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Viora-Dupont E, Robert F, Chassagne A, Pélissier A, Staraci S, Sanlaville D, Edery P, Lesca G, Putoux A, Pons L, Cadenes A, Baurand A, Sawka C, Bertolone G, Spetchian M, Yousfi M, Salvi D, Gautier E, Vitobello A, Denommé-Pichon AS, Bruel AL, Tran Mau-Them F, Faudet A, Keren B, Labalme A, Chatron N, Abel C, Dupuis-Girod S, Poisson A, Buratti J, Mignot C, Afenjar A, Whalen S, Charles P, Heide S, Mouthon L, Moutton S, Sorlin A, Nambot S, Briffaut AS, Asensio ML, Philippe C, Thauvin-Robinet C, Héron D, Rossi M, Meunier-Bellard N, Gargiulo M, Peyron C, Binquet C, Faivre L. Expectations, needs and mid-term outcomes in people accessing to secondary findings from ES: 1st French mixed study (FIND Study). Eur J Hum Genet 2024; 32:1166-1183. [PMID: 38802530 PMCID: PMC11368951 DOI: 10.1038/s41431-024-01616-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/01/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024] Open
Abstract
Generation and subsequently accessibility of secondary findings (SF) in diagnostic practice is a subject of debate around the world and particularly in Europe. The French FIND study has been set up to assess patient/parent expectations regarding SF from exome sequencing (ES) and to collect their real-life experience until 1 year after the delivery of results. 340 patients who had ES for undiagnosed developmental disorders were included in this multicenter mixed study (quantitative N = 340; qualitative N = 26). Three groups of actionable SF were rendered: predisposition to late-onset actionable diseases; genetic counseling; pharmacogenomics. Participants expressed strong interest in obtaining SF and a high satisfaction level when a SF is reported. The medical actionability of the SF reinforced parents' sense of taking action for their child and was seen as an opportunity. While we observed no serious psychological concerns, we showed that these results could have psychological consequences, in particular for late-onset actionable diseases SF, within families already dealing with rare diseases. This study shows that participants remain in favor of accessing SF despite the potential psychological, care, and lifestyle impacts, which are difficult to anticipate. The establishment of a management protocol, including the support of a multidisciplinary team, would be necessary if national policy allows the reporting of these data.
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Affiliation(s)
- Eléonore Viora-Dupont
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France.
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France.
| | - Françoise Robert
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- Clinical Psychology Lab., Psychopathology, Psychoanalysis (EA4056, ED 261), University of Paris, Sorbonne Paris City, Paris, France
| | - Aline Chassagne
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- Laboratory of Sociology and Anthropology (LaSA, EA3189), University of Burgundy-Franche-Comté, Besançon, France
| | - Aurore Pélissier
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- Laboratory of economy (LEDi), University of Burgundy, Dijon, France
| | - Stéphanie Staraci
- Genetics Department, Reference Center for Hereditary Cardiac Disorders, GH APHP, Paris, France
| | - Damien Sanlaville
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- Univ Lyon, Univ Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Patrick Edery
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- INSERM U1028, CNRS UMR5292, CRNL, GENDEV Team, University of Claude Bernard Lyon 1, Bron, France
| | - Gaetan Lesca
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- Univ Lyon, Univ Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Audrey Putoux
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- INSERM U1028, CNRS UMR5292, CRNL, GENDEV Team, University of Claude Bernard Lyon 1, Bron, France
| | - Linda Pons
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
| | - Amandine Cadenes
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
| | - Amandine Baurand
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Caroline Sawka
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Geoffrey Bertolone
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Myrtille Spetchian
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Meriem Yousfi
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Dominique Salvi
- Laboratory of economy (LEDi), University of Burgundy, Dijon, France
| | - Elodie Gautier
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Antonio Vitobello
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
| | | | - Ange-Line Bruel
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
| | | | - Anne Faudet
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Boris Keren
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Audrey Labalme
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
| | - Nicolas Chatron
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- Univ Lyon, Univ Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Carine Abel
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
| | - Sophie Dupuis-Girod
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
| | - Alice Poisson
- Reference Center for Rare Disorders with psychiatric expression C.H. Le Vinatier, Bron, France
- Equipe de recherche AESIO santé, unité de Sant Etienne, Clinique médico chirurgicale mutualiste, Saint Etienne, France
| | - Julien Buratti
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Cyril Mignot
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Alexandra Afenjar
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Sandra Whalen
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Perrine Charles
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Solveig Heide
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Linda Mouthon
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Sébastien Moutton
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Arthur Sorlin
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Sophie Nambot
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Anne-Sophie Briffaut
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- CHU Dijon Bourgogne, INSERM, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, Dijon, France
| | - Marie-Laure Asensio
- CHU Dijon Bourgogne, INSERM, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, Dijon, France
| | | | - Christel Thauvin-Robinet
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- Genetics Department, Reference Center for Intellectual Disabilities, University Hospital, Dijon, France
| | - Delphine Héron
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Massimiliano Rossi
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- INSERM U1028, CNRS UMR5292, CRNL, GENDEV Team, University of Claude Bernard Lyon 1, Bron, France
| | - Nicolas Meunier-Bellard
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- CHU Dijon Bourgogne, INSERM, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, Dijon, France
| | - Marcela Gargiulo
- Clinical Psychology Lab., Psychopathology, Psychoanalysis (EA4056, ED 261), University of Paris, Sorbonne Paris City, Paris, France
- Institute of myology, GH APHP, Paris, France
| | - Christine Peyron
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- Laboratory of economy (LEDi), University of Burgundy, Dijon, France
| | - Christine Binquet
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- CHU Dijon Bourgogne, INSERM, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, Dijon, France
| | - Laurence Faivre
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France.
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France.
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Droin-Mollard M, de Montgolfier S, Gimenez-Roqueplo AP, Flahault C, Petit A, Bourdeaut F, Julia S, Rial-Sebbag E, Coupier I, Simaga F, Brugières L, Guerrini-Rousseau L, Claret B, Cavé H, Strullu M, Hervouet L, Lahlou-Laforêt K. Psychological and ethical issues raised by genomic in paediatric care pathway, a qualitative analysis with parents and childhood cancer patients. Eur J Hum Genet 2024:10.1038/s41431-024-01653-4. [PMID: 38997469 DOI: 10.1038/s41431-024-01653-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/27/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024] Open
Abstract
In paediatric oncology, genomics raises new ethical, legal and psychological issues, as somatic and constitutional situations intersect throughout the care pathway. The discovery of potential predisposition in this context is sometimes carried out outside the usual framework. This article focuses on the views of children, adolescents, and young adults (AYA) with cancer and their parents about their experience with genomic testing. Forty-eight semi-structured interviews were performed with children or AYAs with cancer and one of their parents, before and/or after receiving the genetic test results. The interviews were fully transcribed, coded and thematically analysed using an inductive method. This analysis revealed several themes that are key issues: perceived understanding and consenting, apprehension about the test outcomes (expectations and fears), perception and attitude towards incidental findings. The main expectation was an aetiological explanation. Children and AYAs also emphasised the altruistic meaning of genetic testing, while parents seemed to expect a therapeutic and preventive approach for their child and the rest of the family. Parents were more concerned about a family risk, while patients were more afraid of cancer relapse or transmission to their descendants. Both groups suggested possible feelings of guilt concerning family transmission and imaginary representations of what genomics may allow. Incidental findings were not understood by patients, while some parents perceived the related issues and hesitated between wanting or not to know. A multidisciplinary approach would be an interesting way to help parents and children and AYAs to better grasp the complexity of genetic and/or genomic testing.
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Affiliation(s)
- Marion Droin-Mollard
- UF of Psychology and Liaison and Emergency Psychiatry, DMU Psychiatry and Addictology, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, F-75015, Paris, France
| | - Sandrine de Montgolfier
- IRIS Institut de Recherche Interdisciplinaire sur les Enjeux Sociaux (UMR 8156 CNRS-997 INSERM-EHESS-UPSN), Campus Condorcet, Aubervilliers, France.
- University of Paris Est Créteil, Créteil, France.
- Aix Marseille Universite, Inserm, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l'Information Médicale, ISSPAM, Marseille, France.
| | - Anne-Paule Gimenez-Roqueplo
- Département de Médecine Génomique des Tumeurs et des Cancers, Consultation d'oncogénétique Multidisciplinaire des Cancers Rares, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
- Université Paris Cité, PARCC, INSERM, Paris, France
| | - Cécile Flahault
- UF of Psychology and Liaison and Emergency Psychiatry, DMU Psychiatry and Addictology, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, F-75015, Paris, France
- Université Paris Cité, Laboratoire de Psychopathologie et Processus de Santé UR4057, Paris, France
| | - Arnaud Petit
- Service d'Hématologie et d'Oncologie Pédiatrique, Hôpital Armand Trousseau, APHP, Sorbonne Université, Paris, France
| | - Franck Bourdeaut
- SIREDO Pediatric Oncology Center, Laboratory of Translational Research in Pediatric Oncology-INSERMU830, Institut Curie, Paris Sciences Lettres Research University, Paris, France
- Université Paris-Cité, Paris, France
| | - Sophie Julia
- UMR 1027 INSERM, University of Toulouse & Toulouse University Hospital, Toulouse, France
- Medical Genetics Department, Purpan Hospital, Toulouse, France
| | - Emmanuelle Rial-Sebbag
- UMR 1027 INSERM, University of Toulouse & University Toulouse III-Paul Sabatier, Toulouse, France
| | - Isabelle Coupier
- CHU Montpellier, Hôpital Arnaud de Villeneuve Montpellier, Service de Génétique Médicale et Oncogénétique, Montpellier, France
- INSERM896, CRCM Val d'Aurelle, Montpellier, France
| | | | - Laurence Brugières
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Léa Guerrini-Rousseau
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Molecular Predictors and New Targets in Oncology, Inserm U981 Team "Genomics and Oncogenesis of Pediatric Brain Tumors", Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Béatrice Claret
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Psycho-Oncology Unit, Supportive Care Department, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Hélène Cavé
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, Paris, France
- INSERM UMR_S1131, Institut de Recherche Saint-Louis, Université Paris-Cité, Paris, France
| | - Marion Strullu
- INSERM UMR_S1131, Institut de Recherche Saint-Louis, Université Paris-Cité, Paris, France
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Service d'Hémato-Immunologie Pédiatrique, Paris, France
| | - Lucile Hervouet
- IRIS Institut de Recherche Interdisciplinaire sur les Enjeux Sociaux (UMR 8156 CNRS-997 INSERM-EHESS-UPSN), Campus Condorcet, Aubervilliers, France
| | - Khadija Lahlou-Laforêt
- UF of Psychology and Liaison and Emergency Psychiatry, DMU Psychiatry and Addictology, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, F-75015, Paris, France
- Département de Médecine Génomique des Tumeurs et des Cancers, Consultation d'oncogénétique Multidisciplinaire des Cancers Rares, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
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Donoghue S, Wright J, Voss AK, Lockhart PJ, Amor DJ. The Mendelian disorders of chromatin machinery: Harnessing metabolic pathways and therapies for treatment. Mol Genet Metab 2024; 142:108360. [PMID: 38428378 DOI: 10.1016/j.ymgme.2024.108360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
The Mendelian disorders of chromatin machinery (MDCMs) represent a distinct subgroup of disorders that present with neurodevelopmental disability. The chromatin machinery regulates gene expression by a range of mechanisms, including by post-translational modification of histones, responding to histone marks, and remodelling nucleosomes. Some of the MDCMs that impact on histone modification may have potential therapeutic interventions. Two potential treatment strategies are to enhance the intracellular pool of metabolites that can act as substrates for histone modifiers and the use of medications that may inhibit or promote the modification of histone residues to influence gene expression. In this article we discuss the influence and potential treatments of histone modifications involving histone acetylation and histone methylation. Genomic technologies are facilitating earlier diagnosis of many Mendelian disorders, providing potential opportunities for early treatment from infancy. This has parallels with how inborn errors of metabolism have been afforded early treatment with newborn screening. Before this promise can be fulfilled, we require greater understanding of the biochemical fingerprint of these conditions, which may provide opportunities to supplement metabolites that can act as substrates for chromatin modifying enzymes. Importantly, understanding the metabolomic profile of affected individuals may also provide disorder-specific biomarkers that will be critical for demonstrating efficacy of treatment, as treatment response may not be able to be accurately assessed by clinical measures.
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Affiliation(s)
- Sarah Donoghue
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Biochemical Genetics, Victorian Clinical Genetics Services, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia.
| | - Jordan Wright
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
| | - Anne K Voss
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville 3052, Australia
| | - Paul J Lockhart
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
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Cornelis C, Tibben A, Brilstra E, Bolt I, van Summeren M, Knoers N, Bredenoord AL. Hope, but never expect? Comparing parents' pre- and post-disclosure attitudes toward return of results from diagnostic exome sequencing for their child. Mol Genet Genomic Med 2024; 12:e2341. [PMID: 38366804 PMCID: PMC10958177 DOI: 10.1002/mgg3.2341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Counseling for whole-exome sequencing (WES) could benefit from aligning parents' pre- and post-disclosure attitudes. A few studies have qualitatively compared parents' pre- and post-disclosure attitudes toward receiving WES results for their child in a diagnostic setting. This study explored these attitudes in the context of children with a developmental delay. METHODS Semi-structured interviews were conducted with parents (n = 27) of 16 children undergoing diagnostic WES in trio-analysis, both before and after receiving results. RESULTS Three key insights emerged. First, the distinction between hoping and expecting was relevant for shaping parents' experiences with receiving results related to the primary indication. Second, parents of young children whose development of autonomous capacities was uncertain sometimes found themselves in a situation resembling a Catch-22 when confronted with decisions about unsolicited findings (UFs): an important reason for consenting to WES was to gain a better picture of how the child might develop, but in order to make responsible choices about UFs, some ideas of their child's development is needed. Third, default opt-ins and opt-outs helped parents fathom new kinds of considerations for accepting or declining UFs in different categories, thereby aiding decision-making. CONCLUSION Results from this study are relevant for counseling and policy development.
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Affiliation(s)
- Candice Cornelis
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
- Department of Medical Humanities, Julius CenterUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Aad Tibben
- Department of Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Eva Brilstra
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Ineke Bolt
- Department of Medical Ethics, Philosophy and History of MedicineErasmus Medical CenterRotterdamThe Netherlands
| | - Marieke van Summeren
- Department of General PediatricsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Nine Knoers
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
- Department of GeneticsUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Annelien L. Bredenoord
- Department of Medical Humanities, Julius CenterUniversity Medical Center UtrechtUtrechtThe Netherlands
- Erasmus School of PhilosophyErasmus University RotterdamRotterdamThe Netherlands
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Mandiracioglu B, Ozden F, Kaynar G, Yilmaz MA, Alkan C, Cicek AE. ECOLE: Learning to call copy number variants on whole exome sequencing data. Nat Commun 2024; 15:132. [PMID: 38167256 PMCID: PMC10762021 DOI: 10.1038/s41467-023-44116-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Copy number variants (CNV) are shown to contribute to the etiology of several genetic disorders. Accurate detection of CNVs on whole exome sequencing (WES) data has been a long sought-after goal for use in clinics. This was not possible despite recent improvements in performance because algorithms mostly suffer from low precision and even lower recall on expert-curated gold standard call sets. Here, we present a deep learning-based somatic and germline CNV caller for WES data, named ECOLE. Based on a variant of the transformer architecture, the model learns to call CNVs per exon, using high-confidence calls made on matched WGS samples. We further train and fine-tune the model with a small set of expert calls via transfer learning. We show that ECOLE achieves high performance on human expert labelled data for the first time with 68.7% precision and 49.6% recall. This corresponds to precision and recall improvements of 18.7% and 30.8% over the next best-performing methods, respectively. We also show that the same fine-tuning strategy using tumor samples enables ECOLE to detect RT-qPCR-validated variations in bladder cancer samples without the need for a control sample. ECOLE is available at https://github.com/ciceklab/ECOLE .
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Affiliation(s)
- Berk Mandiracioglu
- Department of Computer and Communication Sciences, EPFL, Lausanne, Switzerland
| | - Furkan Ozden
- Department of Computer Science, Oxford University, Oxford, UK
| | - Gun Kaynar
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | | | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - A Ercument Cicek
- Department of Computer Engineering, Bilkent University, Ankara, Turkey.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, US.
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Richards JL, Knight SJ. Parents' Perspectives on Secondary Genetic Ancestry Findings in Pediatric Genomic Medicine. Clin Ther 2023; 45:719-728. [PMID: 37573223 PMCID: PMC11182349 DOI: 10.1016/j.clinthera.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/17/2023] [Accepted: 06/02/2023] [Indexed: 08/14/2023]
Abstract
PURPOSE With advances in genome sequencing technologies, large-scale genome-wide sequencing has advanced our understanding of disease risk and etiology and contributes to the rapidly expanding genomic health services in pediatric settings. Because it is possible to return ancestry estimates following clinical genomic sequencing, it is important to understand the interest in ancestry results among families who may have the option of receiving these results. METHODS We conducted 26 semi-structured qualitative telephone interviews of parents with children/newborns with likely genetic conditions from two studies of clinical genome sequencing. Using a purposive sampling approach, we selected parents from the SouthSeq cohort, Clinical Sequencing Evidence-Generating Research (CSER Phase 2) project active in Alabama, Mississippi, and Louisiana, or an earlier Clinical Sequencing Exploratory Research (CSER Phase 1) initiative based in the same region. Our interviews focused on parental knowledge about, attitudes on, interest in, and preferences for receiving genetic ancestry results following clinical genome sequencing in the neonatal intensive care unit or in pediatric clinics. FINDINGS Overall, parents prioritized clinical results or results that would help guide the diagnosis and treatment of their child, but they were also interested in any genetic result, including genetic ancestry, that potentially could enhance the meaning of information on disease risk, prevention and screening guidance, or family planning. While parents thought that ancestry results would help them learn about themselves and their heritage, the had concerns over the privacy, security, and accuracy of genetic ancestry information, although parents indicated that they had greater trust in ancestry findings provided as part of clinical care compared with those offered commercially. Parents also wanted ancestry results to be returned in a timely manner by knowledgeable staff, with kid-friendly materials and online tools available to aid, as needed, in the understanding of their results. IMPLICATIONS Taken together, our results highlight that despite being in high-stress situations, such as having a newborn in the neonatal intensive care unit, parents were interested in receiving genetic ancestry results along with their clinically relevant findings.
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Affiliation(s)
- Jaimie L Richards
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sara J Knight
- Department of Internal Medicine, Division of Epidemiology, University of Utah, School of Medicine, Salt Lake City, Utah, USA; Informatics, Decision-Enhancement, and Analytical Sciences Center of Innovation, Salt Lake City VA Healthcare System, Salt Lake City, Utah, USA.
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Smith HS, Bonkowski ES, Hickingbotham MR, Deloge RB, Pereira S. Framing the Family: A Qualitative Exploration of Factors That Shape Family-Level Experience of Pediatric Genomic Sequencing. CHILDREN (BASEL, SWITZERLAND) 2023; 10:774. [PMID: 37238322 PMCID: PMC10217651 DOI: 10.3390/children10050774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/17/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023]
Abstract
Families of children with rare and undiagnosed conditions face many psychosocial and logistical challenges that may affect their approach to decisions about their child's care and their family's well-being. As genomic sequencing (GS) is increasingly incorporated into pediatric diagnostic workups, assessing the family-level characteristics that shape the experience of pediatric GS is crucial to understanding how families approach decision-making about the test and how they incorporate the results into their family life. We conducted semi-structured interviews with parents and other primary caregivers of pediatric patients who were evaluated for a suspected genetic condition and who were recommended to have GS (n = 20) or who had recently completed GS (n = 21). We analyzed qualitative data using multiple rounds of thematic analysis. We organized our thematic findings into three domains of factors that influence the family-level experience of GS: (1) family structure and dynamics; (2) parental identity, relationships, and philosophies; and (3) social and cultural differences. Participants conceptualized their child's family in various ways, ranging from nuclear biological family to support networks made up of friends and communities. Our findings can inform the design and interpretation of preference research to advance family-level value assessment of GS as well as genetic counseling for families.
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Affiliation(s)
- Hadley Stevens Smith
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Emily S. Bonkowski
- Institute for Public Health Genetics, University of Washington School of Public Health, Seattle, WA 98195, USA
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Madison R. Hickingbotham
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Raymond Belanger Deloge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
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Smith HS, Bonkowski ES, Deloge RB, Gutierrez AM, Recinos AM, Lavelle TA, Veenstra DL, McGuire AL, Pereira S. Key drivers of family-level utility of pediatric genomic sequencing: a qualitative analysis to support preference research. Eur J Hum Genet 2023; 31:445-452. [PMID: 36434257 PMCID: PMC10133279 DOI: 10.1038/s41431-022-01245-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/16/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
Given that pediatric genomic sequencing (GS) may have implications for the health and well-being of both the child and family, a clearer understanding of the key drivers of the utility of GS from the family perspective is needed. The purpose of this study is to explore what is important to caregivers of pediatric patients regarding clinical GS, with a focus on family-level considerations. We conducted semi-structured interviews with caregivers (n = 41) of pediatric patients who had been recommended for or completed GS that explored the scope of factors caregivers considered when deciding whether to pursue GS for their child. We analyzed the qualitative data in multiple rounds of coding using thematic analysis. Caregivers raised important family-level considerations, in addition to those specifically for their child, which included wanting the best chance at good quality of life for the family, the ability to learn about family health, the impact on the caregiver's well-being, privacy concerns among family members, and the cost of testing to the family. We developed a framework of key drivers of utility consisting of four domains that influenced caregivers' decision making: underlying values, perceived benefits, perceived risks, and other pragmatic considerations regarding GS. These findings can inform measurement approaches that better capture the utility of pediatric GS for families and improve assessments of the value of clinical GS.
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Affiliation(s)
- Hadley Stevens Smith
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA.
| | - Emily S Bonkowski
- Institute for Public Health Genetics, University of Washington School of Public Health, Seattle, WA, USA
| | | | - Amanda M Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - Alva M Recinos
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Tara A Lavelle
- Center for the Evaluation of Value and Risk in Health (CEVR), Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, USA
| | - David L Veenstra
- Comparative Health Outcomes, Policy & Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
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Mueller R, Lee BM, Callahan KP. Managing Prognosis in Precision Medicine: Utility, Imagination, and Communication. CHILDREN 2023; 10:children10040664. [PMID: 37189913 DOI: 10.3390/children10040664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/22/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Research on how physicians predict and communicate prognosis focuses primarily on end-of-life care. Unsurprisingly, as genomic technology gains traction as a prognostic tool, the focus has also been on terminality, with research focused on how genetic results may be used to terminate pregnancies or redirect care towards palliation for neonates. However, genomic results also have powerful impacts on how patients who live prepare for their futures. Genomic testing provides broad-reaching and early—albeit complex, uncertain, and shifting—prognostic information. In this essay, we argue that as genomic testing occurs earlier and increasingly in a screening context, researchers and clinicians must strive to understand and manage the prognostic implications of results. While our understanding of the psychosocial and communicational aspects of prognosis in symptomatic populations is incomplete, it has progressed further than our understanding in a screening context and therefore provides useful lessons and feasible opportunities for further research. By providing an interdisciplinary and inter-specialty perspective on the psychosocial and communicational aspects of prognosis in genetics, we discuss prognostication with respect to genetics from the neonatal period through adulthood, highlighting medical specialties and patient populations that are especially informative for considering the longitudinal management of prognostic information in genomic medicine.
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Affiliation(s)
- Rebecca Mueller
- Department of Medical Ethics and Health Policy, University of Pennsylvania, Philadelphia, PA 19104, USA
- Masters Genetic Counseling Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brittany M. Lee
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Katharine Press Callahan
- Department of Medical Ethics and Health Policy, University of Pennsylvania, Philadelphia, PA 19104, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Gereis J, Hetherington K, Ha L, Robertson EG, Ziegler DS, Barlow-Stewart K, Tucker KM, Marron JM, Wakefield CE. Parents' understanding of genome and exome sequencing for pediatric health conditions: a systematic review. Eur J Hum Genet 2022; 30:1216-1225. [PMID: 35999452 PMCID: PMC9626631 DOI: 10.1038/s41431-022-01170-2] [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: 01/19/2022] [Revised: 07/13/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Genome and exome sequencing (GS/ES) are increasingly being used in pediatric contexts. We summarize evidence regarding the actual and perceived understanding of GS/ES of parents of a child offered testing for diagnosis and/or management of a symptomatic health condition. We searched four databases (2008-2021) and identified 1264 unique articles, of which 16 met inclusion criteria. We synthesized data from qualitative and quantitative studies and organized results using Ayuso et al. (2013)'s framework of key elements of information for informed consent to GS/ES. Many of the parents represented had prior experience with genetic testing and accessed a form of genetic counseling. Parents' understanding was varied across the domains evaluated. Parents demonstrated understanding of the various potential direct clinical benefits to their child undergoing GS/ES, including in relation to other genetic tests. We found parents had mixed understanding of the nature of potential secondary findings, and of issues related to data privacy, confidentiality, and usage of sequencing results beyond their child's clinical care. Genetic counseling consultations improved understanding. Our synthesis indicates that ES/GS can be challenging for families to understand and underscores the importance of equipping healthcare professionals to explore parents' understanding of ES/GS and the implications of testing for their child.
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Affiliation(s)
- Jessica Gereis
- grid.1005.40000 0004 4902 0432School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW Australia ,grid.414009.80000 0001 1282 788XBehavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Sydney, NSW Australia
| | - Kate Hetherington
- grid.1005.40000 0004 4902 0432School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW Australia ,grid.414009.80000 0001 1282 788XBehavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Sydney, NSW Australia
| | - Lauren Ha
- grid.414009.80000 0001 1282 788XBehavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Sydney, NSW Australia ,grid.1005.40000 0004 4902 0432School of Health Sciences, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW Australia
| | - Eden G. Robertson
- grid.1005.40000 0004 4902 0432School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW Australia
| | - David S. Ziegler
- grid.1005.40000 0004 4902 0432School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW Australia ,grid.414009.80000 0001 1282 788XKids Cancer Centre, Sydney Children’s Hospital, Sydney, NSW Australia ,grid.1005.40000 0004 4902 0432Children’s Cancer Institute, UNSW Sydney, Sydney, NSW Australia
| | - Kristine Barlow-Stewart
- grid.1005.40000 0004 4902 0432School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW Australia ,grid.1005.40000 0004 4902 0432Children’s Cancer Institute, UNSW Sydney, Sydney, NSW Australia ,grid.1013.30000 0004 1936 834XNorthern Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW Australia
| | - Katherine M. Tucker
- grid.1005.40000 0004 4902 0432Prince of Wales Clinical School, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW Australia
| | - Jonathan M. Marron
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.2515.30000 0004 0378 8438Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XCenter for Bioethics, Harvard Medical School, Boston, MA USA
| | - Claire E. Wakefield
- grid.1005.40000 0004 4902 0432School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW Australia ,grid.414009.80000 0001 1282 788XBehavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Sydney, NSW Australia
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Abbott M, McKenzie L, Moran BVG, Heidenreich S, Hernández R, Hocking-Mennie L, Clark C, Gomes J, Lampe A, Baty D, McGowan R, Miedzybrodzka Z, Ryan M. Continuing the sequence? Towards an economic evaluation of whole genome sequencing for the diagnosis of rare diseases in Scotland. J Community Genet 2022; 13:487-501. [PMID: 34415556 PMCID: PMC9530076 DOI: 10.1007/s12687-021-00541-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/15/2021] [Indexed: 11/21/2022] Open
Abstract
Novel developments in genomic medicine may reduce the length of the diagnostic odyssey for patients with rare diseases. Health providers must thus decide whether to offer genome sequencing for the diagnosis of rare conditions in a routine clinical setting. We estimated the costs of singleton standard genetic testing and trio-based whole genome sequencing (WGS), in the context of the Scottish Genomes Partnership (SGP) study. We also explored what users value about genomic sequencing. Insights from the costing and value assessments will inform a subsequent economic evaluation of genomic medicine in Scotland. An average cost of £1,841 per singleton was estimated for the standard genetic testing pathway, with significant variability between phenotypes. WGS cost £6625 per family trio, but this estimate reflects the use of WGS during the SGP project and large cost savings may be realised if sequencing was scaled up. Patients and families valued (i) the chance of receiving a diagnosis (and the peace of mind and closure that brings); (ii) the information provided by WGS (including implications for family planning and secondary findings); and (iii) contributions to future research. Our costings will be updated to address limitations of the current study for incorporation in budget impact modelling and cost-effectiveness analysis (cost per diagnostic yield). Our insights into the benefits of WGS will guide the development of a discrete choice experiment valuation study. This will inform a user-perspective cost-benefit analysis of genome-wide sequencing, accounting for the broader non-health outcomes. Taken together, our research will inform the long-term strategic development of NHS Scotland clinical genetics testing services, and will be of benefit to others seeking to undertake similar evaluations in different contexts.
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Affiliation(s)
- Michael Abbott
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK.
| | - Lynda McKenzie
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK
| | | | - Sebastian Heidenreich
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK
- Evidera Inc., London, UK
| | - Rodolfo Hernández
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK
| | | | - Caroline Clark
- Department of Medical Genetics, University of Aberdeen, Aberdeen, UK
- NHS Grampian Regional Genetics Service, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Joana Gomes
- NHS Grampian Regional Genetics Service, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Anne Lampe
- South East Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, UK
| | - David Baty
- NHS Tayside Regional Genetics Service, Ninewells Hospital, Dundee, UK
| | - Ruth McGowan
- South East Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow, UK
| | | | - Mandy Ryan
- Health Economics Research Unit, University of Aberdeen, Aberdeen, UK
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12
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Perspectives and preferences regarding genomic secondary findings in underrepresented prenatal and pediatric populations: A mixed-methods approach. Genet Med 2022; 24:1206-1216. [PMID: 35396980 DOI: 10.1016/j.gim.2022.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Patients undergoing clinical exome sequencing (ES) are routinely offered the option to receive secondary findings (SF). However, little is known about the views of individuals from underrepresented minority pediatric or prenatal populations regarding SF. METHODS We explored the preferences for receiving hypothetical categories of SF (H-SF) and reasons for accepting or declining actual SF through surveying (n = 149) and/or interviewing (n = 47) 190 families undergoing pediatric or prenatal ES. RESULTS Underrepresented minorities made up 75% of the probands. In total, 150 families (79%) accepted SF as part of their child/fetus's ES. Most families (63%) wanted all categories of H-SF. Those who declined SF as part of ES were less likely to want H-SF across all categories. Interview findings indicate that some families did not recall their SF decision. Preparing for the future was a major motivator for accepting SF, and concerns about privacy, discrimination, and psychological effect drove decliners. CONCLUSION A notable subset of families (37%) did not want at least 1 category of H-SF, suggesting more hesitancy about receiving all available results than previously reported. The lack of recollection of SF decisions suggests a need for alternative communication approaches. Results highlight the importance of the inclusion of diverse populations in genomic research.
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Genetic diagnosis for rare diseases in the Dutch Caribbean: a qualitative study on the experiences and associated needs of parents. Eur J Hum Genet 2022; 30:587-594. [PMID: 35087185 PMCID: PMC9091230 DOI: 10.1038/s41431-022-01039-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 12/30/2022] Open
Abstract
Research on the perspectives of patients and parents regarding genetic testing and its implications has been performed mostly in Europe, Canada, the United States, Australia and New Zealand, even though genetic testing is becoming increasingly available worldwide. We aimed to fill this knowledge gap by exploring the experiences and needs of parents in the Dutch Caribbean who received a genetic diagnosis for the rare disease of their child. We conducted 23 semi-structured interviews with 30 parents of children diagnosed with various rare genetic diseases in Aruba, Bonaire and Curaçao (ABC-islands). Two researchers independently analyzed the interviews using a thematic approach. Main themes identified were: (1) getting a genetic diagnosis, (2) coping, support and perceived social stigma, (3) living on a small island, and (4) needs regarding genetic services. Our results indicate that, despite reported limitations regarding the availability of healthcare and support services, receiving a genetic diagnosis for their child was valuable for most participants. While some of the participants' experiences with and attitudes towards the genetic diagnosis of their child were similar to those reported in previous studies, we identified a number of aspects that are more specifically related to this Dutch Caribbean setting. These include coping through faith and religion, social stigma and being the only one on the island with a specific genetic disorder. The results of this study and the provided recommendations may be useful when developing genetic testing and counseling services in similar settings.
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Hammond J, Klapwijk JE, Riedijk S, Lou S, Ormond KE, Vogel I, Hui L, Sziepe EJ, Buchanan J, Ingvoldstad-Malmgren C, Soller MJ, Harding E, Hill M, Lewis C. Assessing women’s preferences towards tests that may reveal uncertain results from prenatal genomic testing: Development of attributes for a discrete choice experiment, using a mixed-methods design. PLoS One 2022; 17:e0261898. [PMID: 35089945 PMCID: PMC8797177 DOI: 10.1371/journal.pone.0261898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 12/14/2021] [Indexed: 11/19/2022] Open
Abstract
Prenatal DNA tests, such as chromosomal microarray analysis or exome sequencing, increase the likelihood of receiving a diagnosis when fetal structural anomalies are identified. However, some parents will receive uncertain results such as variants of uncertain significance and secondary findings. We aimed to develop a set of attributes and associated levels for a discrete-choice experiment (DCE) that will examine parents’ preferences for tests that may reveal uncertain test results. A two phase mixed-methods approach was used to develop attributes for the DCE. In Phase 1, a “long list” of candidate attributes were identified via two approaches: 1) a systematic review of the literature around parental experiences of uncertainty following prenatal testing; 2) 16 semi-structured interviews with parents who had experienced uncertainty during pregnancy and 25 health professionals who return uncertain prenatal results. In Phase 2, a quantitative scoring exercise with parents prioritised the candidate attributes. Clinically appropriate levels for each attribute were then developed. A final set of five attributes and levels were identified: likelihood of getting a result, reporting of variants of uncertain significance, reporting of secondary findings, time taken to receive results, and who tells you about your result. These attributes will be used in an international DCE study to investigate preferences and differences across countries. This research will inform best practice for professionals supporting parents to manage uncertainty in the prenatal setting.
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Affiliation(s)
- Jennifer Hammond
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, United Kingdom
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | | | - Sam Riedijk
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Stina Lou
- Center for Fetal Diagnostics, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Kelly E. Ormond
- Department of Genetics and Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, United States America
| | - Ida Vogel
- Center for Fetal Diagnostics, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
- Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria, Australia
- Department of Obstetrics and Gynaecology, Northern Health, Epping, VIC, Australia
| | - Emma-Jane Sziepe
- Reproductive Epidemiology, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, England, United Kindom
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, England, United Kindom
| | - Charlotta Ingvoldstad-Malmgren
- Department of Clinical Genetics, Karolinska Hospital and Karolinska Institutet, Stockholm, Sweden
- Center for Fetal Medicine, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Maria Johansson Soller
- Department of Clinical Genetics, Karolinska Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Eleanor Harding
- BSc Paediatrics and Child Health, The UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Melissa Hill
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, United Kingdom
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Celine Lewis
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, United Kingdom
- * E-mail:
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Nambot S, Sawka C, Bertolone G, Cosset E, Goussot V, Derangère V, Boidot R, Baurand A, Robert M, Coutant C, Loustalot C, Thauvin-Robinet C, Ghiringhelli F, Lançon A, Populaire C, Damette A, Collonge-Rame MA, Meunier-Beillard N, Lejeune C, Albuisson J, Faivre L. Incidental findings in a series of 2500 gene panel tests for a genetic predisposition to cancer: Results and impact on patients. Eur J Med Genet 2021; 64:104196. [PMID: 33753322 DOI: 10.1016/j.ejmg.2021.104196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/02/2021] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
With next generation sequencing, physicians are faced with more complex and uncertain data, particularly incidental findings (IF). Guidelines for the return of IF have been published by learned societies. However, little is known about how patients are affected by these results in a context of oncogenetic testing. Over 4 years, 2500 patients with an indication for genetic testing underwent a gene cancer panel. If an IF was detected, patients were contacted by a physician/genetic counsellor and invited to take part in a semi-structured interview to assess their understanding of the result, the change in medical care, the psychological impact, and the transmission of results to the family. Fourteen patients (0.56%) were delivered an IF in a cancer predisposition gene (RAD51C, PMS2, SDHC, RET, BRCA2, CHEK2, CDKN2A, CDH1, SUFU). Two patients did not collect the results and another two died before the return of results. Within the 10 patients recontacted, most of them reported surprise at the delivery of IF, but not anxiety. The majority felt they had chosen to obtain the result and enough information to understand it. They all initiated the recommended follow-up and did not regret the procedure. Information regarding the IF was transmitted to their offspring but siblings or second-degree relatives were not consistently informed. No major adverse psychological events were found in our experience. IF will be inherent to the development of sequencing, even for restricted gene panels, so it is important to increase our knowledge on the impact of such results in different contexts.
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Affiliation(s)
- S Nambot
- Centre de Génétique, FHU TRANSLAD, Institut GIMI, CHU Dijon, F-21000, Dijon, France; CGFL, Unité D'oncogénétique et Institut GIMI, F-21000, Dijon, France.
| | - C Sawka
- Centre de Génétique, FHU TRANSLAD, Institut GIMI, CHU Dijon, F-21000, Dijon, France; CGFL, Unité D'oncogénétique et Institut GIMI, F-21000, Dijon, France
| | - G Bertolone
- Centre de Génétique, FHU TRANSLAD, Institut GIMI, CHU Dijon, F-21000, Dijon, France; CGFL, Unité D'oncogénétique et Institut GIMI, F-21000, Dijon, France
| | - E Cosset
- CGFL, Unité D'oncogénétique et Institut GIMI, F-21000, Dijon, France
| | - V Goussot
- Platform of Transfer in Cancer Biology, Department of Biology and Pathology of Tumours, Centre Georges-François Leclerc, Unicancer, F-21000, Dijon, France
| | - V Derangère
- Platform of Transfer in Cancer Biology, Department of Biology and Pathology of Tumours, Centre Georges-François Leclerc, Unicancer, F-21000, Dijon, France
| | - R Boidot
- Platform of Transfer in Cancer Biology, Department of Biology and Pathology of Tumours, Centre Georges-François Leclerc, Unicancer, F-21000, Dijon, France; CNRS, 6302 Unit, Dijon, France
| | - A Baurand
- Centre de Génétique, FHU TRANSLAD, Institut GIMI, CHU Dijon, F-21000, Dijon, France; CGFL, Unité D'oncogénétique et Institut GIMI, F-21000, Dijon, France
| | - M Robert
- Centre de Génétique, FHU TRANSLAD, Institut GIMI, CHU Dijon, F-21000, Dijon, France
| | - C Coutant
- Département de Chirurgie, Centre Georges François Leclerc, F-21000, Dijon, France
| | - C Loustalot
- Département de Chirurgie, Centre Georges François Leclerc, F-21000, Dijon, France
| | - C Thauvin-Robinet
- Centre de Génétique, FHU TRANSLAD, Institut GIMI, CHU Dijon, F-21000, Dijon, France
| | - F Ghiringhelli
- Platform of Transfer in Cancer Biology, Department of Biology and Pathology of Tumours, Centre Georges-François Leclerc, Unicancer, F-21000, Dijon, France; Département D'oncologie Médicale, Centre Georges François Leclerc, Dijon, France; Centre de Recherche INSERM LNC-UMR123, Université de Bourgogne Franche-Comté, F-21000, Dijon, France
| | - A Lançon
- CGFL, Unité D'oncogénétique et Institut GIMI, F-21000, Dijon, France
| | - C Populaire
- Service Génétique et Biologie Du Développement-Histologie, CHU Hôpital Saint-Jacques, Besançon, France
| | - A Damette
- Service Génétique et Biologie Du Développement-Histologie, CHU Hôpital Saint-Jacques, Besançon, France
| | - M A Collonge-Rame
- Service Génétique et Biologie Du Développement-Histologie, CHU Hôpital Saint-Jacques, Besançon, France
| | - N Meunier-Beillard
- INSERM, CIC1432, Module épidémiologie Clinique, Dijon, France; Centre Hospitalier Universitaire Dijon-Bourgogne, Centre D'investigation Clinique, Module épidémiologie Clinique/essais Cliniques, Dijon, France
| | - C Lejeune
- Centre de Recherche INSERM LNC-UMR123, Université de Bourgogne Franche-Comté, F-21000, Dijon, France; INSERM, CIC1432, Module épidémiologie Clinique, Dijon, France; Centre Hospitalier Universitaire Dijon-Bourgogne, Centre D'investigation Clinique, Module épidémiologie Clinique/essais Cliniques, Dijon, France
| | - J Albuisson
- Platform of Transfer in Cancer Biology, Department of Biology and Pathology of Tumours, Centre Georges-François Leclerc, Unicancer, F-21000, Dijon, France; Centre de Recherche INSERM LNC-UMR123, Université de Bourgogne Franche-Comté, F-21000, Dijon, France
| | - L Faivre
- Centre de Génétique, FHU TRANSLAD, Institut GIMI, CHU Dijon, F-21000, Dijon, France; CGFL, Unité D'oncogénétique et Institut GIMI, F-21000, Dijon, France.
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Tibben A, Dondorp W, Cornelis C, Knoers N, Brilstra E, van Summeren M, Bolt I. Parents, their children, whole exome sequencing and unsolicited findings: growing towards the child's future autonomy. Eur J Hum Genet 2021; 29:911-919. [PMID: 33456055 DOI: 10.1038/s41431-020-00794-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 10/07/2020] [Accepted: 11/26/2020] [Indexed: 01/09/2023] Open
Abstract
In a previous study we found that parents of children with developmental delay (DD) favoured acceptance of unsolicited findings (UFs) for medically actionable conditions in childhood, but that preferences diverged for UFs with no medical actionability, or only in adulthood, and regarding carrier status. Sometimes the child's future autonomy formed a reason for withholding UFs for the present, despite an unfavourable prognosis concerning the child's cognitive capabilities. This might be different for children undergoing whole exome sequencing (WES) for reasons other than DD and who are expected to exert future autonomy. This is the focus of the current study. We conducted nine qualitative, semi-structured interviews with parents of children, ages <1-15, after consenting to WES, but prior to feedback of results, and with three adolescent children. Several parents wished to receive any information that might in whatever way be relevant to the health and well-being of their child, and to a lesser extent wished the inclusion of information about non-actionable disorders and information concerning carrier status of autosomal recessive disorders. Although parents understood the rationale behind the centre's UFs disclosure policy, they also felt that they needed this information in order to be able to exert their parental responsibility and take good care of a child still dependent on them. Parents reason from their notion of parental responsibility but are also inclined to take adolescent children's preferences seriously and acknowledge the child's incipient autonomy as a ground for granting an increasing degree of self-determination on the road to adulthood.
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Affiliation(s)
- Aad Tibben
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Wybo Dondorp
- Department of Health, Ethics & Society, Research School for Public Health & Primary Care (CAPHRI), Maastricht University, Maastricht, the Netherlands
| | - Candice Cornelis
- Ethics Institute, Utrecht University, Utrecht, the Netherlands.,Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nine Knoers
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Eva Brilstra
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marieke van Summeren
- Department of General Pediatrics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ineke Bolt
- Ethics Institute, Utrecht University, Utrecht, the Netherlands.,Department of Medical Ethics, Philosophy and History of Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
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17
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Hayeems RZ, Dimmock D, Bick D, Belmont JW, Green RC, Lanpher B, Jobanputra V, Mendoza R, Kulkarni S, Grove ME, Taylor SL, Ashley E. Clinical utility of genomic sequencing: a measurement toolkit. NPJ Genom Med 2020; 5:56. [PMID: 33319814 PMCID: PMC7738524 DOI: 10.1038/s41525-020-00164-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022] Open
Abstract
Whole-genome sequencing (WGS) is positioned to become one of the most robust strategies for achieving timely diagnosis of rare genomic diseases. Despite its favorable diagnostic performance compared to conventional testing strategies, routine use and reimbursement of WGS are hampered by inconsistencies in the definition and measurement of clinical utility. For example, what constitutes clinical utility for WGS varies by stakeholder's perspective (physicians, patients, families, insurance companies, health-care organizations, and society), clinical context (prenatal, pediatric, critical care, adult medicine), and test purpose (diagnosis, screening, treatment selection). A rapidly evolving technology landscape and challenges associated with robust comparative study design in the context of rare disease further impede progress in this area of empiric research. To address this challenge, an expert working group of the Medical Genome Initiative was formed. Following a consensus-based process, we align with a broad definition of clinical utility and propose a conceptually-grounded and empirically-guided measurement toolkit focused on four domains of utility: diagnostic thinking efficacy, therapeutic efficacy, patient outcome efficacy, and societal efficacy. For each domain of utility, we offer specific indicators and measurement strategies. While we focus on diagnostic applications of WGS for rare germline diseases, this toolkit offers a flexible framework for best practices around measuring clinical utility for a range of WGS applications. While we expect this toolkit to evolve over time, it provides a resource for laboratories, clinicians, and researchers looking to characterize the value of WGS beyond the laboratory.
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Affiliation(s)
- Robin Z Hayeems
- Program in Child Health Evaluative Sciences, The Hospital for Sick Children and the Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, ON, Canada.
| | - David Dimmock
- Rady Children's Hospital Institute for Genomic Medicine, San Diego, CA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Robert C Green
- Brigham and Women's Hospital Broad Institute and Harvard Medical School, Boston, MA, USA
| | | | - Vaidehi Jobanputra
- New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology Columbia University Medical Center, New York, NY, USA
| | - Roberto Mendoza
- The Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Shashi Kulkarni
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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18
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D. Graf W. Exome Sequencing and Molecular Diagnosis. DEUTSCHES ARZTEBLATT INTERNATIONAL 2019; 116:195-196. [PMID: 31056084 PMCID: PMC6514380 DOI: 10.3238/arztebl.2019.0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Affiliation(s)
- William D. Graf
- Connecticut Children‘s Medical Center, University of Connecticut, USA
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