Table 2.

Median squared error and P-value from the t test comparing SNP weights between python and Julia implementations for a single run.

SNP count
Median square errorP-valueGWASPolygenic risk score
Asthma2.07 × 10−110.898,270,130494,889
Body mass index6.55 × 10−111.002,529,253719,311
Coronary artery disease6.83 × 10−110.918,440,435782,510
eGFR3.22 × 10−110.9317,393,472774,105
HDL3.29 × 10−110.952,433,797696,196
LDL3.19 × 10−110.972,424,334695,115
Total cholesterol3.25 × 10−110.872,433,332696,147
Triglycerides3.17 × 10−110.862,425,960695,255
Type 2 diabetes mellitus2.00 × 10−110.8535,369,247780,627
  • eGFR, estimated glomerular filtration rate; GWAS, genome-wide association study; HDL, high-density lipoprotein; LDL, low-density lipoprotein; SNP, single nucleotide polymorphism.