Table 1.
Discovery GWAS used to compute polygenic scores with PRS-CS
| Trait | Discovery GWAS | GWAS ancestry | GWAS sample sizea for PRS-CS | SNP countb for PNC PGS calculations | SNP count for ABCD PGS calculations |
|---|---|---|---|---|---|
| PTSD | Nievergelt et al.39 (Freeze 2 PGC) |
AFR | 11,321 | 1,162,502 | 1,064,574 |
| EUR | 70,237 | 1,087,435 | 1,016,161 | ||
| Duncan et al.38 (Freeze 1 PGC) |
AFR | 9,691 | 1,157,302 | 1,059,197 | |
| EUR | 9,954 | 1,086,644 | 1,015,369 | ||
| T2D | Chen et al.42 | AFR | 4,146 | 1,114,936 | 1,020,579 |
| Scott et al.40 (DIAGRAM) |
EUR | 152,599 | 1,087,724 | 1,016,440 | |
| Mahajan et al.41 (DIAGRAM) |
EUR | 231,420 | 1,089,613 | 1,018,372 | |
| Height | Marouli et al.44 (GIANT) |
AFR | 27,494 | 18,580 | 15,720 |
| EUR | 381,625 | 18,035 | 15,767 | ||
| Wood et al.43 (GIANT) |
EUR | 252,048 | 987,760 | 920,889 |
PTSD, post-traumatic stress disorder; T2D, type 2 diabetes; PNC, Philadelphia Neurodevelopmental Cohort; PGS, polygenic score; ABCD, Adolescent Brain Cognitive Development study; PGC, Psychiatric Genomics Consortium; DIAGRAM, Diabetes Genetics Replication and Meta-Analysis Consortium; GIANT, Genetic Investigation of Anthropometric Traits Consortium.
a
PRS-CS requires a single GWAS sample size; see supplemental methods for how we derived this measure when the sample size varied by SNP.
b
The "SNP count" is the number of SNPs in common between the discovery GWAS, the PRS-CS LD panel, and the genomic dataset.