Internal validation inferences of significant genomic features in genome-wide screening

Although validation of classification and prediction models has been a long-standing topic in Statistics and computer learning, the concept of statistical validation in genome-wide screening studies has been vague. Internal validation generally refers to validation procedures solely based on the study dataset. A popular approach to internal validation of identified genomic features has been the split-dataset validation. Contrast to this approach, internal validation in genome-wide association screening studies is precisely defined through the concepts of association profile and profile significance. A general procedure and two specific profile significance measures are developed and are compared with the split-dataset validation approach by a simulation study. The simulation results clearly demonstrate the strength and limitations of the profile significance approach to internal validation, especially its enormous gain in sensitivity (power) and stability over the split-dataset validation. The proposed methodology is illustrated by an example of genome-wide SNP association analysis in genetic epidemiology.