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. Author manuscript; available in PMC: 2020 Oct 1.
Published in final edited form as: Hum Genet. 2019 Jul 24;138(10):1155–1169. doi: 10.1007/s00439-019-02049-x

Table 3:

Performance of optimal PGS in each ancestry

Ancestry p-value cut-off # SNPs Cohort PGS R2 (model R2) p-valuea
European 0.00035 341 Tuning (n=1,000) 0.014 (0.14) 9.3×10−5
Validation (n=8,569) 0.0098 (0.17) 1.1×10−23
African 0.01265 32,269 Tuning (n=57) 0.029 (0.49) 0.11
Validation (n=1,042) 0.002 (0.03) 0.15
African 1.0 NAb Full-Independent (n=1,099) 0.003 (0.04) 0.05

Abbreviations: SNPs, single nucleotide polymorphism; PGS, polygenic score

a

p-value for association between PGS and log[25(OH)D]

b

this PGS was created via mega-analysis of three cohorts; # SNPs varies by cohort