Subgroups at high risk for ischaemic heart disease:identification and validation in 67 000 individuals from the general population

An Application of the Patient Rule-Induction Method to Detect Clinically Meaningful Subgroups from Failed Phase III Clinical Trials

Background

Phase III superiority clinical trials have negative results (new treatment is not statistically better than standard of care) due to a number of factors, including patient and disease heterogeneity. However, even a treatment regime that fails to show population-level clinical improvement will have a subgroup of patients that attain a measurable clinical benefit.

Objective

The goal of this paper is to modify the Patient Rule-Induction Method to identify statistically significant subgroups, defined by clinical and/or demographic factors, of the clinical trial population where the experimental treatment performs better than the standard of care and better than observed in the entire clinical trial sample.

Results

We illustrate this method using part A of the SUCCESS clinical trial, which showed no overall difference between treatment arms: HR (95% CI) = 0.97 (0.78, 1.20). Using PRIM, we identified one subgroup defined by the mutational profile in BRCA1 which resulted in a significant benefit for adding Gemcitabine to the standard treatment: HR (95% CI) = 0.59 (0.40, 0.87).

Conclusion

This result demonstrates that useful information can be extracted from existing databases that could provide insight into why a phase III trial failed and assist in the design of future clinical trials involving the experimental treatment.

Systematic Functional Testing of Rare Variants: Contributions of CFI to Age-Related Macular Degeneration

Purpose

Genome-wide association (GWAS) and sequencing studies for AMD have highlighted the importance of coding variants at loci that encode components of the complement pathway. However, assessing the contribution of such alleles to AMD, especially when they are rare, remains coarse, in part because of the persistent challenge in establishing their functional relevance. Others and we have shown previously that rare alleles in complement factor I (CFI) can be tested functionally using a surrogate in vivo assay of retinal vascularization in zebrafish embryos. Here, we have implemented and scaled these tools to assess the overall contribution of rare alleles in CFI to AMD.

Methods

We performed targeted sequencing of CFI in 731 AMD patients, followed by replication in a second patient cohort of 511 older healthy individuals. Systematic functional testing of all alleles and post-hoc statistical analysis of functional variants was also performed.

Results

We discovered 20 rare coding nonsynonymous variants, including the previously reported G119R allele. In vivo testing led to the identification of nine variants that alter CFI; six of which are associated with hypoactive complement factor I (FI). Post-hoc analysis in ethnically matched, population controls showed six of these to be present exclusively in cases.

Conclusions

Taken together, our data argue that multiple rare and ultra-rare alleles in CFI contribute to AMD pathogenesis; they improve the precision of the assessment of the contribution of CFI to AMD; and they offer a rational route to establishing both causality and direction of allele effect for genes associated with this disorder.