Fine mapping studies of quantitative trait loci for baseline platelet count in mice and humans

Abstract

Platelet count is a complex trait with a substantial genetic contribution. Platelets have a fundamental role in normal haemostasis, with both increases and decreases of the platelet count associated with significant mortality and morbidity. Despite the significant genetic component contributing to variation in baseline platelet count, the precise mechanisms remain incompletely understood. A detailed knowledge of these genetic and biochemical pathways could potentially lead to the development of new therapies for disorders of platelet number. The aim of this project has been to fine map quantitative trait loci previously identified in a murine F2 cross, of which two (Pltct1 and Pltct2) had been found to reach genome-wide statistical significance. Fine mapping was attempted by three independent approaches. First, a human association study for platelet count was performed, and a cross-species comparison conducted to identify regions where human associations and murine linkage peaks might coincide. Although this association study did not unequivocally identify syntenic regions associated with platelet count in humans where linkage was identified in the murine F2 cross, potentially suggestive associations were identified. Next, fine mapping of the murine regions was undertaken by QTL analysis in a murine F11 advanced intercross line. This approach successfully narrowed the support interval for pltct2. Although linkage at the pltct1 locus was also replicated, this failed to reach genome-wide significance in the F11 study. Next, an in-silico association analysis was undertaken where the methodology included the novel development of an underlying genetic similarity matrix index to correct for population stratification. The results from this in-silico association were then correlated with expression array data from parental samples and five genes were prioritised for more detailed analysis by resequencing. Two potential variants in these candidate genes were identified which merit further investigation for causal effects on platelet count. This work highlights the complexity of mapping genetic variants contributing to thrombopoiesis, despite the significant progresses which have been made at the technological, methodological and statistical levels in the field of complex trait mapping.