logit regression analysis. RESULTS Surveys from 1239 women (Australia: n = 178; China: n = 179; Denmark: n = 88; Netherlands: n = 177; Singapore: n = 90; Sweden: n = 178; UK: n = 174; USA: n = 175) were analyzed. The key attribute affecting preferences was a test with the highest diagnostic yield (p < 0.01). Women preferred tests with short turnaround times (p < 0.01), and tests reporting variants of uncertain significance (VUS; p < 0.01) and secondary findings (SFs; p < 0.01). Several country-specific differences were identified, including time to get a result, who explains the result, and the return of VUS and SFs. CONCLUSION Most women want maximum information from prenatal genomic tests, but our findings highlight country-based differences. Global consensus on how to return uncertain results is not necessarily realistic or desirable.
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Affiliation(s)
- James Buchanan
- Nuffield Department of Population Health, Health Economics Research Centre, University of Oxford, Oxford, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Melissa Hill
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Caroline M Vass
- Manchester Centre for Health Economics, The University of Manchester, Manchester, UK.,RTI Health Solutions, Manchester, UK
| | - Jennifer Hammond
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sam Riedijk
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Eleanor Harding
- BSc Paediatrics and Child Health, The UCL Great Ormond Street Institute of Child Health, London, UK
| | - Stina Lou
- Center for Fetal Diagnostics, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,DEFACTUM - Public Health & Health Services Research, Central Denmark Region, Aarhus, Denmark
| | - Ida Vogel
- Center for Fetal Diagnostics, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Lisa Hui
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Department of Obstetrics and Gynaecology, Northern Health, Epping, Victoria, Australia
| | - Charlotta Ingvoldstad-Malmgren
- Center for Research and Bioethics, Uppsala University, Uppsala, Sweden.,Center for Fetal Medicine, Karolinska University Hospital, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska Hospital and Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Maria Johansson Soller
- Department of Clinical Genetics, Karolinska Hospital and Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kelly E Ormond
- Department of Genetics and Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, California, USA.,Department of Health Sciences and Technology, Health Ethics and Policy Lab, ETH Zurich, Zurich, Switzerland
| | - Mahesh Choolani
- Department of Obstetrics & Gynaecology, National University Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Qian Zheng
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK
| | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Celine Lewis
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK.,Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, UK
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Ward AJ, Murphy D, Marron R, McGrath V, Bolz-Johnson M, Cullen W, Daly A, Hardiman O, Lawlor A, Lynch SA, MacLachlan M, McBrien J, Ni Bhriain S, O'Byrne JJ, O'Connell SM, Turner J, Treacy EP. Designing rare disease care pathways in the Republic of Ireland: a co-operative model. Orphanet J Rare Dis 2022; 17:162. [PMID: 35410222 PMCID: PMC8996209 DOI: 10.1186/s13023-022-02309-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/24/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Rare diseases (RDs) are often complex, serious, chronic and multi-systemic conditions, associated with physical, sensory and intellectual disability. Patients require follow-up management from multiple medical specialists and health and social care professionals involving a high level of integrated care, service coordination and specified care pathways. METHODS AND OBJECTIVES This pilot study aimed to explore the best approach for developing national RD care pathways in the Irish healthcare system in the context of a lack of agreed methodology. Irish clinical specialists and patient/lived experience experts were asked to map existing practice against evidence-based clinical practice guidelines (CPGs) and best practice recommendations from the European Reference Networks (ERNs) to develop optimal care pathways. The study focused on the more prevalent, multisystemic rare conditions that require multidisciplinary care, services, supports and therapeutic interventions. RESULTS 29 rare conditions were selected across 18 ERNs, for care pathway development. Multidisciplinary input from multiple specialisms was relevant for all pathways. A high level of engagement was experienced from clinical leads and patient organisations. CPGs were identified for 26 of the conditions. Nurse specialist, Psychology, Medical Social Work and Database Manager roles were deemed essential for all care pathways. Access to the therapeutic Health Service Professionals: Physiotherapy, Occupational Therapy, and Speech and Language Therapy were seen as key requirements for holistic care. Genetic counselling was highlighted as a core discipline in 27 pathways demonstrating the importance of access to Clinical Genetics services for many people with RDs. CONCLUSIONS This study proposes a methodology for Irish RD care pathway development, in collaboration with patient/service user advocates. Common RD patient needs and health care professional interventions across all pathways were identified. Key RD stakeholders have endorsed this national care pathway initiative. Future research focused on the implementation of such care pathways is a priority.
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Affiliation(s)
- A J Ward
- National Rare Diseases Office, Mater Misericordiae University Hospital, Eccles St, Dublin 7, Ireland
| | - D Murphy
- National Rare Diseases Office, Mater Misericordiae University Hospital, Eccles St, Dublin 7, Ireland
| | - R Marron
- National Rare Diseases Office, Mater Misericordiae University Hospital, Eccles St, Dublin 7, Ireland
| | - V McGrath
- Rare Diseases Ireland, Carmichael House, North Brunswick St, Dublin 7, Ireland
| | - M Bolz-Johnson
- European Organisation for Rare Diseases (EURORDIS), Paris, France
| | - W Cullen
- Division of Urban General Practice, School of Medicine, University College, Dublin, Ireland
| | - A Daly
- European Organisation for Rare Diseases (EURORDIS), Paris, France
| | - O Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College, Dublin, Ireland
- Department of Neurology, Beaumont Hospital, Beaumont, Dublin, Ireland
| | - A Lawlor
- 22Q11 Ireland, North Brunswick Street, Dublin, Ireland
| | - S A Lynch
- Clinical Genetics, Children's Health Ireland (CHI) at Crumlin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - M MacLachlan
- Disability Services, Health Service Executive, Dublin, Ireland
- Psychology and Social Inclusion, Assisting Living and Learning Institute, Maynooth University, Maynooth, Ireland
| | - J McBrien
- Department of General Paediatrics and Neurodisability, CHI at Temple Street, Dublin, Ireland
| | - S Ni Bhriain
- Office of the National Lead for Integrated Care, Health Service Executive, Dr. Steeven's Hospital, Dublin, Ireland
| | - J J O'Byrne
- School of Medicine, University College Dublin, Dublin, Ireland
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- National Centre for Inherited Metabolic Disorders, Mater Misericordiae University Hospital, Dublin, Ireland
| | - S M O'Connell
- Department of Diabetes and Endocrinology, Children's Health Ireland (CHI) at Crumlin, Dublin, Ireland
- Department of Paediatrics, Royal College of Surgeons of Ireland (RCSI), Dublin, Ireland
| | - J Turner
- National Rare Diseases Office, Mater Misericordiae University Hospital, Eccles St, Dublin 7, Ireland
| | - E P Treacy
- National Rare Diseases Office, Mater Misericordiae University Hospital, Eccles St, Dublin 7, Ireland.
- School of Medicine, University College Dublin, Dublin, Ireland.
- School of Medicine, Trinity College Dublin, Dublin, Ireland.
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Austin-Tse CA, Jobanputra V, Perry DL, Bick D, Taft RJ, Venner E, Gibbs RA, Young T, Barnett S, Belmont JW, Boczek N, Chowdhury S, Ellsworth KA, Guha S, Kulkarni S, Marcou C, Meng L, Murdock DR, Rehman AU, Spiteri E, Thomas-Wilson A, Kearney HM, Rehm HL. Best practices for the interpretation and reporting of clinical whole genome sequencing. NPJ Genom Med 2022; 7:27. [PMID: 35395838 PMCID: PMC8993917 DOI: 10.1038/s41525-022-00295-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/17/2022] [Indexed: 01/19/2023] Open
Abstract
Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.
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Affiliation(s)
- Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Vaidehi Jobanputra
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ted Young
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah Barnett
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Nicole Boczek
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Saurav Guha
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Shashikant Kulkarni
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cherisse Marcou
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linyan Meng
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David R Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Atteeq U Rehman
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Elizabeth Spiteri
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, CA, USA
| | | | - Hutton M Kearney
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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60
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Zhu J, Stephenson KAJ, Farrar GJ, Turner J, O’Byrne JJ, Keegan D. Management of significant secondary genetic findings in an ophthalmic genetics clinic. Eye (Lond) 2022; 36:896-898. [PMID: 33941876 PMCID: PMC8956566 DOI: 10.1038/s41433-021-01557-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/09/2021] [Accepted: 04/13/2021] [Indexed: 02/02/2023] Open
Affiliation(s)
- Julia Zhu
- grid.411596.e0000 0004 0488 8430Mater Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Kirk A J Stephenson
- grid.411596.e0000 0004 0488 8430Mater Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - G. Jane Farrar
- grid.8217.c0000 0004 1936 9705Ocular Genetics Unit, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Jacqueline Turner
- grid.411596.e0000 0004 0488 8430Mater Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - James J. O’Byrne
- grid.411596.e0000 0004 0488 8430Mater Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - David Keegan
- grid.411596.e0000 0004 0488 8430Mater Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
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Goddard KAB, Lee K, Buchanan AH, Powell BC, Hunter JE. Establishing the Medical Actionability of Genomic Variants. Annu Rev Genomics Hum Genet 2022; 23:173-192. [PMID: 35363504 PMCID: PMC10184682 DOI: 10.1146/annurev-genom-111021-032401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Actionability is an important concept in medicine that does not have a well-accepted standard definition, nor is there a general consensus on how to establish it. Medical actionability is often conflated with clinical utility, a related but distinct concept. This lack of clarity contributes to practice variation and inconsistent coverage decisions in genomic medicine, leading to the potential for systematic bias in the use of evidence-based interventions. We clarify how medical actionability and clinical utility are distinct and then discuss the spectrum of actionability, including benefits for the person, the family, and society. We also describe applications across the life course, including prediction, diagnosis, and treatment. Current challenges in assessing the medical actionability of identified genomic variants include gaps in the evidence, limited contexts with practice guidelines, and subjective aspects of medical actionability. A standardized and authoritative assessment of medical actionability is critical to implementing genomic medicine in a fashion that improves population health outcomes and reduces health disparities. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Katrina A B Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Kristy Lee
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Adam H Buchanan
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Bradford C Powell
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
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Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal Dystrophies. Int J Mol Sci 2022; 23:ijms23073905. [PMID: 35409265 PMCID: PMC8999823 DOI: 10.3390/ijms23073905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 12/15/2022] Open
Abstract
The inherited retinal dystrophies (IRDs) are a clinically and genetically complex group of disorders primarily affecting the rod and cone photoreceptors or other retinal neuronal layers, with emerging therapies heralding the need for accurate molecular diagnosis. Targeted capture and panel-based strategies examining the partial or full exome deliver molecular diagnoses in many IRD families tested. However, approximately one in three families remain unsolved and unable to obtain personalised recurrence risk or access to new clinical trials or therapy. In this study, we investigated whole genome sequencing (WGS), focused assays and functional studies to assist with unsolved IRD cases and facilitate integration of these approaches to a broad molecular diagnostic clinical service. The WGS approach identified variants not covered or underinvestigated by targeted capture panel-based clinical testing strategies in six families. This included structural variants, with notable benefit of the WGS approach in repetitive regions demonstrated by a family with a hybrid gene and hemizygous missense variant involving the opsin genes, OPN1LW and OPN1MW. There was also benefit in investigation of the repetitive GC-rich ORF15 region of RPGR. Further molecular investigations were facilitated by focused assays in these regions. Deep intronic variants were identified in IQCB1 and ABCA4, with functional RNA based studies of the IQCB1 variant revealing activation of a cryptic splice acceptor site. While targeted capture panel-based methods are successful in achieving an efficient molecular diagnosis in a proportion of cases, this study highlights the additional benefit and clinical value that may be derived from WGS, focused assays and functional genomics in the highly heterogeneous IRDs.
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63
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Biesecker LG. Invited Commentary on "My Research Results: a program to facilitate return of clinically actionable genomic research findings" by Willis et al. Eur J Hum Genet 2022; 30:256-257. [PMID: 34803162 PMCID: PMC8904623 DOI: 10.1038/s41431-021-01003-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Leslie G. Biesecker
- grid.280128.10000 0001 2233 9230Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 MD USA
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64
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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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65
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Petrova D, Cruz M, Sánchez MJ. BRCA1/2 testing for genetic susceptibility to cancer after 25 years: A scoping review and a primer on ethical implications. Breast 2022; 61:66-76. [PMID: 34920368 PMCID: PMC8686063 DOI: 10.1016/j.breast.2021.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Mutations in the genes called BRCA1 and BRCA2 are associated with significantly elevated lifetime risk of developing breast and ovarian cancer. This year marks 25 years since genetic tests for BRCA1/2 mutations became available to the public. Currently, comprehensive guidelines exist regarding BRCA1/2 testing and preventive measures in mutation carriers. As such, BRCA1/2 testing represents a precedent not only in genetic testing and management of genetic cancer risk, but also in bioethics. The goal of the current research was to offer a review and an ethical primer of the main ethical challenges related to BRCA testing. METHOD A systematic scoping review was undertaken following the PRISMA Extension for Scoping Reviews (PRISMA-ScR). Four databases were searched and 18 articles that met the inclusion criteria were synthetized narratively into a conceptual map. RESULTS Ethical discussions revolved around the BRCA1/2 gene discovery, how tests are distributed for clinical use, the choice to undergo testing, unresolved issues in receiving and disclosing test results, reproductive decision-making, and culture-specific ethics. Several unique properties of the latest developments in testing circumstances (e.g., incorporation of BRCA1/2 testing in multi-gene or whole genome sequence panels and tests sold directly to consumers) significantly raised the complexity of ethical debates. CONCLUSIONS Multidisciplinary ethical discussion is necessary to guide not only individual decision making but also societal practices and medical guidelines in light of the new technologies available and the latest results regarding psychological, social, and health outcomes in cancer previvors and survivors affected by BRCA mutations.
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Affiliation(s)
- Dafina Petrova
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain; Escuela Andaluza de Salud Pública, Granada, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain.
| | - Maite Cruz
- Escuela Andaluza de Salud Pública, Granada, Spain
| | - María-José Sánchez
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain; Escuela Andaluza de Salud Pública, Granada, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain; Department of Preventive Medicine and Public Health, University of Granada, Granada, Spain
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66
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Murray MF. Enabling Diagnostic Resulting as a New Category of Secondary Genomic Findings. J Pers Med 2022; 12:jpm12020158. [PMID: 35207647 PMCID: PMC8878546 DOI: 10.3390/jpm12020158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/19/2021] [Accepted: 12/30/2021] [Indexed: 02/01/2023] Open
Abstract
Over the past decade, the secondary analysis of existing DNA datasets for clinical resulting has become an established practice. However, this established practice is typically limited to only one category of secondary genomic findings, the identification of “disease risk”. Diagnostic resulting has been left out of secondary genomic findings. In medical practice, diagnostic resulting is triggered when a test is ordered for a patient based on a recognizable clinical indication for evaluation; most genetic and genomic testing is carried out in support of diagnostic evaluations. The secondary analysis of existing DNA data has the potential to cost less and have more rapid turnaround times for diagnostic results compared to current DNA diagnostic approaches that typically generate a new dataset with every test ordered. Worldwide, innovative health systems could position themselves to deliver valid secondary genomic finding results in both the established category of disease risk results, as well as a new category of diagnostic results. To support the ongoing delivery of both categories of secondary findings, health systems will need comprehensive genomic datasets for patients and secure workflows that allow for repeated access to that data for on-demand secondary analysis.
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Affiliation(s)
- Michael F Murray
- Yale Center for Genomic Health, Yale School of Medicine, New Haven, CT 06510, USA
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67
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Vears D, Amor DJ. A framework for reporting secondary and incidental findings in prenatal sequencing: When and for whom? Prenat Diagn 2022; 42:697-704. [PMID: 35032068 PMCID: PMC9306573 DOI: 10.1002/pd.6097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/03/2022] [Accepted: 01/09/2022] [Indexed: 12/27/2022]
Abstract
As the use of genomic sequencing (GS) in the prenatal setting becomes more widespread, laboratories and clinicians will be tasked with making decisions about whether to offer incidental and secondary findings to expectant parents and, if so, which ones. Unfortunately, few guidelines or position statements issued by professional bodies address the return of secondary findings specifically in the context of prenatal GS, nor do they offer clear guidance on whether, and which types of incidental findings should be reported. Laboratories and clinicians will also need to navigate other challenges, such as how to obtain sufficiently informed consent, workload burdens for both laboratories and clinicians, and funding. Here we discuss these, and other challenges associated with offering incidental and secondary findings in the context of prenatal GS. We outline existing guidelines for return of these findings, prenatally and in children. We review the existing literature on stakeholder perspectives on return of incidental and secondary findings and discuss the main practical and ethical challenges that require consideration. We then propose a framework to help guide decision-making, suggesting a baseline routine analysis, with additional layers of analysis that could be offered, according to local laboratory policy, with additional opt-in consent from the parents.
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Affiliation(s)
- Danya Vears
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Melbourne Law School, University of Melbourne, Carlton, Victoria, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia
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68
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Baranova EE, Fedulova KD, Glotov AS, Izhevskaya VL. Guidelines for genetic testing of healthy adults who deposit samples and related data in bioresource collections and biobanks. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2022. [DOI: 10.15829/1728-8800-2021-3120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Currently, a significant part of research in the fields of human and medical genetics is carried out using tissue samples, genealogical, population, medical and personal data. Their use is of particular relevance in the “genome era”, since only joint analysis of genomic data and health status of the population is crucial for understanding how genes are associated with health and disease. Genetic studies of adults without symptoms of diseases are carried out to obtain data on a possible predisposition to multifactorial diseases, to establish the carrier status of autosomal recessive mutations as part of preconception care and to assess individual sensitivity to drugs. In addition, healthy individuals can be tested to detect an inherited disease at presymptomatic stage. This situation increasingly emphasizes the importance of storing data on genome sequencing or any other patient tests for subsequent data reanalysis, as well as their safety, including biosamples from an individual and one’s family. The review article, based on international experience, summarizes guidelines for genetic testing of healthy individuals. The options for storing biological samples and related data are considered.
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Affiliation(s)
- E. E. Baranova
- Russian Medical Academy of Continuous Professional Education; LLC Evogen
| | | | - A. S. Glotov
- D.O. Ott Research Institute of Obstetrics, Gynecology, and Reproductology
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69
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Pezzoli L, Pezzani L, Bonanomi E, Marrone C, Scatigno A, Cereda A, Bedeschi MF, Selicorni A, Gasperini S, Bini P, Maitz S, Maccioni C, Pedron C, Colombo L, Marchetti D, Bellini M, Lincesso AR, Perego L, Pingue M, Della Malva N, Mangili G, Ferrazzi P, Iascone M. Not Only Diagnostic Yield: Whole-Exome Sequencing in Infantile Cardiomyopathies Impacts on Clinical and Family Management. J Cardiovasc Dev Dis 2021; 9:jcdd9010002. [PMID: 35050212 PMCID: PMC8780486 DOI: 10.3390/jcdd9010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 12/26/2022] Open
Abstract
Whole-exome sequencing (WES) is a powerful and comprehensive tool for the genetic diagnosis of rare diseases, but few reports describe its timely application and clinical impact on infantile cardiomyopathies (CM). We conducted a retrospective analysis of patients with infantile CMs who had trio (proband and parents)-WES to determine whether results contributed to clinical management in urgent and non-urgent settings. Twenty-nine out of 42 enrolled patients (69.0%) received a definitive molecular diagnosis. The mean time-to-diagnosis was 9.7 days in urgent settings, and 17 out of 24 patients (70.8%) obtained an etiological classification. In non-urgent settings, the mean time-to-diagnosis was 225 days, and 12 out of 18 patients (66.7%) had a molecular diagnosis. In 37 out of 42 patients (88.1%), the genetic findings contributed to clinical management, including heart transplantation, palliative care, or medical treatment, independent of the patient’s critical condition. All 29 patients and families with a definitive diagnosis received specific counseling about recurrence risk, and in seven (24.1%) cases, the result facilitated diagnosis in parents or siblings. In conclusion, genetic diagnosis significantly contributes to patients’ clinical and family management, and trio-WES should be performed promptly to be an essential part of care in infantile cardiomyopathy, maximizing its clinical utility.
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Affiliation(s)
- Laura Pezzoli
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (L.P.); (D.M.); (M.B.); (A.R.L.); (L.P.); (M.P.); (N.D.M.)
| | - Lidia Pezzani
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (L.P.); (D.M.); (M.B.); (A.R.L.); (L.P.); (M.P.); (N.D.M.)
- Pediatria ad Alta Intensità di Cura, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Ezio Bonanomi
- Terapia Intensiva Pediatrica, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy;
| | - Chiara Marrone
- Cardiologia Pediatrica, Fondazione G. Monasterio, 54100 Massa, Italy;
| | - Agnese Scatigno
- Pediatria, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (A.S.); (A.C.)
| | - Anna Cereda
- Pediatria, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (A.S.); (A.C.)
| | - Maria Francesca Bedeschi
- Genetica Medica, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy;
| | | | - Serena Gasperini
- Malattie Metaboliche Rare, Dipartimento di Pediatria, Fondazione MBBM, ASST, 20900 Monza, Italy;
| | - Paolo Bini
- Terapia Intensiva Neonatale, ASST Lariana, 22100 Como, Italy;
| | - Silvia Maitz
- Ambulatorio di Genetica Pediatrica, Clinica Pediatrica, Fondazione MBBM, Ospedale S. Gerardo, 20900 Monza, Italy;
| | - Carla Maccioni
- Terapia Intensiva Neonatale, Ospedale A. Manzoni, ASST, 23900 Lecco, Italy;
| | - Cristina Pedron
- Cardiologia, Ospedale di Bolzano, Azienda Sanitaria dell’Alto Adige, 39100 Bolzano, Italy;
| | - Lorenzo Colombo
- NICU Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy;
| | - Daniela Marchetti
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (L.P.); (D.M.); (M.B.); (A.R.L.); (L.P.); (M.P.); (N.D.M.)
| | - Matteo Bellini
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (L.P.); (D.M.); (M.B.); (A.R.L.); (L.P.); (M.P.); (N.D.M.)
| | - Anna Rita Lincesso
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (L.P.); (D.M.); (M.B.); (A.R.L.); (L.P.); (M.P.); (N.D.M.)
| | - Loredana Perego
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (L.P.); (D.M.); (M.B.); (A.R.L.); (L.P.); (M.P.); (N.D.M.)
| | - Monica Pingue
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (L.P.); (D.M.); (M.B.); (A.R.L.); (L.P.); (M.P.); (N.D.M.)
| | - Nunzia Della Malva
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (L.P.); (D.M.); (M.B.); (A.R.L.); (L.P.); (M.P.); (N.D.M.)
| | - Giovanna Mangili
- Patologia Neonatale, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy;
| | - Paolo Ferrazzi
- Centro Cardiomiopatia Ipertrofica, Policlinico di Monza, 20900 Monza, Italy;
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (L.P.); (D.M.); (M.B.); (A.R.L.); (L.P.); (M.P.); (N.D.M.)
- Correspondence: ; Tel.: +39-0352678112
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70
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Hirsch S, Dikow N, Pfister SM, Pajtler KW. Cancer predisposition in pediatric neuro-oncology-practical approaches and ethical considerations. Neurooncol Pract 2021; 8:526-538. [PMID: 34594567 DOI: 10.1093/nop/npab031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A genetic predisposition to tumor development can be identified in up to 10% of pediatric patients with central nervous system (CNS) tumors. For some entities, the rate of an underlying predisposition is even considerably higher. In recent years, population-based approaches have helped to further delineate the role of cancer predisposition in pediatric oncology. Investigations for cancer predisposition syndrome (CPS) can be guided by clinical signs and family history leading to directed testing of specific genes. The increasingly adopted molecular analysis of tumor and often parallel blood samples with multi-gene panel, whole-exome, or whole-genome sequencing identifies additional patients with or without clinical signs. Diagnosis of a genetic predisposition may put an additional burden on affected families. However, information on a given cancer predisposition may be critical for the patient as potentially influences treatment decisions and may offer the patient and healthy carriers the chance to take part in intensified surveillance programs aiming at early tumor detection. In this review, we discuss some of the practical and ethical challenges resulting from the widespread use of new diagnostic techniques and the most important CPS that may manifest with brain tumors in childhood.
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Affiliation(s)
- Steffen Hirsch
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
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71
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Ridnõi K, Muru K, Keernik M, Pajusalu S, Ustav EL, Tammur P, Mölter-Väär T, Kahre T, Šamarina U, Asser K, Szirko F, Reimand T, Õunap K. A two-year prospective study assessing the performance of fetal chromosomal microarray analysis and next-generation sequencing in high-risk pregnancies. Mol Genet Genomic Med 2021; 9:e1787. [PMID: 34486251 PMCID: PMC8580097 DOI: 10.1002/mgg3.1787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/22/2021] [Accepted: 08/13/2021] [Indexed: 12/16/2022] Open
Abstract
Background Introduction of cell‐free fetal DNA (cff‐DNA) testing in maternal blood opened possibilities to improve the performance of combined first‐trimester screening (cFTS) in terms of better detection of trisomies and lowering invasive testing rate. The use of new molecular methods, such as chromosomal microarray analysis (CMA) and next‐generation sequencing (NGS), has shown benefits in prenatal diagnosis of chromosomal and genetic diseases, which are not detectable with cff‐DNA screening, but require an invasive procedure. Methods The objective of this study was to evaluate prospectively during two years performance of CMA and NGS in high‐risk pregnancies. Initially, we investigated 14,566 singleton pregnancies with cFTS. A total of 334 high‐risk pregnancies were selected for CMA diagnostic performance evaluation and 28 cases of highly dysmorphic fetuses for NGS analysis. CMA study group was divided into two groups based on the indications for testing; group A patients with high‐risk for trisomies after cFTS, but normal ultrasound and group B patients who met criteria for CMA as a first‐tier diagnostic test. Results The diagnostic yield of CMA was overall 3.6% (1.6% in Group A and 6.0% in Group B). In NGS analysis group, we report diagnostic yield of 17.9%. Conclusion The use of CMA in high‐risk pregnancies is justified and provides relevant clinical information in 3.6% of the cases. NGS analysis in fetuses with multiple anomalies shows promising results, but more investigations are needed for a better understanding of practical applications of this molecular diagnosis method in prenatal settings.
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Affiliation(s)
- Konstantin Ridnõi
- Centre for Perinatal Care, Women's Clinic, East-Tallinn Central Hospital, Tallinn, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kai Muru
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Maria Keernik
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Pille Tammur
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Triin Mölter-Väär
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Tiina Kahre
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Ustina Šamarina
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Karin Asser
- Radiology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Ferenc Szirko
- Centre for Perinatal Care, Women's Clinic, East-Tallinn Central Hospital, Tallinn, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
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72
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Ménard T, Barros A, Ganter C. Clinical Quality Considerations when Using Next-Generation Sequencing (NGS) in Clinical Drug Development. Ther Innov Regul Sci 2021; 55:1066-1074. [PMID: 34046876 PMCID: PMC8332578 DOI: 10.1007/s43441-021-00308-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/19/2021] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing (NGS) and decreased costs of genomic testing are changing the paradigm in precision medicine and continue to fuel innovation. Integration of NGS into clinical drug development has the potential to accelerate clinical trial conduct and ultimately will shape the landscape of clinical care by making it easier to identify patients who would benefit from particular therapy(ies) and to monitor treatment outcomes with less invasive tests. This has led to an increased use of NGS service providers by pharmaceutical sponsors: to screen patients for clinical trials eligibility and for patient stratification, expanded Companion Diagnostic (CDx) development for treatment recommendations and Comprehensive Genomic profiling (CGP). These changes are reshaping the face of clinical quality considerations for precision medicine. Although some clinical quality considerations do exist in Health Authorities (HA) guidances and regulations (e.g., International Conference of Harmonization Good Clinical Practices-GCP), there is currently no holistic GxP-like detailed framework for pharmaceutical sponsors using NGS service providers in clinical trials, or for the development of CDx and CGP. In this research, we identified existing and applicable regulations, guidelines and recommendations that could be translated into clinical quality considerations related to technology, data quality, patients and oversight. We propose these considerations as a basis for pharmaceutical sponsors using NGS service providers in clinical drug development to develop a set of guidelines for NGS clinical quality.
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Affiliation(s)
| | - Alaina Barros
- Genentech Inc. - A Member of the Roche Group, South San Francisco, USA
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73
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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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74
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Lewis ACF, Knoppers BM, Green RC. An international policy on returning genomic research results. Genome Med 2021; 13:115. [PMID: 34266500 PMCID: PMC8281644 DOI: 10.1186/s13073-021-00928-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 11/10/2022] Open
Abstract
The Global Alliance for Genomics and Health has approved a policy for the return of clinically actionable genomic research results, the first such policy approved by an international body. The policy acknowledges the potential medical benefits to millions of individuals who are participating in genomics research. It ties the pace of implementation to each country's clinical standards, including for the return of secondary findings, and urges funders to set aside resources to support responsible return.
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Affiliation(s)
- Anna C F Lewis
- E J Safra Center for Ethics, Harvard University, 124 Mount Auburn Street, Suite 520 N, Cambridge, MA, 02138, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | | | - Robert C Green
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Ariadne Labs, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
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75
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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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76
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Remec ZI, Trebusak Podkrajsek K, Repic Lampret B, Kovac J, Groselj U, Tesovnik T, Battelino T, Debeljak M. Next-Generation Sequencing in Newborn Screening: A Review of Current State. Front Genet 2021; 12:662254. [PMID: 34122514 PMCID: PMC8188483 DOI: 10.3389/fgene.2021.662254] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/13/2021] [Indexed: 12/27/2022] Open
Abstract
Newborn screening was first introduced at the beginning of the 1960s with the successful implementation of the first phenylketonuria screening programs. Early expansion of the included disorders was slow because each additional disorder screened required a separate test. Subsequently, the technological advancements of biochemical methodology enabled the scaling-up of newborn screening, most notably with the implementation of tandem mass spectrometry. In recent years, we have witnessed a remarkable progression of high-throughput sequencing technologies, which has resulted in a continuous decrease of both cost and time required for genetic analysis. This has enabled more widespread use of the massive multiparallel sequencing. Genomic sequencing is now frequently used in clinical applications, and its implementation in newborn screening has been intensively advocated. The expansion of newborn screening has raised many clinical, ethical, legal, psychological, sociological, and technological concerns over time. This review provides an overview of the current state of next-generation sequencing regarding newborn screening including current recommendations and potential challenges for the use of such technologies in newborn screening.
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Affiliation(s)
- Ziga I. Remec
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Katarina Trebusak Podkrajsek
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
| | - Barbka Repic Lampret
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Jernej Kovac
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Urh Groselj
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Chair of Pediatrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tine Tesovnik
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tadej Battelino
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Chair of Pediatrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Marusa Debeljak
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
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77
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Vrijenhoek T, Tonisson N, Kääriäinen H, Leitsalu L, Rigter T. Clinical genetics in transition-a comparison of genetic services in Estonia, Finland, and the Netherlands. J Community Genet 2021; 12:277-290. [PMID: 33704686 PMCID: PMC7948164 DOI: 10.1007/s12687-021-00514-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/18/2021] [Indexed: 11/25/2022] Open
Abstract
Genetics has traditionally enabled the reliable diagnosis of patients with rare genetic disorders, thus empowering the key role of today's clinical geneticists in providing healthcare. With the many novel technologies that have expanded the genetic toolkit, genetics is increasingly evolving beyond rare disease diagnostics. When placed in a transition context-like we do here-clinical genetics is likely to become a fully integral part of future healthcare and clinical genetic expertise will be required increasingly outside traditional clinical genetic settings. We explore transition effects on the thinking (culture), organizing (structure), and performing (practice) in clinical genetics, taking genetic healthcare in Estonia, Finland, and the Netherlands as examples. Despite clearly distinct healthcare histories, all three countries have initially implemented genetic healthcare in a rather similar fashion: as a diagnostic tool for predominantly rare congenital diseases, with clinical geneticists as the main providers. Dynamics at different levels, such as emerging technologies, biobanks and data infrastructure, and legislative frameworks, may require development of a new system attuned with the demands and (historic) context of specific countries. Here, we provide an overview of genetic service provisions in Estonia, Finland, and the Netherlands to consider the impact of historic and recent events on prospective developments in genetic healthcare.
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Affiliation(s)
- T Vrijenhoek
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - N Tonisson
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Dept. of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - H Kääriäinen
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - L Leitsalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - T Rigter
- Department of Clinical Genetics, Section Community Genetics & Amsterdam Public Health Research Institute, Amsterdam University Medical Centre, Location VUmc, Amsterdam, The Netherlands.
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78
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Berichte aus den GfH-Kommissionen und von den Delegierten. MED GENET-BERLIN 2021; 33:91-105. [PMID: 38836201 PMCID: PMC11110114 DOI: 10.1515/medgen-2021-2066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
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79
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Widening the lens of actionability: A qualitative study of primary care providers' views and experiences of managing secondary genomic findings. Eur J Hum Genet 2021; 30:595-603. [PMID: 33776058 PMCID: PMC9091250 DOI: 10.1038/s41431-021-00876-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/22/2022] Open
Abstract
Most secondary genomic findings (SFs) fall in the scope of primary care practice. However, primary care providers' (PCPs) capacity to manage these findings is not well understood. We explored PCPs' views and experiences of managing SFs through a qualitative study. PCPs participated in semi-structured interviews about SFs from a patient in their practice or a hypothetical patient. The interpretive descriptive methodology was used to analyze transcripts thematically through constant comparison. Fifteen family physicians from Ontario, Canada participated (ten females; 6-40 years in practice across community and academic settings). PCPs made sense of SFs through the lens of actionability: they actively looked for clinical relevance by considering a wide range of immediate and future actions, including referrals, genetic testing, screening, lifestyle changes, counseling about family planning, informing family members, future medication choice, increased vigilance/surveillance, and managing results in the electronic medical record. PCPs saw clinical actionability as the main benefit mitigating the potential harms of learning SFs, namely patient anxiety and unnecessary investigations. PCPs conceptualized actionability more broadly than it is traditionally defined in medical genetics. Further research will be needed to determine if PCPs' emphasis on actionability conflicts with patients' expectations of SFs and if it leads to overutilization of healthcare resources.
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80
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Stakeholder views on opportunistic genomic screening in the Netherlands: a qualitative study. Eur J Hum Genet 2021; 29:949-956. [PMID: 33619333 DOI: 10.1038/s41431-021-00828-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 01/21/2021] [Accepted: 02/04/2021] [Indexed: 11/08/2022] Open
Abstract
Genome sequencing can be used to actively search for genetic variants unrelated to the initial clinical question. While such 'opportunistic genomic screening' (OGS) has been proposed in the USA, a European discussion on the ethics of OGS is only starting. Should testing for selected 'secondary findings' be offered to patients who need genetic sequencing? Using focus groups and interviews, we explored views on OGS in adults and minors from three perspectives: policy experts (n = 9), health professionals (n = 8) and patient representatives (n = 7). A thematic approach was used to analyze the data. There was consensus that OGS should be evaluated in terms of the classical 'screening' framework, rather than as a form of 'good patient care'. Accordingly, stakeholders agreed that professionals do not have a 'fiduciary duty' to look for secondary findings. Adding screening to clinical care was only conceivable with the patient's informed consent. In general, stakeholders were reluctant towards OGS. Arguments for regarding OGS being premature included lack of evidence regarding its clinical utility, also in view of uncertainties regarding general population penetrance, and concerns about both its psychosocial impact and respect for autonomy. All groups agreed that OGS means unequal access, which was seen as problematic. Yet, despite their concerns, stakeholders felt that offering screening for certain actionable pathogenic variants with known high penetrance could potentially be valuable in certain contexts for both adults and minors. Pharmacogenetic variants were regarded as a category by itself, for which OGS could potentially be beneficial.
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81
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Kelly MA, Leader JB, Wain KE, Bodian D, Oetjens MT, Ledbetter DH, Martin CL, Strande NT. Leveraging population-based exome screening to impact clinical care: The evolution of variant assessment in the Geisinger MyCode research project. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2021; 187:83-94. [PMID: 33576083 DOI: 10.1002/ajmg.c.31887] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023]
Abstract
Exome and genome sequencing are increasingly utilized in research studies and clinical care and can provide clinically relevant information beyond the initial intent for sequencing, including medically actionable secondary findings. Despite ongoing debate about sharing this information with patients and participants, a growing number of clinical laboratories and research programs routinely report secondary findings that increase the risk for selected diseases. Recently, there has been a push to maximize the potential benefit of this practice by implementing proactive genomic screening at the population level irrespective of medical history, but the feasibility of deploying population-scale proactive genomic screening requires scaling key elements of the genomic data evaluation process. Herein, we describe the motivation, development, and implementation of a population-scale variant-first screening pipeline combining bioinformatics-based filtering with a manual review process to screen for clinically relevant findings in research exomes generated through the DiscovEHR collaboration within Geisinger's MyCode® research project. Consistent with other studies, this pipeline yields a screen-positive detection rate between 2.1 and 2.6% (depending on inclusion of those with prior indication-based testing) in 130,048 adult MyCode patient-participants screened for clinically relevant findings in 60 genes. Our variant-first pipeline affords cost and time savings by filtering out negative cases, thereby avoiding analysis of each exome one-by-one, as typically employed in the diagnostic setting. While research is still needed to fully appreciate the benefits of population genomic screening, MyCode provides the first demonstration of a program at scale to help shape how population genomic screening is integrated into routine clinical care.
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Affiliation(s)
| | | | - Karen E Wain
- Geisinger Medical Center, Danville, Pennsylvania, USA
| | - Dale Bodian
- Geisinger Medical Center, Danville, Pennsylvania, USA
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