Table 1. . Genome-wide association study input studies for the warfarin experiment.
| PMID | Phenotype class | Phenotype | Sample size | Population ancestry | SNPs |
|---|---|---|---|---|---|
| 18535201 | Response | Warfarin maintenance dose | 555 | European | 3 |
| 19300499 | Response | Warfarin maintenance dose | 1641 | European | 4 |
| 20833655 | Response | Warfarin maintenance dose | 1952 | Japanese | 5 |
| 23755828 | Response | Warfarin maintenance dose | 965 | African–American | 1 |
| 26265036 | Response | Warfarin maintenance dose | 2967 | Brazilian, European, Japanese, African American | 16 |
| 22443383 | ADEs | Hemostatic factors and hematological phenotypes | 951 | European | 9 |
| 23381943 | ADEs | End-stage coagulation | 2100 | European | 23 |
| 24357727 | ADEs | Thrombin-generation potential phenotypes | 3224 | European | 4 |
| 19278955 | Disease/background | Venous thromboembolism | 4884 | European | 1 |
| 20212171 | Disease/background | C4b binding protein levels | 352 | European | 1 |
| 20303064 | Disease/background | Activated partial thromboplastin time | 1431 | European | 3 |
| 21980494 | Disease/background | Venous thromboembolism | 2652 | European | 4 |
| 22216198 | Disease/background | Anticoagulant levels | 397 | European | 8 |
| 22701019 | Disease/background | Factor XI | 997 | European | 0 |
| 22703881 | Disease/background | Prothrombin time | 3569 | European | 2 |
| 22703881 | Disease/background | Activated partial thromboplastin time | 11851 | European | 9 |
| 22672568 | Disease/background | Venous thromboembolism | 5787 | European and other | 5 |
| 23267103 | Disease/background | Coagulation factor levels | 3250 | European | 7 |
| 23509962 | Disease/background | Venous thromboembolism (SNP × SNP interaction) | 4291 | European | 37 |
| 23650146 | Disease/background | Venous thromboembolism | 51266 | European | 8 |
| 25240745 | Disease/background | Mitochondrial DNA levels | 386 | European | 21 |
| 25772935 | Disease/background | Venous thromboembolism | 65734 | European | 10 |
| 22550155 | Disease/background | Platelet thrombus formation | 241 | European, African–American | 6 |
A total of 23 associations from 22 genome-wide association studies (GWAS) [39–60] met the criteria for inclusion in the warfarin experiment, and their significant associations were rendered into the MVF and organized into phenotypic classes, along with 23 additional variants annotated by the Pharmacogenomics Knowledge Base (PharmGKB®) [61]. The 23 additional variants included all variants annotated by the PharmGKB as of September 2016, with a significant association with warfarin response, and were not already included in the list of variants identified from GWAS. Population descriptions are taken from the summary annotations in the original papers and the GWAS Catalog [62] , but in the PIP input files they are represented in 1000 Genomes format to replicate the detailed descriptions in the original papers as precisely as possible. Although they represent a variety of ancestries, European ancestry predominated among 17 out of 22 (77%) of the study populations.
ADE: Adverse drug event; MVF: Master variant file; PIP: Pharmacoepigenomics informatics pipeline; PMID: PubMed ID.