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Rosenberger A, Crossland RE, Dressel R, Kube D, Wolff D, Wulf G, Bickeböller H, Dickinson A, Holler E. A genome-wide association study on hematopoietic stem cell transplantation reveals novel genomic loci associated with transplant outcomes. Front Immunol 2024; 15:1280876. [PMID: 38384455 PMCID: PMC10879589 DOI: 10.3389/fimmu.2024.1280876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction Data on genomic susceptibility for adverse outcomes after hematopoietic stem cell transplantation (HSCT) for recipients are scarce. Methods We performed a genome wide association study (GWAS) to identify genes associated with survival/mortality, relapse, and severe graft-versus-host disease (sGvHD), fitting proportional hazard and subdistributional models to data of n=1,392 recipients of European ancestry from three centres. Results The single nucleotide polymorphism (SNP) rs17154454, intronic to the neuronal growth guidant semaphorin 3C gene (SEMA3C), was genome-wide significantly associated with event-free survival (p=7.0x10-8) and sGvHD (p=7.5x10-8). Further associations were detected for SNPs in the Paxillin gene (PXN) with death without prior relapse or sGvHD, as well as for SNPs of the Plasmacytoma Variant Translocation 1 gene (PVT1, a long non-coding RNA gene), the Melanocortin 5 Receptor (MC5R) gene and the WW Domain Containing Oxidoreductase gene (WWOX), all associated with the occurrence of sGvHD. Functional considerations support the observed associations. Discussion Thus, new genes were identified, potentially influencing the outcome of HSCT.
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Affiliation(s)
- Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Rachel E. Crossland
- Translational & Clinical Research Institute, Faculty of Medical Science, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ralf Dressel
- Department of Cellular and Molecular Immunology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Dieter Kube
- Department of Cellular and Molecular Immunology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Daniel Wolff
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Gerald Wulf
- Hematology and Medical Oncology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - Anne Dickinson
- Translational & Clinical Research Institute, Faculty of Medical Science, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ernst Holler
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
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Sosero YL, Bandres-Ciga S, Ferwerda B, Tocino MTP, Belloso DR, Gómez-Garre P, Faouzi J, Taba P, Pavelka L, Marques TM, Gomes CPC, Kolodkin A, May P, Milanowski LM, Wszolek ZK, Uitti RJ, Heutink P, van Hilten JJ, Simon DK, Eberly S, Alvarez I, Krohn L, Yu E, Freeman K, Rudakou U, Ruskey JA, Asayesh F, Menéndez-Gonzàlez M, Pastor P, Ross OA, Krüger R, Corvol JC, Koks S, Mir P, De Bie RMA, Iwaki H, Gan-Or Z. Dopamine pathway and Parkinson's risk variants are associated with levodopa-induced dyskinesia. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.28.23294610. [PMID: 37790572 PMCID: PMC10543218 DOI: 10.1101/2023.08.28.23294610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background Levodopa-induced dyskinesia (LID) is a common adverse effect of levodopa, one of the main therapeutics used to treat the motor symptoms of Parkinson's disease (PD). Previous evidence suggests a connection between LID and a disruption of the dopaminergic system as well as genes implicated in PD, including GBA1 and LRRK2. Objectives To investigate the effects of genetic variants on risk and time to LID. Methods We performed a genome-wide association study (GWAS) and analyses focused on GBA1 and LRRK2 variants. We also calculated polygenic risk scores including risk variants for PD and variants in genes involved in the dopaminergic transmission pathway. To test the influence of genetics on LID risk we used logistic regression, and to examine its impact on time to LID we performed Cox regression including 1,612 PD patients with and 3,175 without LID. Results We found that GBA1 variants were associated with LID risk (OR=1.65, 95% CI=1.21-2.26, p=0.0017) and LRRK2 variants with reduced time to LID onset (HR=1.42, 95% CI=1.09-1.84, p=0.0098). The fourth quartile of the PD PRS was associated with increased LID risk (ORfourth_quartile=1.27, 95% CI=1.03-1.56, p=0.0210). The third and fourth dopamine pathway PRS quartiles were associated with a reduced time to development of LID (HRthird_quartile=1.38, 95% CI=1.07-1.79, p=0.0128; HRfourth_quartile=1.38, 95% CI=1.06-1.78, p=0.0147). Conclusions This study suggests that variants implicated in PD and in the dopaminergic transmission pathway play a role in the risk/time to develop LID. Further studies will be necessary to examine how these findings can inform clinical care.
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Affiliation(s)
- Yuri L Sosero
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada
| | - Sara Bandres-Ciga
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes on Health, Bethesda, MD, USA
| | - Bart Ferwerda
- Department of Clinical Epidemiology and Biostatistics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Maria T P Tocino
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Dìaz R Belloso
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Pilar Gómez-Garre
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Johann Faouzi
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, Assistance Publique Hôpitaux de Paris, Department of Neurology, Pitié-Salpêtrière Hospital, Paris, France
- CREST, ENSAI, Campus de Ker-Lann, 51 Rue Blaise Pascal - BP 37203 35172 Bruz Cedex, France
| | - Pille Taba
- Department of Neurology and Neurosurgery, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Lukas Pavelka
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
| | - Tainà M Marques
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Clarissa P C Gomes
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alexey Kolodkin
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Patrick May
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
| | - Lukasz M Milanowski
- Department of Neurology Faculty of Health Science, Medical University of Warsaw, Warsaw, Poland
- Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Zbigniew K Wszolek
- Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Ryan J Uitti
- Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida, USA
| | | | | | - David K Simon
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School
| | - Shirley Eberly
- Department of Biostatistics and Computational Biology at the University of Rochester School of Medicine and Dentistry
| | - Ignacio Alvarez
- Department of Neurology, Hospital Universitari Mutua de Terrassa, Barcelona, Spain
| | - Lynne Krohn
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada
| | - Eric Yu
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada
| | - Kathryn Freeman
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada
| | - Uladzislau Rudakou
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada
| | - Jennifer A Ruskey
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Farnaz Asayesh
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Manuel Menéndez-Gonzàlez
- Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Calle Julián Clavería s/n, 33006 Oviedo, Spain
- Department of Neurology, Hospital Universitario Central de Asturias, Avenida Roma s/n, 33011 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Avenida Roma s/n, 33011 Oviedo, Spain
| | - Pau Pastor
- Department of Neurology, Hospital Universitari Mutua de Terrassa, Barcelona, Spain
- Unit of Neurodegenerative Diseases, Department of Neurology, University Hospital Germans Trias i Pujol and The Germans Trias i Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Owen A Ross
- Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Rejko Krüger
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jean-Christophe Corvol
- CREST, ENSAI, Campus de Ker-Lann, 51 Rue Blaise Pascal - BP 37203 35172 Bruz Cedex, France
| | - Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Australia
- Perron Institute for Neurological and Translational Science, Nedlands, Australia
| | - Pablo Mir
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Rob M A De Bie
- Department of Neurology and Clinical Neurophysiology, Amsterdam University Medical Centers, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
| | - Hirotaka Iwaki
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes on Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, District of Columbia, USA
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
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Pedersen EM, Agerbo E, Plana-Ripoll O, Steinbach J, Krebs MD, Hougaard DM, Werge T, Nordentoft M, Børglum AD, Musliner KL, Ganna A, Schork AJ, Mortensen PB, McGrath JJ, Privé F, Vilhjálmsson BJ. ADuLT: An efficient and robust time-to-event GWAS. Nat Commun 2023; 14:5553. [PMID: 37689771 PMCID: PMC10492844 DOI: 10.1038/s41467-023-41210-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 08/28/2023] [Indexed: 09/11/2023] Open
Abstract
Proportional hazards models have been proposed to analyse time-to-event phenotypes in genome-wide association studies (GWAS). However, little is known about the ability of proportional hazards models to identify genetic associations under different generative models and when ascertainment is present. Here we propose the age-dependent liability threshold (ADuLT) model as an alternative to a Cox regression based GWAS, here represented by SPACox. We compare ADuLT, SPACox, and standard case-control GWAS in simulations under two generative models and with varying degrees of ascertainment as well as in the iPSYCH cohort. We find Cox regression GWAS to be underpowered when cases are strongly ascertained (cases are oversampled by a factor 5), regardless of the generative model used. ADuLT is robust to ascertainment in all simulated scenarios. Then, we analyse four psychiatric disorders in iPSYCH, ADHD, Autism, Depression, and Schizophrenia, with a strong case-ascertainment. Across these psychiatric disorders, ADuLT identifies 20 independent genome-wide significant associations, case-control GWAS finds 17, and SPACox finds 8, which is consistent with simulation results. As more genetic data are being linked to electronic health records, robust GWAS methods that can make use of age-of-onset information will help increase power in analyses for common health outcomes.
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Affiliation(s)
- Emil M Pedersen
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark.
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
| | - Esben Agerbo
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrated Register-based Research at Aarhus University, Aarhus, Denmark
| | - Oleguer Plana-Ripoll
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Department of Clinical Epidemiology, Aarhus University and Aarhus University Hospital, Aarhus, Denmark
| | - Jette Steinbach
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Morten D Krebs
- Institute of Biological Psychiatry, Mental Health Center - Sct Hans, Copenhagen University Hospital - Mental Health Services CPH, Copenhagen, Denmark
| | - David M Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Center - Sct Hans, Copenhagen University Hospital - Mental Health Services CPH, Copenhagen, Denmark
- Department of Clinical Sciences, Copenhagen University, Copenhagen, Denmark
- Section for Geogenetics, GLOBE Institute, Faculty of Health and Medical Science, Copenhagen University, Copenhagen, Denmark
| | - Merete Nordentoft
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- CORE- Copenhagen Centre for Research in Mental Health, Mental Health Center-Copenhagen, Copenhagen University Hospital - Mental Health Services CPH, Copenhagen, Denmark
| | - Anders D Børglum
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine and iSEQ Centre, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, CGPM, Aarhus University, Aarhus, Denmark
| | - Katherine L Musliner
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Department of Affective Disorders, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Center - Sct Hans, Copenhagen University Hospital - Mental Health Services CPH, Copenhagen, Denmark
- Section for Geogenetics, GLOBE Institute, Faculty of Health and Medical Science, Copenhagen University, Copenhagen, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Preben B Mortensen
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - John J McGrath
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - Florian Privé
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Bjarni J Vilhjálmsson
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark.
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, the Broad Institute of MIT and Harvard, Massachusetts, USA.
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4
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Mori Y, Miyake M, Hosoda Y, Miki A, Takahashi A, Muraoka Y, Miyata M, Sato T, Tamura H, Ooto S, Yamada R, Yamashiro K, Nakamura M, Tajima A, Nagasaki M, Honda S, Tsujikawa A. Genome-wide Survival Analysis for Macular Neovascularization Development in Central Serous Chorioretinopathy Revealed Shared Genetic Susceptibility with Polypoidal Choroidal Vasculopathy. Ophthalmology 2022; 129:1034-1042. [PMID: 35490733 DOI: 10.1016/j.ophtha.2022.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/04/2022] [Accepted: 04/22/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE To identify susceptibility genes for macular neovascularization (MNV) development in central serous chorioretinopathy (CSC). DESIGN Genome-wide survival analysis using a longitudinal cohort study. PARTICIPANTS We included 402 and 137 patients with CSC but without MNV at their first visit from the Kyoto CSC Cohort and Kobe CSC dataset, respectively. All patients underwent detailed ophthalmologic examinations, including multimodal imaging, such as fundus autofluorescence, spectral-domain optical coherence tomography, and fluorescein angiography/indocyanine green angiography and/or optimal coherence tomography angiography. METHODS We conducted a genome-wide survival analysis using the Kyoto CSC Cohort. We applied the Cox proportional hazard model to adjust for age, sex, and the first principal component. Single nucleotide polymorphisms (SNPs) with P-values <1.0×10-5 were carried forward to the replication in the Kobe CSC dataset. Moreover, we evaluated the contribution of previously-reported age-related macular degeneration (AMD) susceptibility loci. We used FUMA and ToppFun for the functional enrichment analysis. MAIN OUTCOME MEASURES The association between SNPs and MNV development in patients with CSC. RESULTS Rs370974631 near ARMS2 displayed a genome-wide significant association in the meta-analysis of discovery and replication result (hazard ratio [HR]meta = 3.63; Pmeta = 5.76×10-9). Among previously-reported AMD susceptibility loci, we additionally identified CFH rs800292 (HR = 0.39, P = 2.55×10-4), COL4A3 rs4276018 (HR = 0.26, P = 1.56×10-3), and B3GALTL rs9564692 (HR = 0.56, P = 8.30×10-3) as susceptibility loci for MNV development in CSC. The functional enrichment analysis revealed significant enrichment of eight pathways (GO:0051561, GO:0036444, GO:0008282, GO:1990246, GO:0015272, GO:0030955, GO:0031420, and GO:0005242) related to ion transport. CONCLUSIONS ARMS2, CFH, COL4A3, and B3GALTL were identified as susceptibility genes for MNV development in CSC. The aforementioned four genes are known as susceptibility genes for AMD, whereas COL4A3 and B3GALTL were previously reported to be polypoidal choroidal vasculopathy (PCV)-specific susceptibility genes. Our findings revealed the shared genetic susceptibility between PCV and MNV secondary to CSC.
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Affiliation(s)
- Yuki Mori
- Department of Ophthalmology, Kyoto University Graduate School of Medicine, Kyoto, Japan; Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masahiro Miyake
- Department of Ophthalmology, Kyoto University Graduate School of Medicine, Kyoto, Japan; Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | | | - Akiko Miki
- Department of Surgery, Division of Ophthalmology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ayako Takahashi
- Department of Ophthalmology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuki Muraoka
- Department of Ophthalmology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Manabu Miyata
- Department of Ophthalmology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa Japan
| | - Hiroshi Tamura
- Department of Ophthalmology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Sotaro Ooto
- Department of Ophthalmology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryo Yamada
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Science, Kochi Medical School, Kochi University, Nankoku City, Kochi, Japan
| | - Makoto Nakamura
- Department of Surgery, Division of Ophthalmology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Ishikawa Japan
| | - Masao Nagasaki
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shigeru Honda
- Department of Medical Statistics, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Akitaka Tsujikawa
- Department of Ophthalmology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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5
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Yang L, Qu Q, Hao Z, Sha K, Li Z, Li S. Powerful Identification of Large Quantitative Trait Loci Using Genome-wide R/glmnet-Based Regression. J Hered 2022; 113:472-478. [PMID: 35134967 DOI: 10.1093/jhered/esac006] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/02/2022] [Indexed: 11/14/2022] Open
Abstract
R/glmnet has been successfully applied to jointly-mapped multiple quantitative trait loci for linkage analysis, along with statistical inference for quantitative trait loci candidates with non-zero genetic effects using R/lm for normally distributed traits, R/glm for discrete traits, and R/coxph for survival times. In this study, we extended R/glmnet to a genome-wide association study by means of parallel computation. A multi-locus genome-wide association study for high-throughput single nucleotide polymorphisms was implemented in the "Multi-Runking" software written within the R workspace. This software can better detect common and large quantitative trait nucleotides and more accurately estimate than genome-wide mixed model analysis for one single nucleotide polymorphism at a time and linear mixed models-least absolute shrinkage and selection operator. Its applicability and utility were demonstrated by multi-locus genome-wide association studies for the simulated and real traits distributed normally, binary traits, and survival times.
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Affiliation(s)
- Li'ang Yang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Qiannan Qu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhiyu Hao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Ke Sha
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Ziyu Li
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Shuling Li
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
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6
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Ojavee SE, Kousathanas A, Trejo Banos D, Orliac EJ, Patxot M, Läll K, Mägi R, Fischer K, Kutalik Z, Robinson MR. Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis. Nat Commun 2021; 12:2337. [PMID: 33879782 PMCID: PMC8058085 DOI: 10.1038/s41467-021-22538-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/17/2021] [Indexed: 01/18/2023] Open
Abstract
While recent advancements in computation and modelling have improved the analysis of complex traits, our understanding of the genetic basis of the time at symptom onset remains limited. Here, we develop a Bayesian approach (BayesW) that provides probabilistic inference of the genetic architecture of age-at-onset phenotypes in a sampling scheme that facilitates biobank-scale time-to-event analyses. We show in extensive simulation work the benefits BayesW provides in terms of number of discoveries, model performance and genomic prediction. In the UK Biobank, we find many thousands of common genomic regions underlying the age-at-onset of high blood pressure (HBP), cardiac disease (CAD), and type-2 diabetes (T2D), and for the genetic basis of onset reflecting the underlying genetic liability to disease. Age-at-menopause and age-at-menarche are also highly polygenic, but with higher variance contributed by low frequency variants. Genomic prediction into the Estonian Biobank data shows that BayesW gives higher prediction accuracy than other approaches.
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Affiliation(s)
- Sven E Ojavee
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
| | | | - Daniel Trejo Banos
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Etienne J Orliac
- Scientific Computing and Research Support Unit, University of Lausanne, Lausanne, Switzerland
| | - Marion Patxot
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Kristi Läll
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Krista Fischer
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - Zoltan Kutalik
- University Center for Primary Care and Public Health, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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7
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Bi W, Fritsche LG, Mukherjee B, Kim S, Lee S. A Fast and Accurate Method for Genome-Wide Time-to-Event Data Analysis and Its Application to UK Biobank. Am J Hum Genet 2020; 107:222-233. [PMID: 32589924 DOI: 10.1016/j.ajhg.2020.06.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/03/2020] [Indexed: 12/09/2022] Open
Abstract
With increasing biobanking efforts connecting electronic health records and national registries to germline genetics, the time-to-event data analysis has attracted increasing attention in the genetics studies of human diseases. In time-to-event data analysis, the Cox proportional hazards (PH) regression model is one of the most used approaches. However, existing methods and tools are not scalable when analyzing a large biobank with hundreds of thousands of samples and endpoints, and they are not accurate when testing low-frequency and rare variants. Here, we propose a scalable and accurate method, SPACox (a saddlepoint approximation implementation based on the Cox PH regression model), that is applicable for genome-wide scale time-to-event data analysis. SPACox requires fitting a Cox PH regression model only once across the genome-wide analysis and then uses a saddlepoint approximation (SPA) to calibrate the test statistics. Simulation studies show that SPACox is 76-252 times faster than other existing alternatives, such as gwasurvivr, 185-511 times faster than the standard Wald test, and more than 6,000 times faster than the Firth correction and can control type I error rates at the genome-wide significance level regardless of minor allele frequencies. Through the analysis of UK Biobank inpatient data of 282,871 white British European ancestry samples, we show that SPACox can efficiently analyze large sample sizes and accurately control type I error rates. We identified 611 loci associated with time-to-event phenotypes of 12 common diseases, of which 38 loci would be missed within a logistic regression framework with a binary phenotype defined as event occurrence status during the follow-up period.
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Langdon R, Richmond R, Elliott HR, Dudding T, Kazmi N, Penfold C, Ingarfield K, Ho K, Bretherick A, Haley C, Zeng Y, Walker RM, Pawlita M, Waterboer T, Gaunt T, Smith GD, Suderman M, Thomas S, Ness A, Relton C. Identifying epigenetic biomarkers of established prognostic factors and survival in a clinical cohort of individuals with oropharyngeal cancer. Clin Epigenetics 2020; 12:95. [PMID: 32600451 PMCID: PMC7322918 DOI: 10.1186/s13148-020-00870-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/19/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Smoking status, alcohol consumption and HPV infection (acquired through sexual activity) are the predominant risk factors for oropharyngeal cancer and are thought to alter the prognosis of the disease. Here, we conducted single-site and differentially methylated region (DMR) epigenome-wide association studies (EWAS) of these factors, in addition to ∼ 3-year survival, using Illumina Methylation EPIC DNA methylation profiles from whole blood in 409 individuals as part of the Head and Neck 5000 (HN5000) study. Overlapping sites between each factor and survival were then assessed using two-step Mendelian randomization to assess whether methylation at these positions causally affected survival. RESULTS Using the MethylationEPIC array in an OPC dataset, we found novel CpG associations with smoking, alcohol consumption and ~ 3-year survival. We found no CpG associations below our multiple testing threshold associated with HPV16 E6 serological response (used as a proxy for HPV infection). CpG site associations below our multiple-testing threshold (PBonferroni < 0.05) for both a prognostic factor and survival were observed at four gene regions: SPEG (smoking), GFI1 (smoking), PPT2 (smoking) and KHDC3L (alcohol consumption). Evidence for a causal effect of DNA methylation on survival was only observed in the SPEG gene region (HR per SD increase in methylation score 1.28, 95% CI 1.14 to 1.43, P 2.12 × 10-05). CONCLUSIONS Part of the effect of smoking on survival in those with oropharyngeal cancer may be mediated by methylation at the SPEG gene locus. Replication in data from independent datasets and data from HN5000 with longer follow-up times is needed to confirm these findings.
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Affiliation(s)
- Ryan Langdon
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Rebecca Richmond
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hannah R. Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom Dudding
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Chris Penfold
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and University of Bristol, Bristol, UK
| | - Kate Ingarfield
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and University of Bristol, Bristol, UK
| | - Karen Ho
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Scotland Bristol, EH4 2XU UK
| | - Chris Haley
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Scotland Bristol, EH4 2XU UK
| | - Yanni Zeng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Scotland Bristol, EH4 2XU UK
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Rosie M. Walker
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Michael Pawlita
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tom Gaunt
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and University of Bristol, Bristol, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Steve Thomas
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and University of Bristol, Bristol, UK
| | - Andy Ness
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and University of Bristol, Bristol, UK
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9
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Hughey JJ, Rhoades SD, Fu DY, Bastarache L, Denny JC, Chen Q. Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record. BMC Genomics 2019; 20:805. [PMID: 31684865 PMCID: PMC6829851 DOI: 10.1186/s12864-019-6192-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Background The growth of DNA biobanks linked to data from electronic health records (EHRs) has enabled the discovery of numerous associations between genomic variants and clinical phenotypes. Nonetheless, although clinical data are generally longitudinal, standard approaches for detecting genotype-phenotype associations in such linked data, notably logistic regression, do not naturally account for variation in the period of follow-up or the time at which an event occurs. Here we explored the advantages of quantifying associations using Cox proportional hazards regression, which can account for the age at which a patient first visited the healthcare system (left truncation) and the age at which a patient either last visited the healthcare system or acquired a particular phenotype (right censoring). Results In comprehensive simulations, we found that, compared to logistic regression, Cox regression had greater power at equivalent Type I error. We then scanned for genotype-phenotype associations using logistic regression and Cox regression on 50 phenotypes derived from the EHRs of 49,792 genotyped individuals. Consistent with the findings from our simulations, Cox regression had approximately 10% greater relative sensitivity for detecting known associations from the NHGRI-EBI GWAS Catalog. In terms of effect sizes, the hazard ratios estimated by Cox regression were strongly correlated with the odds ratios estimated by logistic regression. Conclusions As longitudinal health-related data continue to grow, Cox regression may improve our ability to identify the genetic basis for a wide range of human phenotypes.
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Affiliation(s)
- Jacob J Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA. .,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
| | - Seth D Rhoades
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Darwin Y Fu
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qingxia Chen
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
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Rizvi AA, Karaesmen E, Morgan M, Preus L, Wang J, Sovic M, Hahn T, Sucheston-Campbell LE. gwasurvivr: an R package for genome-wide survival analysis. Bioinformatics 2018; 35:1968-1970. [PMID: 30395168 PMCID: PMC7963072 DOI: 10.1093/bioinformatics/bty920] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/26/2018] [Accepted: 11/01/2018] [Indexed: 01/31/2023] Open
Abstract
SUMMARY To address the limited software options for performing survival analyses with millions of SNPs, we developed gwasurvivr, an R/Bioconductor package with a simple interface for conducting genome-wide survival analyses using VCF (outputted from Michigan or Sanger imputation servers), IMPUTE2 or PLINK files. To decrease the number of iterations needed for convergence when optimizing the parameter estimates in the Cox model, we modified the R package survival; covariates in the model are first fit without the SNP, and those parameter estimates are used as initial points. We benchmarked gwasurvivr with other software capable of conducting genome-wide survival analysis (genipe, SurvivalGWAS_SV and GWASTools). gwasurvivr is significantly faster and shows better scalability as sample size, number of SNPs and number of covariates increases. AVAILABILITY AND IMPLEMENTATION gwasurvivr, including source code, documentation and vignette are available at: http://bioconductor.org/packages/gwasurvivr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Martin Morgan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Leah Preus
- Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Junke Wang
- Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Michael Sovic
- Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Theresa Hahn
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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