PRSice: Polygenic Risk Score software.
paper
Cited
Public
- Authors
- Euesden, Jack; Lewis, Cathryn M; O'Reilly, Paul F
- Year
- 2015
- Journal
- Bioinformatics (Oxford, England)
- PMID
- 25550326
- DOI
- 10.1093/bioinformatics/btu848
- PMCID
- PMC4410663
SUMMARY: A polygenic risk score (PRS) is a sum of trait-associated alleles across many genetic loci, typically weighted by effect sizes estimated from a genome-wide association study. The application of PRS has grown in recent years as their utility for detecting shared genetic aetiology among traits has become appreciated; PRS can also be used to establish the presence of a genetic signal in underpowered studies, to infer the genetic architecture of a trait, for screening in clinical trials, and can act as a biomarker for a phenotype. Here we present the first dedicated PRS software, PRSice ('precise'), for calculating, applying, evaluating and plotting the results of PRS. PRSice can calculate PRS at a large number of thresholds ("high resolution") to provide the best-fit PRS, as well as provide results calculated at broad P-value thresholds, can thin Single Nucleotide Polymorphisms (SNPs) according to linkage disequilibrium and P-value or use all SNPs, handles genotyped and imputed data, can calculate and incorporate ancestry-informative variables, and can apply PRS across multiple traits in a single run. We exemplify the use of PRSice via application to data on schizophrenia, major depressive disorder and smoking, illustrate the importance of identifying the best-fit PRS and estimate a P-value significance threshold for high-resolution PRS studies. AVAILABILITY AND IMPLEMENTATION: PRSice is written in R, including wrappers for bash data management scripts and PLINK-1.9 to minimize computational time. PRSice runs as a command-line program with a variety of user-options, and is freely available for download from http://PRSice.info CONTACT: jack.euesden@kcl.ac.uk or paul.oreilly@kcl.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Bar plot from PRSice showing results at broad P-value thresholds for Schizophrenia PRS predicting MDD status. A bar for the best-fit PRS from the high-resolution run is also included
High-resolution PRSice plot for SCZ predicting MDD status. The thick line connects points at the broad P-value thresholds of Fig.1
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| Polygenic risk scores: the future of cancer risk prediction, screening, and precision prevention. | Wang Y et al. | β | 2021 | β |
| Polygenic risk scoring to assess genetic overlap and protective factors influencing posttraumatic stress, depression, and chronic pain after motor vehicle collision trauma. | Lobo JJ et al. | β | 2021 | β |
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| Role of Common Genetic Variants for Drug-Resistance to Specific Anti-Seizure Medications. | Wolking S et al. | β | 2021 | β |
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| T cell composition and polygenic multiple sclerosis risk: A population-based study in children. | de Mol CL et al. | β | 2021 | β |
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| A Polygenic and Phenotypic Risk Prediction for Polycystic Ovary Syndrome Evaluated by Phenome-Wide Association Studies. | Joo YY et al. | β | 2020 | β |
| A polygenic biomarker to identify patients with severe hypercholesterolemia of polygenic origin. | Leal LG et al. | β | 2020 | β |
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| Assessing the Relationship Between Gut Microbiota and Bone Mineral Density. | Cheng S et al. | β | 2020 | β |
| Assessing the Relationship Between Leukocyte Telomere Length and Cancer Risk/Mortality in UK Biobank and TCGA Datasets With the Genetic Risk Score and Mendelian Randomization Approaches. | Gao Y et al. | β | 2020 | β |
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| Association Between Polygenic Risk Score and Risk of Myopia. | Ghorbani Mojarrad N et al. | β | 2020 | β |
| A trans-ethnic two-stage polygenetic scoring analysis detects genetic correlation between osteoporosis and schizophrenia. | Liu L et al. | β | 2020 | β |
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| Cancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks. | Fritsche LG et al. | β | 2020 | β |
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| Comparison of Genetic Liability for Sleep Traits Among Individuals With Bipolar Disorder I or II and Control Participants. | Lewis KJS et al. | β | 2020 | β |
| Composite Measures of Physical Fitness to Discriminate Between Healthy Aging and Heart Failure: The COmPLETE Study. | Wagner J et al. | β | 2020 | β |
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| Contribution of Genetic Background and Data Collection on Adverse Events of Anti-human Immunodeficiency Virus (HIV) Drugs (D:A:D) Clinical Risk Score to Chronic Kidney Disease in Swiss HIV-infected Persons With Normal Baseline Estimated Glomerular Filtration Rate. | Dietrich LG et al. | β | 2020 | β |
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| Genetic contributions to two special factors of neuroticism are associated with affluence, higher intelligence, better health, and longer life. | Hill WD et al. | β | 2020 | β |
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| Genetic Modifiers of Cystic Fibrosis-Related Diabetes Have Extensive Overlap With Type 2 Diabetes and Related Traits. | Aksit MA et al. | β | 2020 | β |
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| Genome-Wide Association Study of Opioid Cessation. | Cox JW et al. | β | 2020 | β |
| Genome-wide association study of self-reported walking pace suggests beneficial effects of brisk walking on health and survival. | Timmins IR et al. | β | 2020 | β |
| Genome-Wide Association Study of Suicide Death and Polygenic Prediction of Clinical Antecedents. | Docherty AR et al. | β | 2020 | β |
| Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis. | Allen RJ et al. | β | 2020 | β |
| Genome-wide association study of word reading: Overlap with risk genes for neurodevelopmental disorders. | Price KM et al. | β | 2020 | β |
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| Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits. | Zhou H et al. | β | 2020 | β |
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| Investigating Causality Between Blood Metabolites and Emotional and Behavioral Responses to Traumatic Stress: a Mendelian Randomization Study. | Carvalho CM et al. | β | 2020 | β |
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| Letter to the editor: Is polygenic risk for Parkinson's disease associated with less risk of first episode psychosis? | Quattrone D et al. | β | 2020 | β |
| Leveraging genome-wide data to investigate differences between opioid use vs. opioid dependence in 41,176 individuals from the Psychiatric Genomics Consortium. | Polimanti R et al. | β | 2020 | β |
| Low cardiac vagal control is associated with genetic liability for elevated triglycerides and risky health behaviors. | Martin JD et al. | β | 2020 | β |
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| Mitonuclear interactions influence Alzheimer's disease risk. | Andrews SJ et al. | β | 2020 | β |
| Molecular Genetic Risk for Psychosis Is Associated With Psychosis Risk Symptoms in a Population-Based UK Cohort: Findings From Generation Scotland. | Docherty AR et al. | β | 2020 | β |
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| Pharmacological enrichment of polygenic risk for precision medicine in complex disorders. | Reay WR et al. | β | 2020 | β |
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| Polygenic risk for autism spectrum disorder affects left amygdala activity and negative emotion in schizophrenia. | Qin Y et al. | β | 2020 | β |
| Polygenic risk for autism spectrum disorder associates with anger recognition in a neurodevelopment-focused phenome-wide scan of unaffected youths from a population-based cohort. | Wendt FR et al. | β | 2020 | β |
| Polygenic risk score for obesity and the quality, quantity, and timing of workplace food purchases: A secondary analysis from the ChooseWell 365 randomized trial. | Dashti HS et al. | β | 2020 | β |
| Polygenic risk score for schizophrenia was not associated with glycemic level (HbA1c) in patients with non-affective psychosis: Genetic Risk and Outcome of Psychosis (GROUP) cohort study. | Habtewold TD et al. | β | 2020 | β |
| Polygenic Risk Scores for Developmental Disorders, Neuromotor Functioning During Infancy, and Autistic Traits in Childhood. | Serdarevic F et al. | β | 2020 | β |
| Polygenic Risk Scores in Alzheimer's Disease: Current Applications and Future Directions. | Baker E et al. | β | 2020 | β |
| Polygenic risk scores indicates genetic overlap between peripheral pain syndromes and chronic postsurgical pain. | van Reij RRI et al. | β | 2020 | β |
| Polygenic risk scores in schizophrenia with clinically significant copy number variants. | Taniguchi S et al. | β | 2020 | β |
| Polygenic risk scores of several subtypes of epilepsies in a founder population. | Moreau C et al. | β | 2020 | β |
| Polygenic Score for Body Mass Index Is Associated with Disordered Eating in a General Population Cohort. | Abdulkadir M et al. | β | 2020 | β |
| Polygenic score for sleep duration. Association with cognition. | Tsapanou A et al. | β | 2020 | β |
| Population phenomena inflate genetic associations of complex social traits. | Morris TT et al. | β | 2020 | β |
| Prediction of Nephrotoxicity Associated With Cisplatin-Based Chemotherapy in Testicular Cancer Patients. | Garcia SL et al. | β | 2020 | β |
| Predictive Utility of Polygenic Risk Scores for Coronary Heart Disease in Three Major Racial and Ethnic Groups. | Dikilitas O et al. | β | 2020 | β |
| Psychiatric Polygenic Risk Scores as Predictor for Attention Deficit/Hyperactivity Disorder and Autism Spectrum Disorder in a Clinical Child and Adolescent Sample. | Jansen AG et al. | β | 2020 | β |
| Psychotic-like experiences, polygenic risk scores for schizophrenia, and structural properties of the salience, default mode, and central-executive networks in healthy participants from UK Biobank. | Alloza C et al. | β | 2020 | β |
| Recent advances in sarcoidosis genomics: epigenetics, gene expression, and gene by environment (GβΓβE) interaction studies. | Garman L et al. | β | 2020 | β |
| Reproducible Genetic Risk Loci for Anxiety: Results From βΌ200,000 Participants in the Million Veteran Program. | Levey DF et al. | β | 2020 | β |
| Schizophrenia polygenic risk predicts general cognitive deficit but not cognitive decline in healthy older adults. | KΔpiΕska AP et al. | β | 2020 | β |
| Self-reported hearing loss questions provide a good measure for genetic studies: a polygenic risk score analysis from UK Biobank. | Cherny SS et al. | β | 2020 | β |
| Sequential screening nominates the Parkinson's disease associated kinase LRRK2 as a regulator of Clathrin-mediated endocytosis. | Heaton GR et al. | β | 2020 | β |
| Shared genetic etiology between obsessive-compulsive disorder, obsessive-compulsive symptoms in the population, and insulin signaling. | Bralten J et al. | β | 2020 | β |
| Shared polygenic risk for ADHD, executive dysfunction and other psychiatric disorders. | Chang S et al. | β | 2020 | β |
| Sibling comparisons elucidate the associations between educational attainment polygenic scores and alcohol, nicotine and cannabis. | Salvatore JE et al. | β | 2020 | β |
| Similar burden of pathogenic coding variants in exceptionally long-lived individuals and individuals without exceptional longevity. | Gutman D et al. | β | 2020 | β |
| Stratifying major depressive disorder by polygenic risk for schizophrenia in relation to structural brain measures. | Harris MA et al. | β | 2020 | β |
| Studying individual risk factors for self-harm in the UK Biobank: A polygenic scoring and Mendelian randomisation study. | Lim KX et al. | β | 2020 | β |
| The Association with Quantitative Response to Attention-Deficit/Hyperactivity Disorder Medication of the Previously Identified Neurodevelopmental Network Genes. | Zhong Y et al. | β | 2020 | β |
| The behavioral, cellular and immune mediators of HIV-1 acquisition: New insights from population genetics. | Powell TR et al. | β | 2020 | β |
| The ChinaMAP analytics of deep whole genome sequences in 10,588 individuals. | Cao Y et al. | β | 2020 | β |
| The emerging landscape of health research based on biobanks linked to electronic health records: Existing resources, statistical challenges, and potential opportunities. | Beesley LJ et al. | β | 2020 | β |
| The influence of common polygenic risk and gene sets on social skills group training response in autism spectrum disorder. | Li D et al. | β | 2020 | β |
| The interplay of sun damage and genetic risk in Australian multiple and single primary melanoma cases and controls. | McMeniman EK et al. | β | 2020 | β |
| The Role of Eating Behaviours in Genetic Susceptibility to Obesity. | Herle M et al. | β | 2020 | β |
| The role of polygenic susceptibility to obesity among carriers of pathogenic mutations in MC4R in the UK Biobank population. | Chami N et al. | β | 2020 | β |
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| Tutorial: a guide to performing polygenic risk score analyses. | Choi SW et al. | β | 2020 | β |
| Using common genetic variation to examine phenotypic expression and risk prediction in 22q11.2 deletion syndrome. | Davies RW et al. | β | 2020 | β |
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| Using Genetics to Examine a General Liability to Childhood Psychopathology. | Riglin L et al. | β | 2020 | β |
| Variable prediction accuracy of polygenic scores within an ancestry group. | Mostafavi H et al. | β | 2020 | β |
| A combined analysis of genetically correlated traits identifies 187 loci and a role for neurogenesis and myelination in intelligence. | Hill WD et al. | β | 2019 | β |
| A genome-wide association meta-analysis of prognostic outcomes following cognitive behavioural therapy in individuals with anxiety and depressive disorders. | Rayner C et al. | β | 2019 | β |
| A large-scale genomic investigation of susceptibility to infection and its association with mental disorders in the Danish population. | Nudel R et al. | β | 2019 | β |
| Alzheimer's disease polygenic risk score as a predictor of conversion from mild-cognitive impairment. | Chaudhury S et al. | β | 2019 | β |
| Ancestry-specific polygenic scores and SNP heritability of 25(OH)D in African- and European-ancestry populations. | Hatchell KE et al. | β | 2019 | β |
| Assessing potential shared genetic aetiology between body mass index and sleep duration in 142,209 individuals. | Garfield V et al. | β | 2019 | β |
| Assessing the genetic association between vitamin B6 metabolism and genetic generalized epilepsy. | Stevelink R et al. | β | 2019 | β |
| Association of Economic Status and Educational Attainment With Posttraumatic Stress Disorder: A Mendelian Randomization Study. | Polimanti R et al. | β | 2019 | β |
| Association of Whole-Genome and NETRIN1 Signaling Pathway-Derived Polygenic Risk Scores for Major Depressive Disorder and White Matter Microstructure in the UK Biobank. | Barbu MC et al. | β | 2019 | β |
| A systematic review of associations between functional MRI activity and polygenic risk for schizophrenia and bipolar disorder. | Dezhina Z et al. | β | 2019 | β |
| A validation of the diathesis-stress model for depression in Generation Scotland. | Arnau-Soler A et al. | β | 2019 | β |
| Beyond C4: Analysis of the complement gene pathway shows enrichment for IQ in patients with psychotic disorders and healthy controls. | Holland JF et al. | β | 2019 | β |
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| Genetic association with B-cell acute lymphoblastic leukemia in allogeneic transplant patients differs by age and sex. | Clay-Gilmour AI et al. | β | 2017 | β |
| Genetic factor common to schizophrenia and HIV infection is associated with risky sexual behavior: antagonistic vs. synergistic pleiotropic SNPs enriched for distinctly different biological functions. | Wang Q et al. | β | 2017 | β |
| Genetic Influences on Evening Preference Overlap with Those for Bipolar Disorder in a Sample of Mexican Americans and American Indians. | Melroy-Greif WE et al. | β | 2017 | β |
| Genetic prediction of male pattern baldness. | Hagenaars SP et al. | β | 2017 | β |
| Genetic Risk as a Marker of Amyloid-Ξ² and Tau Burden in Cerebrospinal Fluid. | Voyle N et al. | β | 2017 | β |
| Genetic Stratification to Identify Risk Groups for Alzheimer's Disease. | Marioni RE et al. | β | 2017 | β |
| Genome Wide Association Study (GWAS) between Attention Deficit Hyperactivity Disorder (ADHD) and Obsessive Compulsive Disorder (OCD). | Ritter ML et al. | β | 2017 | β |
| Genome-wide association study identifies four novel loci associated with Alzheimer's endophenotypes and disease modifiers. | Deming Y et al. | β | 2017 | β |
| Genome-wide association study of alcohol consumption and genetic overlap with other health-related traits in UK Biobank (N=112β117). | Clarke TK et al. | β | 2017 | β |
| Genome-wide association study of facial emotion recognition in children and association with polygenic risk for mental health disorders. | Coleman JRI et al. | β | 2017 | β |
| Genome-Wide Polygenic Scores Predict Reading Performance Throughout the School Years. | Selzam S et al. | β | 2017 | β |
| Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations. | Martin AR et al. | β | 2017 | β |
| Integrated molecular landscape of Parkinson's disease. | Klemann CJHM et al. | β | 2017 | β |
| Is a polygenic predictor of antidepressant response a possibility? | Fabbri C | β | 2017 | β |
| Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets. | Lam M et al. | β | 2017 | β |
| Molecular genetic contributions to self-rated health. | Harris SE et al. | β | 2017 | β |
| Pharmacogenetics of antidepressant response: A polygenic approach. | GarcΓa-GonzΓ‘lez J et al. | β | 2017 | β |
| Polygenic risk assessment reveals pleiotropy between sarcoidosis and inflammatory disorders in the context of genetic ancestry. | Lareau CA et al. | β | 2017 | β |
| Polygenic risk for five psychiatric disorders and cross-disorder and disorder-specific neural connectivity in two independent populations. | Wang T et al. | β | 2017 | β |
| Polygenic risk has an impact on the structural plasticity of hippocampal subfields during aerobic exercise combined with cognitive remediation in multi-episode schizophrenia. | Papiol S et al. | β | 2017 | β |
| Polygenic scores via penalized regression on summary statistics. | Mak TSH et al. | β | 2017 | β |
| Predicting educational achievement from DNA. | Selzam S et al. | β | 2017 | β |
| Prefrontal gray matter volume mediates genetic risks for obesity. | Opel N et al. | β | 2017 | β |
| Prospects for using risk scores in polygenic medicine. | Lewis CM et al. | β | 2017 | β |
| Role of 108 schizophrenia-associated loci in modulating psychopathological dimensions in schizophrenia and bipolar disorder. | Fabbri C et al. | β | 2017 | β |
| Separate and combined effects of genetic variants and pre-treatment whole blood gene expression on response to exposure-based cognitive behavioural therapy for anxiety disorders. | Coleman JR et al. | β | 2017 | β |
| Sexual dimorphism in the genetic influence on human childlessness. | Verweij RM et al. | β | 2017 | β |
| Single Nucleotide Polymorphisms Associated with Reading Ability Show Connection to Socio-Economic Outcomes. | Luciano M et al. | β | 2017 | β |
| Statistical methods to detect pleiotropy in human complex traits. | Hackinger S et al. | β | 2017 | β |
| The Relationship Between Mental Health, Disease Severity, and Genetic Risk for Depression in Early Rheumatoid Arthritis. | Euesden J et al. | β | 2017 | β |
| Widespread signatures of positive selection in common risk alleles associated to autism spectrum disorder. | Polimanti R et al. | β | 2017 | β |
| Advances in the genetics of schizophrenia: toward a network and pathway view for drug discovery. | Collier DA et al. | β | 2016 | β |
| Alcohol-related genes show an enrichment of associations with a persistent externalizing factor. | Ashenhurst JR et al. | β | 2016 | β |
| Association, characterisation and meta-analysis of SNPs linked to general reading ability in a German dyslexia case-control cohort. | MΓΌller B et al. | β | 2016 | β |
| Dissection of major depressive disorder using polygenic risk scores for schizophrenia in two independent cohorts. | Whalley HC et al. | β | 2016 | β |
| Exon-focused genome-wide association study of obsessive-compulsive disorder and shared polygenic risk with schizophrenia. | Costas J et al. | β | 2016 | β |
| Genetic and Environmental Risk for Chronic Pain and the Contribution of Risk Variants for Major Depressive Disorder: A Family-Based Mixed-Model Analysis. | McIntosh AM et al. | β | 2016 | β |
| Genetic Risk Scores. | Cooke Bailey JN et al. | β | 2016 | β |
| Genetic variants linked to education predict longevity. | Marioni RE et al. | β | 2016 | β |
| Genome-wide analysis identifies 12 loci influencing human reproductive behavior. | Barban N et al. | β | 2016 | β |
| Genome-Wide Association of Heroin Dependence in Han Chinese. | Kalsi G et al. | β | 2016 | β |
| Genome-wide association study of cognitive functions and educational attainment in UK Biobank (N=112β151). | Davies G et al. | β | 2016 | β |
| Multimarker analysis suggests the involvement of BDNF signaling and microRNA biosynthesis in suicidal behavior. | Pulay AJ et al. | β | 2016 | β |
| Personality Polygenes, Positive Affect, and Life Satisfaction. | Weiss A et al. | β | 2016 | β |
| Phenome-wide analysis of genome-wide polygenic scores. | Krapohl E et al. | β | 2016 | β |
| Pleiotropy between neuroticism and physical and mental health: findings from 108 038 men and women in UK Biobank. | Gale CR et al. | β | 2016 | β |
| Rapporteur summaries of plenary, symposia, and oral sessions from the XXIIIrd World Congress of Psychiatric Genetics Meeting in Toronto, Canada, 16-20 October 2015. | Zai G et al. | β | 2016 | β |
| Role of Cytokine Gene Score in Risk Prediction of Premature Coronary Artery Disease. | Omer W et al. | β | 2016 | β |
| Shared genetic aetiology between cognitive functions and physical and mental health in UK Biobank (N=112β151) and 24 GWAS consortia. | Hagenaars SP et al. | β | 2016 | β |
| SLINGER: large-scale learning for predicting gene expression. | Vervier K et al. | β | 2016 | β |
| Smooth-Threshold Multivariate Genetic Prediction with Unbiased Model Selection. | Ueki M et al. | β | 2016 | β |
| The Genetics of Success: How Single-Nucleotide Polymorphisms Associated With Educational Attainment Relate to Life-Course Development. | Belsky DW et al. | β | 2016 | β |
| The polygenic risk for bipolar disorder influences brain regional function relating to visual and default state processing of emotional information. | Dima D et al. | β | 2016 | β |
| The road to precision psychiatry: translating genetics into disease mechanisms. | Gandal MJ et al. | β | 2016 | β |