Power of a score test for quantitative trait linkage analysis of relative pairs

Total parenteral nutrition leads to alteration of hepatocyte cell cycle gene expression and proliferation in the mouse

Total parenteral nutrition (TPN) is correlated with progressive liver injury. Such injury may be associated with either an increase or decrease in hepatocyte growth. The goal of these experiments was to determine TPN-related alterations in intrahepatic genes, as they relate with the cell cycle, using microarray techniques. After 7 days of infusion of saline or TPN-solution, hepatocyte gene expression was examined with a 5000-cDNA microarray chip. TPN was associated with an up-regulation of the cyclin kinase Cdc25B mRNA, which controls the cell cycle at the G2/M phase. Based on this, our studies were directed at alterations in genes related to mitosis in this phase of the cell cycle. mRNA expression of mitotic phase inducers and inhibitors were examined. Cdc25B1 mRNA expression increased with TPN. TPN also led to additional significant alterations in the expression of other factors which mediate proliferation in this phase of mitosis. Histologically, TPN resulted in a significant decline in hepatocyte proliferation. Coincident with the alteration in cyclin expression was a significant decrease in hepatocytes in the G2/M phase with TPN administration. This study demonstrates significant alterations in cell cycle gene expression with TPN. The findings correlate with a loss of hepatocyte proliferation and may give insight into the potential mechanism of TPN-induced hepatocyte injury.

Power and robustness of a score test for linkage analysis of quantitative traits using identity by descent data on sib pairs

Identification of genes involved in complex traits by traditional (lod score) linkage analysis is difficult due to many complicating factors. An unfortunate drawback of non-parametric procedures in general, though, is their low power to detect genetic effects. Recently, Dudoit and Speed [2000] proposed using a (likelihood-based) score test for detecting linkage with IBD data on sib pairs. This method uses the likelihood for theta, the recombination fraction between a trait locus and a marker locus, conditional on the phenotypes of the two sibs to test the null hypothesis of no linkage (theta = (1/2)). Although a genetic model must be specified, the approach offers several advantages. This paper presents results of simulation studies characterizing the power and robustness properties of this score test for linkage, and compares the power of the test to the Haseman-Elston and modified Haseman-Elston tests. The score test is seen to have impressively high power across a broad range of true and assumed models, particularly under multiple ascertainment. Assuming an additive model with a moderate allele frequency, in the range of p = 0.2 to 0.5, along with heritability H = 0.3 and a moderate residual correlation rho = 0.2 resulted in a very good overall performance across a wide range of trait-generating models. Generally, our results indicate that this score test for linkage offers a high degree of protection against wrong assumptions due to its strong robustness when used with the recommended additive model.