A review of statistical designs for improving the efficiency of phase II studies in oncology

Phase II oncology trials are carried out to assess whether an experimental anti-cancer treatment shows sufficient signs of effectiveness to justify being tested in a phase III trial. Traditionally such trials are conducted as single-arm studies using a binary response rate as the primary endpoint. In this article, we review and contrast alternative approaches for such studies. Each approach uses only data that are necessary for the traditional analysis. We consider two broad classes of methods: ones that aim to improve the efficiency using novel design ideas, such as multi-stage and multi-arm multi-stage designs; and ones that aim to improve the analysis, by making better use of the richness of the data that is ignored in the traditional analysis. The former class of methods provides considerable gains in efficiency but also increases the administrative and logistical issues in running the trial. The second class consists of viable alternatives to the standard analysis that come with little additional requirements and provide considerable gains in efficiency

Comparison of multimarker logistic regression models, with application to a genomewide scan of schizophrenia.

BACKGROUND: Genome-wide association studies (GWAS) are a widely used study design for detecting genetic causes of complex diseases. Current studies provide good coverage of common causal SNPs, but not rare ones. A popular method to detect rare causal variants is haplotype testing. A disadvantage of this approach is that many parameters are estimated simultaneously, which can mean a loss of power and slower fitting to large datasets.Haplotype testing effectively tests both the allele frequencies and the linkage disequilibrium (LD) structure of the data. LD has previously been shown to be mostly attributable to LD between adjacent SNPs. We propose a generalised linear model (GLM) which models the effects of each SNP in a region as well as the statistical interactions between adjacent pairs. This is compared to two other commonly used multimarker GLMs: one with a main-effect parameter for each SNP; one with a parameter for each haplotype. RESULTS: We show the haplotype model has higher power for rare untyped causal SNPs, the main-effects model has higher power for common untyped causal SNPs, and the proposed model generally has power in between the two others. We show that the relative power of the three methods is dependent on the number of marker haplotypes the causal allele is present on, which depends on the age of the mutation. Except in the case of a common causal variant in high LD with markers, all three multimarker models are superior in power to single-SNP tests.Including the adjacent statistical interactions results in lower inflation in test statistics when a realistic level of population stratification is present in a dataset.Using the multimarker models, we analyse data from the Molecular Genetics of Schizophrenia study. The multimarker models find potential associations that are not found by single-SNP tests. However, multimarker models also require stricter control of data quality since biases can have a larger inflationary effect on multimarker test statistics than on single-SNP test statistics. CONCLUSIONS: Analysing a GWAS with multimarker models can yield candidate regions which may contain rare untyped causal variants. This is useful for increasing prior odds of association in future whole-genome sequence analyses.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are