Byrnes J.K

Nov 22, 2023 | cell.com | Byrnes J.K |Byrska-Bishop M |Francesco Ravasini |Francesco Montinaro

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Sep 18, 2023 | cell.com | Byrska-Bishop M |Byrnes J.K |Diego Ortega-Del Vecchyo |Luis Pablo Cruz-Hervert

SummaryDemographic models of Latin American populations often fail to fully capture their complex evolutionary history, which has been shaped by both recent admixture and deeper-in-time demographic events. To address this gap, we used high-coverage whole-genome data from Indigenous American ancestries in present-day Mexico and existing genomes from across Latin America to infer multiple demographic models that capture the impact of different timescales on genetic diversity.

Feb 11, 2023 | cell.com | Byrnes J.K |Lerato Majara |Cape Town

SummaryAfrican populations are vastly underrepresented in genetic studies but have the most genetic variation and face wide-ranging environmental exposures globally. Because systematic evaluations of genetic prediction had not yet been conducted in ancestries that span African diversity, we calculated polygenic risk scores (PRSs) in simulations across Africa and in empirical data from South Africa, Uganda, and the United Kingdom to better understand the generalizability of genetic studies.

Feb 11, 2023 | cell.com | Byrnes J.K |Lerato Majara |Cape Town

Polygenic score calculationPruning and thresholdingAll PRSs were calculated in plink2 or in hail using custom scripts. For pruning and thresholding approaches, all clumping was done in plink2 using an LD threshold of r2 = 0.1 and a window size of 500 kb with discovery cohort population-specific reference panels. We calculated PRS using plink2 with the --score and --q-score-range flags for AGVP simulations and DCHS.