1
|
Kunkel D, Sørensen P, Shankar V, Morgante F. Improving polygenic prediction from summary data by learning patterns of effect sharing across multiple phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592745. [PMID: 38766136 PMCID: PMC11100663 DOI: 10.1101/2024.05.06.592745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Polygenic prediction of complex trait phenotypes has become important in human genetics, especially in the context of precision medicine. Recently, Morgante et al. introduced mr.mash, a flexible and computationally efficient method that models multiple phenotypes jointly and leverages sharing of effects across such phenotypes to improve prediction accuracy. However, a drawback of mr.mash is that it requires individual-level data, which are often not publicly available. In this work, we introduce mr.mash-rss, an extension of the mr.mash model that requires only summary statistics from Genome-Wide Association Studies (GWAS) and linkage disequilibrium (LD) estimates from a reference panel. By using summary data, we achieve the twin goal of increasing the applicability of the mr.mash model to data sets that are not publicly available and making it scalable to biobank-size data. Through simulations, we show that mr.mash-rss is competitive with, and often outperforms, current state-of-the-art methods for single- and multi-phenotype polygenic prediction in a variety of scenarios that differ in the pattern of effect sharing across phenotypes, the number of phenotypes, the number of causal variants, and the genomic heritability. We also present a real data analysis of 16 blood cell phenotypes in UK Biobank, showing that mr.mash-rss achieves higher prediction accuracy than competing methods for the majority of traits, especially when the data has smaller sample size.
Collapse
Affiliation(s)
- Deborah Kunkel
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC, United States of America
| | - Peter Sørensen
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Vijay Shankar
- Center for Human Genetics, Clemson University, Greenwood, SC, United States of America
| | - Fabio Morgante
- Center for Human Genetics, Clemson University, Greenwood, SC, United States of America
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States of America
| |
Collapse
|
2
|
Ramos-Lopez O. Genotype-based precision nutrition strategies for the prediction and clinical management of type 2 diabetes mellitus. World J Diabetes 2024; 15:142-153. [PMID: 38464367 PMCID: PMC10921165 DOI: 10.4239/wjd.v15.i2.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/07/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024] Open
Abstract
Globally, type 2 diabetes mellitus (T2DM) is one of the most common metabolic disorders. T2DM physiopathology is influenced by complex interrelationships between genetic, metabolic and lifestyle factors (including diet), which differ between populations and geographic regions. In fact, excessive consumptions of high fat/high sugar foods generally increase the risk of developing T2DM, whereas habitual intakes of plant-based healthy diets usually exert a protective effect. Moreover, genomic studies have allowed the characterization of sequence DNA variants across the human genome, some of which may affect gene expression and protein functions relevant for glucose homeostasis. This comprehensive literature review covers the impact of gene-diet interactions on T2DM susceptibility and disease progression, some of which have demonstrated a value as biomarkers of personal responses to certain nutritional interventions. Also, novel genotype-based dietary strategies have been developed for improving T2DM control in comparison to general lifestyle recommendations. Furthermore, progresses in other omics areas (epigenomics, metagenomics, proteomics, and metabolomics) are improving current understanding of genetic insights in T2DM clinical outcomes. Although more investigation is still needed, the analysis of the genetic make-up may help to decipher new paradigms in the pathophysiology of T2DM as well as offer further opportunities to personalize the screening, prevention, diagnosis, management, and prognosis of T2DM through precision nutrition.
Collapse
Affiliation(s)
- Omar Ramos-Lopez
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana 22390, Baja California, Mexico
| |
Collapse
|
4
|
Albiñana C, Zhu Z, Schork AJ, Ingason A, Aschard H, Brikell I, Bulik CM, Petersen LV, Agerbo E, Grove J, Nordentoft M, Hougaard DM, Werge T, Børglum AD, Mortensen PB, McGrath JJ, Neale BM, Privé F, Vilhjálmsson BJ. Multi-PGS enhances polygenic prediction by combining 937 polygenic scores. Nat Commun 2023; 14:4702. [PMID: 37543680 PMCID: PMC10404269 DOI: 10.1038/s41467-023-40330-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/21/2023] [Indexed: 08/07/2023] Open
Abstract
The predictive performance of polygenic scores (PGS) is largely dependent on the number of samples available to train the PGS. Increasing the sample size for a specific phenotype is expensive and takes time, but this sample size can be effectively increased by using genetically correlated phenotypes. We propose a framework to generate multi-PGS from thousands of publicly available genome-wide association studies (GWAS) with no need to individually select the most relevant ones. In this study, the multi-PGS framework increases prediction accuracy over single PGS for all included psychiatric disorders and other available outcomes, with prediction R2 increases of up to 9-fold for attention-deficit/hyperactivity disorder compared to a single PGS. We also generate multi-PGS for phenotypes without an existing GWAS and for case-case predictions. We benchmark the multi-PGS framework against other methods and highlight its potential application to new emerging biobanks.
Collapse
Affiliation(s)
- Clara Albiñana
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark.
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark.
| | - Zhihong Zhu
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
| | - Andrew J Schork
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, 2100, Denmark
- The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Andrés Ingason
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, 2100, Denmark
| | - Hugues Aschard
- Department of Computational Biology, Institut Pasteur, Université de Paris, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Isabell Brikell
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Department of Biomedicine and Center for Integrative Sequencing, iSEQ, Aarhus University, 8000, Aarhus C, Denmark
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Cynthia M Bulik
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Liselotte V Petersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
| | - Esben Agerbo
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Department of Biomedicine and Center for Integrative Sequencing, iSEQ, Aarhus University, 8000, Aarhus C, Denmark
- Center for Genomics and Personalized Medicine, Aarhus University, 8000, Aarhus C, Denmark
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus C, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Copenhagen Research Centre on Mental Health (CORE), University of Copenhagen, Copenhagen, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, 2300, Copenhagen S, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, 2100, Denmark
- Lundbeck Foundation Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350, Copenhagen K, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Department of Biomedicine and Center for Integrative Sequencing, iSEQ, Aarhus University, 8000, Aarhus C, Denmark
- Center for Genomics and Personalized Medicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
| | - John J McGrath
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD, 4076, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Florian Privé
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
| | - Bjarni J Vilhjálmsson
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark.
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark.
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus C, Denmark.
- Novo Nordisk Foundation Center for Genomic Mechanisms, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
6
|
Kloeve-Mogensen K, Rohde PD, Twisttmann S, Nygaard M, Koldby KM, Steffensen R, Dahl CM, Rytter D, Overgaard MT, Forman A, Christiansen L, Nyegaard M. Polygenic Risk Score Prediction for Endometriosis. FRONTIERS IN REPRODUCTIVE HEALTH 2021; 3:793226. [PMID: 36303976 PMCID: PMC9580817 DOI: 10.3389/frph.2021.793226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/09/2021] [Indexed: 12/19/2022] Open
Abstract
Endometriosis is a major health care challenge because many young women with endometriosis go undetected for an extended period, which may lead to pain sensitization. Clinical tools to better identify candidates for laparoscopy-guided diagnosis are urgently needed. Since endometriosis has a strong genetic component, there is a growing interest in using genetics as part of the clinical risk assessment. The aim of this work was to investigate the discriminative ability of a polygenic risk score (PRS) for endometriosis using three different cohorts: surgically confirmed cases from the Western Danish endometriosis referral Center (249 cases, 348 controls), cases identified from the Danish Twin Registry (DTR) based on ICD-10 codes from the National Patient Registry (140 cases, 316 controls), and replication analysis in the UK Biobank (2,967 cases, 256,222 controls). Patients with adenomyosis from the DTR (25 cases) and from the UK Biobank (1,883 cases) were included for comparison. The PRS was derived from 14 genetic variants identified in a published genome-wide association study with more than 17,000 cases. The PRS was associated with endometriosis in surgically confirmed cases [odds ratio (OR) = 1.59, p = 2.57× 10−7] and in cases from the DTR biobank (OR = 1.50, p = 0.0001). Combining the two Danish cohorts, each standard deviation increase in PRS was associated with endometriosis (OR = 1.57, p = 2.5× 10−11), as well as the major subtypes of endometriosis; ovarian (OR = 1.72, p = 6.7× 10−5), infiltrating (OR = 1.66, p = 2.7× 10−9), and peritoneal (OR = 1.51, p = 2.6 × 10−3). These findings were replicated in the UK Biobank with a much larger sample size (OR = 1.28, p < 2.2× 10−16). The PRS was not associated with adenomyosis, suggesting that adenomyosis is not driven by the same genetic risk variants as endometriosis. Our results suggest that a PRS captures an increased risk of all types of endometriosis rather than an increased risk for endometriosis in specific locations. Although the discriminative accuracy is not yet sufficient as a stand-alone clinical utility, our data demonstrate that genetics risk variants in form of a simple PRS may add significant new discriminatory value. We suggest that an endometriosis PRS in combination with classical clinical risk factors and symptoms could be an important step in developing an urgently needed endometriosis risk stratification tool.
Collapse
Affiliation(s)
- Kirstine Kloeve-Mogensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Palle Duun Rohde
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Simone Twisttmann
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Marianne Nygaard
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | | | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Christian Møller Dahl
- Department of Business and Economics, University of Southern Denmark, Odense, Denmark
| | - Dorte Rytter
- Research Unit for Epidemiology, Department of Public Health, Aarhus University, Aarhus, Denmark
| | | | - Axel Forman
- Department of Gynecology and Obstetrics, Aarhus University Hospital, Skejby, Denmark
| | - Lene Christiansen
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- *Correspondence: Mette Nyegaard
| |
Collapse
|