Comparing the effect of imputation reference panel composition in four distinct Latin American cohorts.
| العنوان: | Comparing the effect of imputation reference panel composition in four distinct Latin American cohorts. |
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| المؤلفون: | French JN; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD., Pua VB; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD.; University of Maryland Institute for Health Computing, Rockville, MD., Laboulaye R; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD., Leal TP; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA., Olivas MC; Neurogenetics Working Group, Universidad Cientifica del Sur, Lima, Peru.; Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru., Lima-Costa MF; Instituto de Pesquisa René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG, Brasil., Horta BL; Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil., Barreto ML; Center for Data and Knowledge Integration for Health (CIDACS), Gonçalo Moniz Institute (IGM), Oswaldo Cruz Foundation (FIOCRUZ-BA), Salvador, Bahia, Brazil.; Collective Health Institute, Federal University of Bahia (UFBA), Salvador, Bahia, Brazil., Tarazona-Santos E; Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil., Mata I; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA., O'Connor TD; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD.; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD.; Program in Health Equity and Population Health, University of Maryland School of Medicine. |
| المصدر: | BioRxiv : the preprint server for biology [bioRxiv] 2024 Apr 15. Date of Electronic Publication: 2024 Apr 15. |
| نوع المنشور: | Preprint |
| اللغة: | English |
| بيانات الدورية: | Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE |
| مستخلص: | Genome-wide association studies have been useful in identifying genetic risk factors for various phenotypes. These studies rely on imputation and many existing panels are largely composed of individuals of European ancestry, resulting in lower levels of imputation quality in underrepresented populations. We aim to analyze how the composition of imputation reference panels affects imputation quality in four target Latin American cohorts. We compared imputation quality for chromosomes 7 and X when altering the imputation reference panel by: 1) increasing the number of Latin American individuals; 2) excluding either Latin American, African, or European individuals, or 3) increasing the Indigenous American (IA) admixture proportions of included Latin Americans. We found that increasing the number of Latin Americans in the reference panel improved imputation quality in the four populations; however, there were differences between chromosomes 7 and X in some cohorts. Excluding Latin Americans from analysis resulted in worse imputation quality in every cohort, while differential effects were seen when excluding Europeans and Africans between and within cohorts and between chromosomes 7 and X. Finally, increasing IA-like admixture proportions in the reference panel increased imputation quality at different levels in different populations. The difference in results between populations and chromosomes suggests that existing and future reference panels containing Latin American individuals are likely to perform differently in different Latin American populations. |
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| معلومات مُعتمدة: | R01 NS112499 United States NS NINDS NIH HHS; R35 HG010692 United States HG NHGRI NIH HHS; T32 AG000262 United States AG NIA NIH HHS |
| تواريخ الأحداث: | Date Created: 20240425 Latest Revision: 20240429 |
| رمز التحديث: | 20240429 |
| مُعرف محوري في PubMed: | PMC11042191 |
| DOI: | 10.1101/2024.04.11.589057 |
| PMID: | 38659746 |
| قاعدة البيانات: | MEDLINE |
| DOI: | 10.1101/2024.04.11.589057 |
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