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Grigoroiu-Serbanescu M, van der Veen T, Bigdeli T, Herms S, Diaconu CC, Neagu AI, Bass N, Thygesen J, Forstner AJ, Nöthen MM, McQuillin A. Schizophrenia polygenic risk scores, clinical variables and genetic pathways as predictors of phenotypic traits of bipolar I disorder. J Affect Disord 2024; 356:507-518. [PMID: 38640977 DOI: 10.1016/j.jad.2024.04.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/05/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
AIM We investigated the predictive value of polygenic risk scores (PRS) derived from the schizophrenia GWAS (Trubetskoy et al., 2022) (SCZ3) for phenotypic traits of bipolar disorder type-I (BP-I) in 1878 BP-I cases and 2751 controls from Romania and UK. METHODS We used PRSice-v2.3.3 and PRS-CS for computing SCZ3-PRS for testing the predictive power of SCZ3-PRS alone and in combination with clinical variables for several BP-I subphenotypes and for pathway analysis. Non-linear predictive models were also used. RESULTS SCZ3-PRS significantly predicted psychosis, incongruent and congruent psychosis, general age-of-onset (AO) of BP-I, AO-depression, AO-Mania, rapid cycling in univariate regressions. A negative correlation between the number of depressive episodes and psychosis, mainly incongruent and an inverse relationship between increased SCZ3-SNP loading and BP-I-rapid cycling were observed. In random forest models comparing the predictive power of SCZ3-PRS alone and in combination with nine clinical variables, the best predictions were provided by combinations of SCZ3-PRS-CS and clinical variables closely followed by models containing only clinical variables. SCZ3-PRS performed worst. Twenty-two significant pathways underlying psychosis were identified. LIMITATIONS The combined RO-UK sample had a certain degree of heterogeneity of the BP-I severity: only the RO sample and partially the UK sample included hospitalized BP-I cases. The hospitalization is an indicator of illness severity. Not all UK subjects had complete subphenotype information. CONCLUSION Our study shows that the SCZ3-PRS have a modest clinical value for predicting phenotypic traits of BP-I. For clinical use their best performance is in combination with clinical variables.
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Affiliation(s)
- Maria Grigoroiu-Serbanescu
- Psychiatric Genetics Research Unit, Alexandru Obregia Clinical Psychiatric Hospital, Bucharest, Romania.
| | - Tracey van der Veen
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - Tim Bigdeli
- SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Stefan Herms
- Department of Biomedicine, University of Basel, Basel, Switzerland; Institute of Human Genetics, University of Bonn, School of Medicine, University Hospital Bonn, Germany
| | | | | | - Nicholas Bass
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - Johan Thygesen
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK; Institute of Health Informatics, University College London, London, UK
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, School of Medicine, University Hospital Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine, University Hospital Bonn, Germany
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
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2
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Joo YY, Lee E, Kim BG, Kim G, Seo J, Cha J. Polygenic architecture of brain structure and function, behaviors, and psychopathologies in children. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595444. [PMID: 38826224 PMCID: PMC11142157 DOI: 10.1101/2024.05.22.595444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The human brain undergoes structural and functional changes during childhood, a critical period in cognitive and behavioral development. Understanding the genetic architecture of the brain development in children can offer valuable insights into the development of the brain, cognition, and behaviors. Here, we integrated brain imaging-genetic-phenotype data from over 8,600 preadolescent children of diverse ethnic backgrounds using multivariate statistical techniques. We found a low-to-moderate level of SNP-based heritability in most IDPs, which is lower compared to the adult brain. Using sparse generalized canonical correlation analysis (SGCCA), we identified several covariation patterns among genome-wide polygenic scores (GPSs) of 29 traits, 7 different modalities of brain imaging-derived phenotypes (IDPs), and 266 cognitive and psychological phenotype data. In structural MRI, significant positive associations were observed between total grey matter volume, left ventral diencephalon volume, surface area of right accumbens and the GPSs of cognition-related traits. Conversely, negative associations were found with the GPSs of ADHD, depression and neuroticism. Additionally, we identified a significant positive association between educational attainment GPS and regional brain activation during the N-back task. The BMI GPS showed a positive association with fractional anisotropy (FA) of connectivity between the cerebellum cortex and amygdala in diffusion MRI, while the GPSs for educational attainment and cannabis use were negatively associated with the same IDPs. Our GPS-based prediction models revealed substantial genetic contributions to cognitive variability, while the genetic basis for many mental and behavioral phenotypes remained elusive. This study delivers a comprehensive map of the relationships between genetic profiles, neuroanatomical diversity, and the spectrum of cognitive and behavioral traits in preadolescence.
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Affiliation(s)
- Yoonjung Yoonie Joo
- Department of Psychology, Seoul National University
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, South Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Eunji Lee
- Department of Psychology, Seoul National University
| | - Bo-Gyeom Kim
- Department of Psychology, Seoul National University
| | - Gakyung Kim
- Department of Brain and Cognitive Sciences, Seoul National University
| | - Jungwoo Seo
- Department of Brain and Cognitive Sciences, Seoul National University
| | - Jiook Cha
- Department of Psychology, Seoul National University
- Department of Brain and Cognitive Sciences, Seoul National University
- Institute of Psychological Science, Seoul National University, Seoul, South Korea
- Graduate School of Artificial Intelligence, Seoul National University, Seoul, South Korea
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3
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Duarte RRR, Pain O, Bendall ML, de Mulder Rougvie M, Marston JL, Selvackadunco S, Troakes C, Leung SK, Bamford RA, Mill J, O'Reilly PF, Srivastava DP, Nixon DF, Powell TR. Integrating human endogenous retroviruses into transcriptome-wide association studies highlights novel risk factors for major psychiatric conditions. Nat Commun 2024; 15:3803. [PMID: 38778015 PMCID: PMC11111684 DOI: 10.1038/s41467-024-48153-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are repetitive elements previously implicated in major psychiatric conditions, but their role in aetiology remains unclear. Here, we perform specialised transcriptome-wide association studies that consider HERV expression quantified to precise genomic locations, using RNA sequencing and genetic data from 792 post-mortem brain samples. In Europeans, we identify 1238 HERVs with expression regulated in cis, of which 26 represent expression signals associated with psychiatric disorders, with ten being conditionally independent from neighbouring expression signals. Of these, five are additionally significant in fine-mapping analyses and thus are considered high confidence risk HERVs. These include two HERV expression signatures specific to schizophrenia risk, one shared between schizophrenia and bipolar disorder, and one specific to major depressive disorder. No robust signatures are identified for autism spectrum conditions or attention deficit hyperactivity disorder in Europeans, or for any psychiatric trait in other ancestries, although this is likely a result of relatively limited statistical power. Ultimately, our study highlights extensive HERV expression and regulation in the adult cortex, including in association with psychiatric disorder risk, therefore providing a rationale for exploring neurological HERV expression in complex neuropsychiatric traits.
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Affiliation(s)
- Rodrigo R R Duarte
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| | - Oliver Pain
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Matthew L Bendall
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | - Jez L Marston
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sashika Selvackadunco
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Claire Troakes
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Szi Kay Leung
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Rosemary A Bamford
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Paul F O'Reilly
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Douglas F Nixon
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Timothy R Powell
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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4
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Beck JJ, Slunecka JL, Johnson BN, Van Asselt AJ, Finnicum CT, Ageton C, Krie A, Nickles H, Cowan K, Maxwell J, Boomsma DI, de Geus E, Ehli EA, Hottenga JJ. Breast Cancer Polygenic Risk Score Validation and Effects of Variable Imputation. Cancers (Basel) 2024; 16:1578. [PMID: 38672660 PMCID: PMC11048743 DOI: 10.3390/cancers16081578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/30/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Breast cancer (BC) is a complex disease affecting one in eight women in the USA. Advances in population genomics have led to the development of polygenic risk scores (PRSs) with the potential to augment current risk models, but replication is often limited. We evaluated 2 robust PRSs with 313 and 3820 SNPs and the effects of multiple genotype imputation replications in BC cases and control populations. Biological samples from BC cases and cancer-free controls were drawn from three European ancestry cohorts. Genotyping on the Illumina Global Screening Array was followed by stringent quality control measures and 20 genotype imputation replications. A total of 468 unrelated cases and 4337 controls were scored, revealing significant differences in mean PRS percentiles between cases and controls (p < 0.001) for both SNP sets (313-SNP PRS: 52.81 and 48.07; 3820-SNP PRS: 55.45 and 49.81), with receiver operating characteristic curve analysis showing area under the curve values of 0.596 and 0.603 for the 313-SNP and 3820-SNP PRS, respectively. PRS fluctuations (from ~2-3% up to 9%) emerged across imputation iterations. Our study robustly reaffirms the predictive capacity of PRSs for BC by replicating their performance in an independent BC population and showcases the need to average imputed scores for reliable outcomes.
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Affiliation(s)
- Jeffrey J. Beck
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - John L. Slunecka
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Brandon N. Johnson
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Austin J. Van Asselt
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Casey T. Finnicum
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | | | - Amy Krie
- Avera Cancer Institute, Sioux Falls, SD 57105, USA
| | | | - Kenneth Cowan
- Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer at University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Jessica Maxwell
- Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer at University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (J.-J.H.)
| | - Eco de Geus
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (J.-J.H.)
| | - Erik A. Ehli
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (J.-J.H.)
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5
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Grebe TA, Khushf G, Greally JM, Turley P, Foyouzi N, Rabin-Havt S, Berkman BE, Pope K, Vatta M, Kaur S. Clinical utility of polygenic risk scores for embryo selection: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2024; 26:101052. [PMID: 38393332 DOI: 10.1016/j.gim.2023.101052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 02/25/2024] Open
Affiliation(s)
- Theresa A Grebe
- Phoenix Children's, Phoenix, AZ; Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ
| | - George Khushf
- Department of Philosophy, University of South Carolina, Columbia, SC
| | - John M Greally
- Departments of Genetics and Pediatrics, Albert Einstein College of Medicine, Bronx, NY
| | - Patrick Turley
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA; Department of Economics, University of Southern California, Los Angeles, CA
| | | | - Sara Rabin-Havt
- Department of OB/GYN, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY
| | - Benjamin E Berkman
- Department of Bioethics, National Institutes of Health; National Human Genome Research Institute, Bethesda, MD
| | - Kathleen Pope
- Department of Pediatrics, Nemours Children's Hospital, Orlando, FL; University of South Florida College of Public Health, Tampa, FL
| | | | - Shagun Kaur
- Phoenix Children's, Phoenix, AZ; Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ
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6
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Laplana M, Lopez-Ortega R, Fibla J. Polygenic risk score comparator (PRScomp): Test population vs. worldwide populations. Int J Med Inform 2024; 183:105333. [PMID: 38184939 DOI: 10.1016/j.ijmedinf.2023.105333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND Polygenic risk scores (PRS) are a powerful tool for predicting an individual's genetic risk for complex diseases. METHODS We have developed a web service (PRScomp) as a user-friendly tool to evaluate PRS of the user own population and compare it with worldwide populations. RESULTS A disease/trait database has been constructed from GWAS Catalog summary statistics. Genotype data of test population is uploaded and merged with the reference dataset (1000 Genome Project and Human Genome Diversity Project) to obtain a file including the common SNPs. The user can select a disease/trait from the database and a curated set of risk markers is used to calculate summatory PRS. Distribution of z-scored PRS values is presented in publication-ready plots and text files that can be downloaded. DISCUSSION PRScomp can be useful for public health decision-making by identifying population-specific genetic risk factors and informing the development of targeted interventions for at-risk populations.
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Affiliation(s)
- Marina Laplana
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida, Spain.
| | - Ricard Lopez-Ortega
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida, Spain; Unitat de Citogenètica i Genètica Mèdica, Hospital Universitari Arnau de Vilanova, IRBLleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida, Spain
| | - Joan Fibla
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida, Spain.
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7
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Uffelmann E, Price AL, Posthuma D, Peyrot WJ. Estimating Disorder Probability Based on Polygenic Prediction Using the BPC Approach. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.12.24301157. [PMID: 38260678 PMCID: PMC10802765 DOI: 10.1101/2024.01.12.24301157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Polygenic Scores (PGSs) summarize an individual's genetic propensity for a given trait in a single value, based on SNP effect sizes derived from Genome-Wide Association Study (GWAS) results. Methods have been developed that apply Bayesian approaches to improve the prediction accuracy of PGSs through optimization of estimated effect sizes. While these methods are generally well-calibrated for continuous traits (implying the predicted values are on average equal to the true trait values), they are not well-calibrated for binary disorder traits in ascertained samples. This is a problem because well-calibrated PGSs are needed to reliably compute the absolute disorder probability for an individual to facilitate future clinical implementation. Here we introduce the Bayesian polygenic score Probability Conversion (BPC) approach, which computes an individual's predicted disorder probability using GWAS summary statistics, an existing Bayesian PGS method (e.g. PRScs, SBayesR), the individual's genotype data, and a prior disorder probability. The BPC approach transforms the PGS to its underlying liability scale, computes the variances of the PGS in cases and controls, and applies Bayes' Theorem to compute the absolute disorder probability; it is practical in its application as it does not require a tuning dataset with both genotype and phenotype data. We applied the BPC approach to extensive simulated data and empirical data of nine disorders. The BPC approach yielded well-calibrated results that were consistently better than the results of another recently published approach.
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Affiliation(s)
- Emil Uffelmann
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam
| | | | | | - Alkes L. Price
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam
- Department of Child and Adolescent Psychiatry and Pediatric Psychology, Section Complex, Trait Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Wouter J. Peyrot
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam
- Department of Psychiatry, Amsterdam UMC, The Netherlands
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8
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Nakase T, Guerra G, Ostrom QT, Ge T, Melin B, Wrensch M, Wiencke JK, Jenkins RB, Eckel-Passow JE, Bondy ML, Francis SS, Kachuri L. Genome-wide Polygenic Risk Scores Predict Risk of Glioma and Molecular Subtypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.10.24301112. [PMID: 38260701 PMCID: PMC10802631 DOI: 10.1101/2024.01.10.24301112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background Polygenic risk scores (PRS) aggregate the contribution of many risk variants to provide a personalized genetic susceptibility profile. Since sample sizes of glioma genome-wide association studies (GWAS) remain modest, there is a need to find efficient ways of capturing genetic risk factors using available germline data. Methods We developed a novel PRS (PRS-CS) that uses continuous shrinkage priors to model the joint effects of over 1 million polymorphisms on disease risk and compared it to an approach (PRS-CT) that selects a limited set of independent variants that reach genome-wide significance (P<5×10-8). PRS models were trained using GWAS results stratified by histological (10,346 cases, 14,687 controls) and molecular subtype (2,632 cases, 2,445 controls), and validated in two independent cohorts. Results PRS-CS was consistently more predictive than PRS-CT across glioma subtypes with an average increase in explained variance (R2) of 21%. Improvements were particularly pronounced for glioblastoma tumors, with PRS-CS yielding larger effect sizes (odds ratio (OR)=1.93, P=2.0×10-54 vs. OR=1.83, P=9.4×10-50) and higher explained variance (R2=2.82% vs. R2=2.56%). Individuals in the 95th percentile of the PRS-CS distribution had a 3-fold higher lifetime absolute risk of IDH mutant (0.63%) and IDH wildtype (0.76%) glioma relative to individuals with average PRS. PRS-CS also showed high classification accuracy for IDH mutation status among cases (AUC=0.895). Conclusions Our novel genome-wide PRS may improve the identification of high-risk individuals and help distinguish between prognostic glioma subtypes, increasing the potential clinical utility of germline genetics in glioma patient management.
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Affiliation(s)
- Taishi Nakase
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Geno Guerra
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Quinn T. Ostrom
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology Umeå University, Umeå, Sweden
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - John K. Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Robert B. Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Melissa L. Bondy
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen S. Francis
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Linda Kachuri
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
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9
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Kachuri L, Chatterjee N, Hirbo J, Schaid DJ, Martin I, Kullo IJ, Kenny EE, Pasaniuc B, Witte JS, Ge T. Principles and methods for transferring polygenic risk scores across global populations. Nat Rev Genet 2024; 25:8-25. [PMID: 37620596 PMCID: PMC10961971 DOI: 10.1038/s41576-023-00637-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2023] [Indexed: 08/26/2023]
Abstract
Polygenic risk scores (PRSs) summarize the genetic predisposition of a complex human trait or disease and may become a valuable tool for advancing precision medicine. However, PRSs that are developed in populations of predominantly European genetic ancestries can increase health disparities due to poor predictive performance in individuals of diverse and complex genetic ancestries. We describe genetic and modifiable risk factors that limit the transferability of PRSs across populations and review the strengths and weaknesses of existing PRS construction methods for diverse ancestries. Developing PRSs that benefit global populations in research and clinical settings provides an opportunity for innovation and is essential for health equity.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jibril Hirbo
- Department of Medicine Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel J Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Iman Martin
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bogdan Pasaniuc
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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10
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Hamilton OS, Steptoe A, Ajnakina O. Polygenic predisposition, sleep duration, and depression: evidence from a prospective population-based cohort. Transl Psychiatry 2023; 13:323. [PMID: 37857612 PMCID: PMC10587060 DOI: 10.1038/s41398-023-02622-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
Suboptimal sleep durations and depression frequently cooccur. Short-sleep and long-sleep are commonly thought of as symptoms of depression, but a growing literature suggests that they may be prodromal. While each represents a process of mutual influence, the directionality between them remains unclear. Using polygenic scores (PGS), we investigate the prospective direction involved in suboptimal sleep durations and depression. Male and female participants, aged ≥50, were recruited from the English Longitudinal Study of Ageing (ELSA). PGS for sleep duration, short-sleep, and long-sleep were calculated using summary statistics data from the UK Biobank cohort. Sleep duration, categorised into short-sleep ("≤5 h"), optimal-sleep (">5 to <9 h"), and long-sleep ("≥9 h"), was measured at baseline and across an average 8-year follow-up. Subclinical depression (Centre for Epidemiological Studies Depression Scale [≥4 of 7]) was also ascertained at baseline and across an average 8-year follow-up. One standard deviation increase in PGS for short-sleep was associated with 14% higher odds of depression onset (95% CI = 1.03-1.25, p = 0.008). However, PGS for sleep duration (OR = 0.92, 95% CI = 0.84-1.00, p = 0.053) and long-sleep (OR = 0.97, 95% CI = 0.89-1.06, p = 0.544) were not associated with depression onset during follow-up. During the same period, PGS for depression was not associated with overall sleep duration, short-sleep, or long-sleep. Polygenic predisposition to short-sleep was associated with depression onset over an average 8-year period. However, polygenic predisposition to depression was not associated with overall sleep duration, short-sleep or long-sleep, suggesting different mechanisms underlie the relationship between depression and the subsequent onset of suboptimal sleep durations in older adults.
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Affiliation(s)
- Odessa S Hamilton
- Department of Behavioural Science and Health, University College London, 1-19 Torrington Place, London, WC1E 7HB, UK.
| | - Andrew Steptoe
- Department of Behavioural Science and Health, University College London, 1-19 Torrington Place, London, WC1E 7HB, UK
| | - Olesya Ajnakina
- Department of Behavioural Science and Health, University College London, 1-19 Torrington Place, London, WC1E 7HB, UK
- Department of Biostatistics & Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 16 De Crespigny Park, London, SE5 8AF, UK
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Biernacka JM. Do Polygenic Scores Inform Psychiatric Disease Risk After Considering Family History? Am J Psychiatry 2023; 180:256-258. [PMID: 37002695 DOI: 10.1176/appi.ajp.20230116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Affiliation(s)
- Joanna M Biernacka
- Department of Psychiatry and Psychology and Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minn
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12
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Affiliation(s)
- Cathryn M Lewis
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Lewis, Vassos); Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London (Lewis)
| | - Evangelos Vassos
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, and Neuroscience, King's College London (Lewis, Vassos); Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London (Lewis)
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13
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Kullo IJ, Lewis CM, Inouye M, Martin AR, Ripatti S, Chatterjee N. Polygenic scores in biomedical research. Nat Rev Genet 2022; 23:524-532. [PMID: 35354965 PMCID: PMC9391275 DOI: 10.1038/s41576-022-00470-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2022] [Indexed: 12/12/2022]
Abstract
Public health strategies aimed at disease prevention or early detection and intervention have the potential to advance human health worldwide. However, their success depends on the identification of risk factors that underlie disease burden in the general population. Genome-wide association studies (GWAS) have implicated thousands of single-nucleotide polymorphisms (SNPs) in common complex diseases or traits. By calculating a weighted sum of the number of trait-associated alleles harboured by an individual, a polygenic score (PGS), also called a polygenic risk score (PRS), can be constructed that reflects an individual’s estimated genetic predisposition for a given phenotype. Here, we ask six experts to give their opinions on the utility of these probabilistic tools, their strengths and limitations, and the remaining barriers that need to be overcome for their equitable use.
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Affiliation(s)
- Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre & Department of Medical & Molecular, King's College London, London, UK.
| | - Michael Inouye
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Samuli Ripatti
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.
- Department of Public Health, University of Helsinki, Helsinki, Finland.
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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14
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Wang Y, Tsuo K, Kanai M, Neale BM, Martin AR. Challenges and Opportunities for Developing More Generalizable Polygenic Risk Scores. Annu Rev Biomed Data Sci 2022; 5:293-320. [PMID: 35576555 PMCID: PMC9828290 DOI: 10.1146/annurev-biodatasci-111721-074830] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Polygenic risk scores (PRS) estimate an individual's genetic likelihood of complex traits and diseases by aggregating information across multiple genetic variants identified from genome-wide association studies. PRS can predict a broad spectrum of diseases and have therefore been widely used in research settings. Some work has investigated their potential applications as biomarkers in preventative medicine, but significant work is still needed to definitively establish and communicate absolute risk to patients for genetic and modifiable risk factors across demographic groups. However, the biggest limitation of PRS currently is that they show poor generalizability across diverse ancestries and cohorts. Major efforts are underway through methodological development and data generation initiatives to improve their generalizability. This review aims to comprehensively discuss current progress on the development of PRS, the factors that affect their generalizability, and promising areas for improving their accuracy, portability, and implementation.
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Affiliation(s)
- Ying Wang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Kristin Tsuo
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA,Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA,Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Benjamin M. Neale
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Alicia R. Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
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Dauyey K, Saitou N. Inferring intelligence of ancient people based on modern genomic studies. J Hum Genet 2022; 67:527-532. [PMID: 35534677 PMCID: PMC9402434 DOI: 10.1038/s10038-022-01039-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/26/2022]
Abstract
Quantification of ancient human intelligence has become possible with recent advances in polygenic prediction. Intelligence is a complex trait that has both environmental and genetic components and high heritability. Large-scale genome-wide association studies based on ~270,000 individuals have demonstrated highly significant single-nucleotide polymorphisms (SNPs) associated with intelligence in present-day humans. We utilized those previously reported 12,037 SNPs to estimate a genetic component of intelligence in ancient Funadomari Jomon individual from 3700 years BP as well as four individuals of Afanasievo nuclear family from about 4100 years BP and who are considered anatomically modern humans. We have demonstrated that ancient individuals could have been not inferior in intelligence compared to present-day humans through assessment of the genetic component of intelligence. We have also confirmed that alleles associated with intelligence tend to spread equally between ancestral and derived origin suggesting that intelligence may be a neutral trait in human evolution.
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Good genotype-phenotype relationships in rare disease are hard to find. Eur J Hum Genet 2022; 30:251. [PMID: 35260823 PMCID: PMC8904513 DOI: 10.1038/s41431-022-01062-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Driver MN, Kuo SIC, Petronio L, Brockman D, Dron JS, Austin J, Dick DM. Evaluating the impact of a new educational tool on understanding of polygenic risk scores for alcohol use disorder. Front Psychiatry 2022; 13:1025483. [PMID: 36506445 PMCID: PMC9726708 DOI: 10.3389/fpsyt.2022.1025483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION As gene identification efforts have advanced in psychiatry, so have aspirations to use genome-wide polygenic information for prevention and intervention. Although polygenic risk scores (PRS) for substance use and psychiatric outcomes are not yet available in clinical settings, individuals can access their PRS through online direct-to-consumer resources. One of these widely used websites reports that alcohol use disorder is the third most requested PRS out of >1,000 conditions. However, data indicate that there are misunderstandings about complex genetic concepts, with a lower understanding of PRS being associated with a more negative impact of receiving polygenic risk information. There is a need to develop and evaluate educational tools to increase understanding of PRS. METHODS We conducted a randomized controlled trial to evaluate the impact of web-based educational information on understanding of PRS for alcohol use disorder. A total of 325 college students (70.4% female; 43.6% White; mean age = 18.9 years) from an urban, diverse university completed the study. RESULTS Overall, participants were highly satisfied with the educational information. Results from a one-way ANOVA indicated that there was a significant increase in overall understanding of PRS for alcohol use disorder (p-value < 0.001), among individuals who received educational information about PRS and alcohol use disorder, as compared to receiving no accompanying information (adj. p-value < 0.001), or educational information about alcohol use disorder only (adj. p-value < 0.001). DISCUSSION These findings suggest that the web-based educational tool could be provided alongside polygenic risk information in order to enhance understanding and interpretation of the information. CLINICAL TRIAL REGISTRATION [ClinicalTrials.gov], identifier [NCT05143073].
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Affiliation(s)
- Morgan N Driver
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States
| | - Sally I-Chun Kuo
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Lia Petronio
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | | | - Jacqueline S Dron
- Department of Medicine, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Jehannine Austin
- Department of Psychiatry, The University of British Columbia, Vancouver, BC, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Danielle M Dick
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States.,Rutgers Addiction Research Center, Brain Health Institute, Rutgers University, Piscataway, NJ, United States
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