1
|
Ross JP, Akçimen F, Liao C, Kwan K, Phillips DE, Schmilovich Z, Spiegelman D, Genge A, Dupré N, Dion PA, Farhan SMK, Rouleau GA. Rare-variant and polygenic analyses of amyotrophic lateral sclerosis in the French-Canadian genome. Genet Med 2024; 26:100967. [PMID: 37638500 DOI: 10.1016/j.gim.2023.100967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023] Open
Abstract
PURPOSE The genetic etiology of amyotrophic lateral sclerosis (ALS) includes few rare, large-effect variants and potentially many common, small-effect variants per case. The genetic risk liability for ALS might require a threshold comprised of a certain amount of variants. Here, we tested the degree to which risk for ALS was affected by rare variants in ALS genes, polygenic risk score, or both. METHODS 335 ALS cases and 356 controls from Québec, Canada were concurrently tested by microarray genotyping and targeted sequencing of ALS genes known at the time of study inception. ALS genome-wide association studies summary statistics were used to estimate an ALS polygenic risk score (PRS). Cases and controls were subdivided into rare-variant heterozygotes and non-heterozygotes. RESULTS Risk for ALS was significantly associated with PRS and rare variants independently in a logistic regression model. Although ALS PRS predicted a small amount of ALS risk overall, the effect was most pronounced between ALS cases and controls that were not heterozygous for a rare variant in the ALS genes surveyed. CONCLUSION Both PRS and rare variants in ALS genes impact risk for ALS. PRS for ALS is most informative when rare variants are not observed in ALS genes.
Collapse
Affiliation(s)
- Jay P Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Fulya Akçimen
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Calwing Liao
- Department of Medicine, Harvard Medical School, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA
| | - Karina Kwan
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, QC, Canada
| | - Daniel E Phillips
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Biology, McGill University, Montréal, QC, Canada
| | - Zoe Schmilovich
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Dan Spiegelman
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Angela Genge
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Nicolas Dupré
- Division of Neurosciences, CHU de Québec, Université Laval, Québec City, QC, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Québec City, QC, Canada
| | - Patrick A Dion
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Sali M K Farhan
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada; Montréal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada.
| |
Collapse
|
2
|
Schmilovich Z, Bourque VR, Douard E, Huguet G, Poulain C, Ross JP, Alipour P, Castonguay CÉ, Younis N, Jean-Louis M, Saci Z, Pausova Z, Paus T, Schuman G, Porteous D, Davies G, Redmond P, Harris SE, Deary IJ, Whalley H, Hayward C, Dion PA, Jacquemont S, Rouleau GA. Copy-number variants and polygenic risk for intelligence confer risk for autism spectrum disorder irrespective of their effects on cognitive ability. medRxiv 2023:2023.11.29.23299190. [PMID: 38076919 PMCID: PMC10705642 DOI: 10.1101/2023.11.29.23299190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Rare copy number variants (CNVs) and polygenic risk for intelligence (PRS-IQ) both confer risk for autism spectrum disorder (ASD) but have opposing effects on cognitive ability. The field has struggled to disentangle the effects of these two classes of genomic variants on cognitive ability from their effects on ASD risk, in part because previous studies did not include controls with cognitive measures. We aim to investigate the impact of these genomic variants on ASD risk while adjusting for their known effects on cognitive ability. In a cohort of 8,426 subjects with ASD and 169,804 controls with cognitive assessments, we found that rare coding CNVs and PRS-IQ increased ASD risk, even after adjusting for their effects on cognitive ability. Bottom decile PRS-IQ and CNVs both decreased cognitive ability but had opposing effects on ASD risk. Models combining both classes of variants showed that the effects of rare CNVs and PRS-IQ on ASD risk and cognitive ability were largely additive, further suggesting that risk for ASD is conferred independently from its effects on cognitive ability. Despite imparting mostly additive effects on ASD risk, rare CNVs and PRS-IQ showed opposing effects on core and associated features and developmental history among subjects with ASD. Our findings suggest that cognitive ability itself may not be the factor driving the underlying risk for ASD conferred by these two classes of genomic variants. In other words, ASD risk and cognitive ability may be two distinct manifestations of CNVs and PRS-IQ. This study also highlights the challenge of understanding how genetic risk for ASD maps onto its dimensional traits.
Collapse
Affiliation(s)
- Zoe Schmilovich
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Vincent-Raphaël Bourque
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Elise Douard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guillaume Huguet
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Cécile Poulain
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jay P. Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Paria Alipour
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Charles-Étienne Castonguay
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
| | - Nadine Younis
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Martineau Jean-Louis
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zohra Saci
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Tomas Paus
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Departments of Psychiatry of Neuroscience, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Gunter Schuman
- Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, England
| | - David Porteous
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Gail Davies
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Sarah E. Harris
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Ian J. Deary
- Lothian Birth Cohorts group, Department of Psychology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, Edinburgh, UK
| | - Heather Whalley
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, UK
| | - Patrick A. Dion
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Canada
| | - Sébastien Jacquemont
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Canada
| |
Collapse
|
3
|
Tesfaye R, Huguet G, Schmilovich Z, Renne T, Loum MA, Douard E, Saci Z, Jean-Louis M, Martineau JL, Whelan R, Desrivieres S, Heinz A, Schumann G, Hayward C, Elsabbagh M, Jacquemont S. Investigating the contributions of circadian pathway and insomnia risk genes to autism and sleep disturbances. Transl Psychiatry 2022; 12:424. [PMID: 36192372 PMCID: PMC9529939 DOI: 10.1038/s41398-022-02188-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 12/12/2022] Open
Abstract
Sleep disturbance is prevalent in youth with Autism Spectrum Disorder (ASD). Researchers have posited that circadian dysfunction may contribute to sleep problems or exacerbate ASD symptomatology. However, there is limited genetic evidence of this. It is also unclear how insomnia risk genes identified through GWAS in general populations are related to ASD and common sleep problems like insomnia traits in ASD. We investigated the contribution of copy number variants (CNVs) encompassing circadian pathway genes and insomnia risk genes to ASD risk as well as sleep disturbances in children with ASD. We studied 5860 ASD probands and 2092 unaffected siblings from the Simons Simplex Collection (SSC) and MSSNG database, as well as 7509 individuals from two unselected populations (IMAGEN and Generation Scotland). Sleep duration and insomnia symptoms were parent reported for SSC probands. We identified 335 and 616 rare CNVs encompassing circadian and insomnia risk genes respectively. Deletions and duplications with circadian genes were overrepresented in ASD probands compared to siblings and unselected controls. For insomnia-risk genes, deletions (not duplications) were associated with ASD in both cohorts. Results remained significant after adjusting for cognitive ability. CNVs containing circadian pathway and insomnia risk genes showed a stronger association with ASD, compared to CNVs containing other genes. Circadian genes did not influence sleep duration or insomnia traits in ASD. Insomnia risk genes intolerant to haploinsufficiency increased risk for insomnia when duplicated. CNVs encompassing circadian and insomnia risk genes increase ASD liability with little to no observable impacts on sleep disturbances.
Collapse
Affiliation(s)
- Rackeb Tesfaye
- McGill University, Neurology and Neurosurgery, Montreal Neurological Institute, Azrieli Centre for Autism Research, Montreal, Canada.
| | - Guillaume Huguet
- UHC Sainte-Justine Research Center, Université de Montréal, Montreal, Canada
| | | | - Thomas Renne
- UHC Sainte-Justine Research Center, Université de Montréal, Montreal, Canada
| | - Mor Absa Loum
- UHC Sainte-Justine Research Center, Université de Montréal, Montreal, Canada
| | - Elise Douard
- UHC Sainte-Justine Research Center, Université de Montréal, Montreal, Canada
| | - Zohra Saci
- UHC Sainte-Justine Research Center, Université de Montréal, Montreal, Canada
| | | | - Jean Luc Martineau
- Institut National de la Santé et de la Recherche Médicale, INSERM U A10 "Trajectoires développementales en psychiatrie", Université Paris-Saclay, Paris-Saclay, CNRS, Centre Borelli, Gif-sur-Yvette, France
| | - Rob Whelan
- Global Brain Health Institute and School of Psychology, Trinity College Dublin, Dublin, Ireland
| | - Sylvane Desrivieres
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute of Psychiatry, Psychology & Neuroscience, SGDP Centre, King's College London, London, United Kingdom
| | - Andreas Heinz
- Department of Psychiatry and Psychotherapy CCM, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Gunter Schumann
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute of Psychiatry, Psychology & Neuroscience, SGDP Centre, King's College London, London, United Kingdom
- PONS Research Group, Dept of Psychiatry and Psychotherapy, Campus Charite Mitte, Humboldt University, Berlin and Leibniz Institute for Neurobiology, Magdeburg, Germany, and Institute for Science and Technology of Brain-inspired Intelligence (ISTBI), Fudan University, Shanghai, People's Republic of China
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, United Kingdom
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, United Kingdom
| | - Mayada Elsabbagh
- McGill University, Neurology and Neurosurgery, Montreal Neurological Institute, Azrieli Centre for Autism Research, Montreal, Canada
| | | |
Collapse
|
4
|
Bell JAH, Schmilovich Z, Buchman DZ, Escaf M, Costello J, Messner HA. First Ready, First to Go: Ethical Priority-Setting of Allogeneic Stem Cell Transplant at a Major Cancer Centre. ACTA ACUST UNITED AC 2021; 15:102-115. [PMID: 32176614 PMCID: PMC7075446 DOI: 10.12927/hcpol.2020.26127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Medical advancements have now made it possible to provide allogeneic stem cell transplantation (allo-SCTs) to older patients and use stem cells from less well-matched donors. This has resulted in access to a life-saving modality for a greater number of patients with imminent life-threatening illnesses. However, resources have not always kept pace with innovation and expanded volumes. During the summer of 2015 in the province of Ontario, Canada, inadequate resources contributed to a capacity crisis, resulting in extended wait-lists for allo-SCT across the province. This situation presented unique ethical challenges, including the need for ongoing negotiations with health system partners and nimble process management to ensure timely delivery of care. This article reports on the process one organization used to determine how to equitably allocate scarce allo-SCT resources. With the ever-expanding landscape of new and emerging medical technologies, our experience has implications for the ethics of translating other increasingly expensive health technologies to clinical care.
Collapse
Affiliation(s)
- Jennifer A H Bell
- Bioethicist and Research Scientist, Princess Margaret Cancer Centre, University Health Network, Toronto, ON
| | - Zoe Schmilovich
- Department of Human Genetics, McGill University, Montreal, QC
| | - Daniel Z Buchman
- Toronto Western Hospital, University Health Network, Toronto, ON
| | - Marnie Escaf
- Senior Vice President, Princess Margaret Cancer Centre, University Health Network, Toronto, ON
| | - Judy Costello
- Senior Clinical Director, Princess Margaret Cancer Centre, University Health Network, Toronto, ON
| | - Hans A Messner
- Former Director of the Allogeneic Stem Cell Transplantation Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON
| |
Collapse
|
5
|
Liao C, Akçimen F, Diez-Fairen M, Houle G, Ross JP, Schmilovich Z, Spiegelman D, Vuokila V, Catoire H, Meijer IA, Pastor P, Rajput A, Dion PA, Rouleau GA. Assessing the NOTCH2NLC GGC expansion in European patients with essential tremor. Brain 2021; 143:e89. [PMID: 33146671 DOI: 10.1093/brain/awaa291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Calwing Liao
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Fulya Akçimen
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Monica Diez-Fairen
- Department of Neurology, Hospital Universitari Mutua de Terrassa, Barcelona, Spain
| | - Gabrielle Houle
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Jay P Ross
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Zoe Schmilovich
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Veikko Vuokila
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Hélène Catoire
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Inge A Meijer
- Department of Neuroscience and Pediatrics, Université de Montréal, Montréal, Quebec, Canada
| | - Pau Pastor
- Department of Neurology, Hospital Universitari Mutua de Terrassa, Barcelona, Spain
| | - Alex Rajput
- Division of Neurology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Patrick A Dion
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| |
Collapse
|