Development of bimodal gene expression analysis and allele-specific competitive PCR for investigation of complex genetic traits, lung cancer risk

The majority of common traits (e.g. cancer predisposition) reside within the paradigm of complex genetic systems. Yet at present, no more than 5% of phenotypic variation in complex genetic traits have been explained. Difficulties in linking individual genetic changes to complex phenotypic traits may be due, in part, to limitations and challenges intrinsic to approaches and methodologies currently employed to study complex genetic phenomena (e.g. genome-wide association studies). The goal of the dissertation presented here was to develop new approaches and methodologies to untangle the intricate web of heritable mechanisms underlying complex genetic traits, using lung cancer predisposition as a model system. The guiding philosophy for the development of new approaches and methods was to investigate: a) novel aspects of the involvement of intermediate phenotypes (e.g. transcript expression) in explaining complex genetic trait penetrance, as well as b) the genetic basis of intermediate phenotypes (e.g. allele-specific expression). Utilization of intermediate phenotypes minimizes the effect of confounding variables when attempting to abstract the effect size (i.e. penetrance) of genetic variation on a complex genetic trait. During the course of my studies I developed bimodal and dispersion-based gene expression analysis, allele-specific competitive PCR methodology as well as an interpretive framework for allele-specific expression signal analysis. In these studies, I demonstrate that bimodal and dispersion gene expression patterns are an important classifying characteristic (intermediate phenotype) for genes with a high degree of likelihood of involvement in lung carcinogenesis. Moreover, using allele-specific competitive PCR and allele-specific expression signal theory I demonstrate the identification of cis-acting genetic variations which alter transcript expression of ERCC5 and CEBPG genes (both important in the progression of lung carcinogenesis) using various in vivo approaches.