Table 1.

Individual and average runtimes for polygenic risk score–continuous shrinkage (PRS-CS) and PRS.jl by phenotype.

PRS-CSPRS.jlAverage
Run 1Run 2Run 3Mean (SD)Run 1Run 2Run 3Mean (SD)Improvementa
Quantitative phenotypes
 Body mass index62:21:2565:12:1659:41:1362:24:58 (1:28:32)12:01:1512:20:3111:19:3211:53:46 (0:31:10)5.3
 Cholesterol56:51:4355:36:3559:12:5957:13:46 (1:49:52)12:07:508:15:2312:34:3810:59:17 (2:22:34)5.2
 eGFR65:52:2069:43:4077:57:5071:11:17 (6:10:36)13:54:2815:57:4014:01:3514:37:54 (1:09:10)4.9
 High-density lipoprotein59:58:1356:39:5659:19:0858:39:06 (1:45:02)8:21:458:16:1310:58:489:12:15 (1:32:19)6.4
 Low-density lipoprotein63:38:0656:17:2456:47:4758:54:26 (4:06:08)8:26:048:18:4712:54:029:52:58 (2:36:51)6.0
 Triglycerides58:00:5256:04:4860:45:4958:17:10 (2:21:13)8:18:018:09:2411:48:259:25:17 (2:04:02)6.2
Binary phenotypes
 Asthma41:58:2640:15:1441:29:0241:14:14 (0:53:10)5:26:446:25:067:27:546:26:35 (1:00:36)6.4
 Coronary artery disease66:59:4566:00:1664:05:3565:41:52 (1:28:32)10:43:5315:05:1513:04:0912:57:46 (2:10:48)5.1
 Type 2 diabetes mellitus68:35:3869:10:2668:08:4368:38:16 (0:30:57)17:03:1820:13:2416:38:3317:58:25 (1:57:33)3.8
All phenotypes combined
544:16:28535:00:35547:28:06542:15:03 (6:28:16)96:23:18103:01:43110:47:36103:24:12 (7:12:35)5.5
  • All runtimes are presented as hour:minutes:seconds.

  • a Average improvement is estimated as the mean PRS-CS/mean PRS.jl.