|Title||GENE-LEVEL PHARMACOGENETIC ANALYSIS ON SURVIVAL OUTCOMES USING GENE-TRAIT SIMILARITY REGRESSION.|
|Publication Type||Journal Article|
|Year of Publication||2014|
|Authors||Tzeng, Jung-Ying, Wenbin Lu, and Fang-Chi Hsu|
|Journal||Ann Appl Stat|
Gene/pathway-based methods are drawing significant attention due to their usefulness in detecting rare and common variants that affect disease susceptibility. The biological mechanism of drug responses indicates that a gene-based analysis has even greater potential in pharmacogenetics. Motivated by a study from the Vitamin Intervention for Stroke Prevention (VISP) trial, we develop a gene-trait similarity regression for survival analysis to assess the effect of a gene or pathway on time-to-event outcomes. The similarity regression has a general framework that covers a range of survival models, such as the proportional hazards model and the proportional odds model. The inference procedure developed under the proportional hazards model is robust against model misspecification. We derive the equivalence between the similarity survival regression and a random effects model, which further unifies the current variance-component based methods. We demonstrate the effectiveness of the proposed method through simulation studies. In addition, we apply the method to the VISP trial data to identify the genes that exhibit an association with the risk of a recurrent stroke. gene was found to be associated with the recurrent stroke risk in the low-dose arm. This gene may impact recurrent stroke risk in response to cofactor therapy.
|Alternate Journal||Ann Appl Stat|
|Original Publication||Gene-level pharmacogenetic analysis on survival outcomes using gene-trait similarity regression.|
|PubMed Central ID||PMC4091797|
|Grant List||P01 CA142538 / CA / NCI NIH HHS / United States |
R01 CA140632 / CA / NCI NIH HHS / United States
R01 MH084022 / MH / NIMH NIH HHS / United States
U01 HG005160 / HG / NHGRI NIH HHS / United States
GENE-LEVEL PHARMACOGENETIC ANALYSIS ON SURVIVAL OUTCOMES USING GENE-TRAIT SIMILARITY REGRESSION.