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Step K, Ndong Sima CAA, Mata I, Bardien S. Exploring the role of underrepresented populations in polygenic risk scores for neurodegenerative disease risk prediction. Front Neurosci 2024; 18:1380860. [PMID: 38859922 PMCID: PMC11163124 DOI: 10.3389/fnins.2024.1380860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/14/2024] [Indexed: 06/12/2024] Open
Affiliation(s)
- Kathryn Step
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Carene Anne Alene Ndong Sima
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ignacio Mata
- Genomic Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
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Saffie Awad P, Makarious MB, Elsayed I, Sanyaolu A, Wild Crea P, Schumacher Schuh AF, Levine KS, Vitale D, Korestky MJ, Kim J, Peixoto Leal T, Perinan MT, Dey S, Noyce AJ, Reyes-Palomares A, Rodriguez-Losada N, Foo JN, Mohamed W, Heilbron K, Norcliffe-Kaufmann L, Rizig M, Okubadejo N, Nalls M, Blauwendraat C, Singleton A, Leonard H, Mata IF, Bandres Ciga S. Insights into Ancestral Diversity in Parkinsons Disease Risk: A Comparative Assessment of Polygenic Risk Scores. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.28.23299090. [PMID: 38076954 PMCID: PMC10705647 DOI: 10.1101/2023.11.28.23299090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Objectives To evaluate and compare different polygenic risk score (PRS) models in predicting Parkinsons disease (PD) across diverse ancestries, focusing on identifying the most suitable approach for each population and potentially contributing to equitable advancements in precision medicine. Methods We constructed a total of 105 PRS across individual level data from seven diverse ancestries. First, a cross-ancestry conventional PRS comparison was implemented by utilizing the 90 known European risk loci with weighted effects from four independent summary statistics including European, East Asian, Latino/Admixed American, and African/Admixed. These models were adjusted by sex, age, and principal components (28 PRS) and by sex, age, and percentage of admixture (28 PRS) for comparison. Secondly, a novel and refined multi-ancestry best-fit PRS approach was then applied across the seven ancestries by leveraging multi-ancestry meta-analyzed summary statistics and using a p-value thresholding approach (49 PRS) to enhance prediction applicability in a global setting. Results European-based PRS models predicted disease status across all ancestries to differing degrees of accuracy. Ashkenazi Jewish had the highest Odds Ratio (OR): 1.96 (95% CI: 1.69-2.25, p < 0.0001) with an AUC (Area Under the Curve) of 68%. Conversely, the East Asian population, despite having fewer predictive variants (84 out of 90), had an OR of 1.37 (95% CI: 1.32-1.42) and an AUC of 62%, illustrating the cross-ancestry transferability of this model. Lower OR alongside broader confidence intervals were observed in other populations, including Africans (OR =1.38, 95% CI: 1.12-1.63, p=0.001). Adjustment by percentage of admixture did not outperform principal components. Multi-ancestry best-fit PRS models improved risk prediction in European, Ashkenazi Jewish, and African ancestries, yet didn't surpass conventional PRS in admixed populations such as Latino/American admixed and African admixed populations. Interpretation The present study represents a novel and comprehensive assessment of PRS performance across seven ancestries in PD, highlighting the inadequacy of a 'one size fits all' approach in genetic risk prediction. We demonstrated that European based PD PRS models are partially transferable to other ancestries and could be improved by a novel best-fit multi-ancestry PRS, especially in non-admixed populations.
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Walker R, Fothergill-Misbah N, Kariuki S, Ojo O, Cilia R, Dekker MCJ, Agabi O, Akpalu A, Amod F, Breckons M, Cham M, Del Din S, Dotchin C, Guggsa S, Kwasa J, Mushi D, Nwaokorie FO, Park T, Rochester L, Rogathi J, Sarfo FS, Shalash A, Ternent L, Urasa S, Okubadejo N. Transforming Parkinson's Care in Africa (TraPCAf): protocol for a multimethodology National Institute for Health and Care Research Global Health Research Group project. BMC Neurol 2023; 23:373. [PMID: 37858118 PMCID: PMC10585779 DOI: 10.1186/s12883-023-03414-0] [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: 06/13/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD) is the second most common neurodegenerative disorder and, according to the Global Burden of Disease estimates in 2015, was the fastest growing neurological disorder globally with respect to associated prevalence, disability, and deaths. Information regarding the awareness, diagnosis, phenotypic characteristics, epidemiology, prevalence, risk factors, treatment, economic impact and lived experiences of people with PD from the African perspective is relatively sparse in contrast to the developed world, and much remains to be learned from, and about, the continent. METHODS Transforming Parkinson's Care in Africa (TraPCAf) is a multi-faceted, mixed-methods, multi-national research grant. The study design includes multiple sub-studies, combining observational (qualitative and quantitative) approaches for the epidemiological, clinical, risk factor and lived experience components, as appropriate, and interventional methods (clinical trial component). The aim of TraPCAf is to describe and gain a better understanding of the current situation of PD in Africa. The countries included in this National Institute for Health and Care Research (NIHR) Global Health Research Group (Egypt, Ethiopia, Ghana, Kenya, Nigeria, South Africa and Tanzania) represent diverse African geographies and genetic profiles, with differing resources, healthcare systems, health and social protection schemes, and policies. The research team is composed of experts in the field with vast experience in PD, jointly led by a UK-based and Africa-based investigator. DISCUSSION Despite the increasing prevalence of PD globally, robust data on the disease from Africa are lacking. Existing data point towards the poor awareness of PD and other neurological disorders on the continent and subsequent challenges with stigma, and limited access to affordable services and medication. This multi-site study will be the first of its kind in Africa. The data collected across the proposed sub-studies will provide novel and conclusive insights into the situation of PD. The selected country sites will allow for useful comparisons and make results relevant to other low- and middle-income countries. This grant is timely, as global recognition of PD and the public health challenge it poses builds. The work will contribute to broader initiatives, including the World Health Organization's Intersectoral global action plan on epilepsy and other neurological disorders. TRIAL REGISTRATION https://doi.org/10.1186/ISRCTN77014546 .
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Affiliation(s)
- R Walker
- Northumbria Healthcare NHS Foundation Trust, Newcastle upon Tyne, UK
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - N Fothergill-Misbah
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK.
| | - S Kariuki
- Neuroscience Unit, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - O Ojo
- College of Medicine, University of Lagos, Lagos, Nigeria
- Lagos University Teaching Hospital, Lagos, Nigeria
| | - R Cilia
- Parkinson and Movement Disorders Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - M C J Dekker
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - O Agabi
- College of Medicine, University of Lagos, Lagos, Nigeria
| | - A Akpalu
- University of Ghana Medical School, Korle Bu Teaching Hospital, Accra, Ghana
| | - F Amod
- University of KwaZulu-Natal, Durban, South Africa
| | - M Breckons
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - M Cham
- Richard Novati Catholic Hospital, Sogakope, Ghana
| | - S Del Din
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre (BRC), Newcastle University and Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - C Dotchin
- Northumbria Healthcare NHS Foundation Trust, Newcastle upon Tyne, UK
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - S Guggsa
- Addis Ababa University, Addis Ababa, Ethiopia
| | - J Kwasa
- Department of Clinical Medicine and Therapeutics, University of Nairobi, Nairobi, Kenya
| | - D Mushi
- Institute of Public Health, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - F O Nwaokorie
- Department of Medical Laboratory Science, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | - T Park
- Parkinson's Africa, Kingston upon Thames, UK
| | - L Rochester
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre (BRC), Newcastle University and Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - J Rogathi
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - F S Sarfo
- Kwame Nkrumah University of Science & Technology, Kumasi, Ghana
| | - A Shalash
- Department of Neurology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - L Ternent
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - S Urasa
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - N Okubadejo
- College of Medicine, University of Lagos, Lagos, Nigeria
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