A Genomic Approach to Warfarin Dose Prescription in Admixed Caribbean Hispanics

Warfarin is an oral anticoagulant and one of the most used drugs in the world accounting for up to 1.5% of prescriptions globally. Warfarin inhibits vitamin K epoxide reductase complex 1 (VKORC1), an enzyme responsible for the vitamin K recycling that is required for the activation of clotting factors. Warfarin is prescribed at an average dose of 5 mg/day for most of the indications but significant inter-patient variability has been observed. Single nucleotide variations at the VKORC1 (GeneID: 79001) and CYP2C9 (GeneID: 1559) genes alone explain from 28 to 35% of variability in warfarin dose requirements and up to 56% when clinical factors (age, gender, body surface area, diabetes and heart valve) are incorporated into regression analysis. However, genetic-guided dosing algorithms are mostly derived from studies in Europeans. The objective of the present study was to identify genetic polymorphisms that can explain variability in warfarin dose requirements among Caribbean Hispanics of Puerto Rico. VKORC1 (GeneID: 79001) and CYP2C9 (GeneID: 1559), the most important genetic predictors of warfarin response, were sequenced using Next Generation sequencing. Other candidate genes in DMET Plus Assay were assessed to identify genetic variants with relevance in warfarin dose requirements among Puerto Ricans. Our study used the Extreme Discordant Phenotype approach to perform a case-control association analysis that were confirmed with univariate and conditioned regressions. Accordingly, patients were stratified based on stable warfarin doses as sensitive (<4 mg/day), control (4-6 mg/day) and resistant (>6 mg/day). Genetic variants associated with warfarin response among the study cohort were used to perform a multivariate regression analyses to develop a genetic-guided dosing algorithm tailored for Puerto Ricans. The CYP2C9rs2860905 SNP was found to be strongly associated with warfarin dose requirements in Puerto Ricans. The CYP2C9 rs2860905 SNP tags four haplotypes that represent the trihybrid admixture of Puerto Ricans. Therefore, haplotypes harboring the rs2860905 variant are more informative in predicting warfarin dose among Puerto Ricans than the common single segregating SNPs (i.e., CYP2C9*2 and CYP2C9*3) relevant to Europeans. DMET Plus array confirmed the strong association of VKORC1 (GeneID: 79001) and CYP2C9 (GeneID: 1559) with warfarin dose requirements, but also identified other polymorphisms in CES2 (GeneID: 8824) and ABCB1 (GeneID: 5243) associated with warfarin resistance (>6 mg/day). Ancestry analysis showed that Puerto Ricans from Veteran Affairs Caribbean Healthcare System (VACHS) using warfarin had higher Native American proportions than Puerto Ricans from the 1000 Genomes project; however, this difference was not significant. Incorporation of rs2860905 in a regression model (R2=0.60 MSE=0.38) that also included additional genetic predictors (i.e., VKORC1-1639G>A; CYP2C9 rs1856908; ABCB1 rs10276036; CES2 rs4783745) and non-genetic factors (i.e., hypertension, diabetes and age) showed better prediction of warfarin dose requirements than CYP2C9*2 and CYP2C9*3 combined (partial R2=0.132 versus 0.023 and 0.007, respectively, p<0.001). Interestingly, deep vein thrombosis and diabetes were found associated with high warfarin dose requirements among Puerto Ricans. Our results support the use of CYP2C9 rs2860905 along with other genetic markers [e.g., VKORC1(GeneID: 79001 )] and clinical covariates to predict warfarin dose in Puerto Ricans. Although our findings need further replication, this study contributes to the field of Pharmacogenetics and to improve anticoagulation therapy among Puerto Ricans.]]>
Warfarin Anticoagulation Therapy in Caribbean Hispanics of Puerto Rico: A Candidate Gene Association StudyVA RESEARCH CONSENT FORMMaterials and MethodsII. Patients recruitment and study designStudy DocumentsStudy Documents ListGraphic overview of the study designRESEARCH PROTOCOL TO BE REVISED BY IRBDMET Plus genotyping array from Affymetrix interrogates 1,931 SNPs in genes that encode for drug metabolizing enzymes. The purpose of the analysis was to identify genes beyond CYP2C9 and VKORC1 that might be involved in warfarin dose requirements (sensitivity and resistance). We performed a case-control association analysis to compare SNP frequencies between sensitive/resistant and non-cases.The purpose of the analysis was to identify SNPs specifically at CYP2C9, VKORC1 and flanking regions that might be involved in warfarin dose requirements (sensitivity and resistance). We performed a case-control association analysis to compare SNP frequencies between sensitive/resistant and non-cases.Inclusion Criteria Hispanic Puerto Rican patients (with at least one of his/her parents from outside Puerto Rico) Age >21, but <90 years old; Stable warfarin dose -three consecutive INRs within therapeutic range (2 - 3 or 2.5 - 3.5, according to indication) for the same dose; Receiving warfarin for therapeutic anti-coagulation in indications such as deep vein thrombosis (DVT) with or without Pulmonary Embolism (PE); atrial fibrillation or other arrhythmias; cardiac valvular replacement; previously diagnosed coagulopathy Hematocrit (Hct) > 40% Exclusion Criteria Non-Hispanic patients (race/ethnicity is self-reported by the patients) Non-Puerto Rican origin patients (with at least one of his/her parents from outside Puerto Rico) No currently enrolled in another active research protocols at the VACHS Hospital BUN/creatinine >30/2.0 mg/dL Active hepatic disease (defined by a Child-Pugh score above 10 points: ascites; total bilirubin above 2.0 mg/dl; serum albumin below 3.5 g/dl; prothrombin time in seconds prolonged over control >4; hepatic encephalopathy) Prolonged diarrhea (three or more days) Nasogastric or enteral feedings Acute illness (e.g., sepsis, infection, anemia) HIV/AIDS, Hepatitis B patients Alcoholism and drug abuse Patients with any cognitive and mental health impairment Liver function test (LFT) <3x Upper Limit of Normal (ULN) Sickle cell patients Active malignancy ]]>
2011: Study started 2012: Publication in Pharmacogenomics where the first algorithm developed for warfarin dosing in Puerto Ricans is presented. 2016: First publication in PLoS One presenting a refinement of the warfarin dosing algorithm that includes the admixture component. 2017: Publication of the first candidate gene association study for warfarin dose requirements in Caribbean Hispanics in Frontiers in Pharmacogenetics ]]>