What's UPDOG? A novel tool for trans-ancestral polygenic score prediction

Polygenic scores provide an indication of an individual's genetic propensity for a trait within a test population. These scores are calculated using results from genetic analysis conducted in discovery populations. However, when the test and discovery populations have different ancestries, predictions are less accurate. As many genetic analyses are conducted using European populations, this hinders the potential for making predictions in many of the underrepresented populations in research. To address this, UP and Downstream Genetic scoring (UPDOG) was developed to consider the genetic architecture of both the discovery and test cohorts before calculating polygenic scores. UPDOG was tested across four ancestries and six phenotypes and benchmarked against five existing tools for polygenic scoring. In approximately two-thirds of cases UPDOG improved trans-ancestral prediction, although the increases were small. Maximising the efficacy of polygenic scores and extending it to the global population is crucial for delivering personalised medicine and universal healthcare equality. ### Competing Interest Statement C.M.L is a member of the Myriad Neuroscience SAB, has received consultancy fees from UCB and speaker fees from SYNLAB. ### Funding Statement D.M.H is supported by a Sir Henry Wellcome Postdoctoral Fellowship (Reference 213674/Z/18/Z). C.M.L acknowledges MRC grant MR/N015746/1. This investigation represents independent research part-funded by the National Institute for Health Research (NIHR) Maudsley Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care. This research was funded in whole, or in part, by the Wellcome Trust [Reference 213674/Z/18/Z]. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study used only openly available human data that were originally located at https://www.ukbiobank.ac.uk/ I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The software used in this study is available at: https://github.com/davemhoward/updog All data produced in the present study are available upon reasonable request to the authors.