Polygenic risk prediction and SNCA haplotype analysis in a Latino Parkinson's disease cohort

Loesch, Douglas P.; Horimoto, Andrea R. V. R.; Sarihan, Elif Irem; Inca-Martinez, Miguel; Mason, Emily; Cornejo-Olivas, Mario; Torres, Luis; Mazzetti, Pilar; Cosentino, Carlos; Sarapura-Castro, Elison; Rivera-Valdivia, Andrea; Medina, Angel C.; Dieguez, Elena; Raggio, Victor; Lescano, Andres; et. al.


Background: Large-scale Parkinson's disease (PD) genome-wide association studies (GWAS) have, until recently, only been conducted on subjects with European -ancestry. Consequently, polygenic risk scores (PRS) constructed using PD GWAS data are likely to be less predictive when applied to non-European cohorts. Methods: Using GWAS data from the largest study to date, we constructed a PD PRS for a Latino PD cohort (1497 subjects from LARGE-PD) and tested it for as-sociation with PD status and age at onset. We validated the PRS performance by testing it in an independent Latino cohort (448 subjects) and by repeating the analysis in LARGE-PD with the addition of 440 external Peruvian controls. We also tested SNCA haplotypes for association with PD risk in LARGE-PD and a European- ancestry PD cohort. Results: The GWAS-significant PD PRS had an area under the receiver-operator curve (AUC) of 0.668 (95% CI: 0.640-0.695) in LARGE-PD. The inclusion of external Peruvian controls mitigated this result, dropping the AUC 0.632 (95% CI: 0.607-0.657). At the SNCA locus, haplotypes differ by ancestry. Ancestry-specific SNCA haplotypes were associated with PD status in both LARGE-PD and the European-ancestry cohort (p-value < 0.05). These haplotypes both include the rs356182 G- allele, but only share 14% of their variants overall. Conclusion: The PD PRS has potential for PD risk prediction in Latinos, but variability caused by admixture patterns and bias in a European-ancestry PD PRS data limits its utility. The inclusion of diverse subjects can help elucidate PD risk loci and improve risk prediction in non-European cohorts.

Más información

Título según WOS: Polygenic risk prediction and SNCA haplotype analysis in a Latino Parkinson's disease cohort
Volumen: 102
Fecha de publicación: 2022
Página de inicio: 7
Página final: 15


Notas: ISI