Relating drug response to epigenetic and genetic markers using a region-based kernel score test

Detecting responses to treatment with fenofibrate in pedigrees

BACKGROUND

Fenofibrate (Fb) is a known treatment for elevated triglyceride (TG) levels. The Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study was designed to investigate potential contributors to the effects of Fb on TG levels. Here, we summarize the analyses of 8 papers whose authors had access to the GOLDN data and were grouped together because they pursued investigations into Fb treatment responses as part of GAW20. These papers report explorations of a variety of genetics, epigenetics, and study design questions. Data regarding treatment with 160 mg of micronized Fb per day for 3 weeks included pretreatment and posttreatment TG and methylation levels (ML) at approximately 450,000 epigenetic markers (cytosine-phosphate-guanine [CpG] sites). In addition, approximately 1 million single-nucleotide polymorphisms (SNPs) were genotyped or imputed in each of the study participants, drawn from 188 pedigrees.

RESULTS

The analyses of a variety of subsets of the GOLDN data used a number of analytic approaches such as linear mixed models, a kernel score test, penalized regression, and artificial neural networks.

CONCLUSIONS

Results indicate that (a) CpG ML are responsive to Fb; (b) CpG ML should be included in models predicting the TG level responses to Fb;