Methods for Pathway Modeling with Application to Folate

描述（由申请人提供）：分子流行病学领域的一个重要挑战是开发用于研究多个基因和多个环境因素作为促成疾病的相互作用因素的方法。该提案的总体目标是开发解决这一问题的新方法，使用叶酸代谢作为结直肠癌发生的重要候选途径，并作为其他候选生化和代谢途径的原型，并将其应用于结直肠癌和结直肠腺瘤的几个数据集。我们有以下具体目标：1.开发一个建模框架，结合生物学对复杂途径结构的理解，以叶酸代谢为例。这将涉及我们的叶酸代谢微分方程模型的扩展，使用该计算机模型的预测来推导我们的分层建模框架的先验协变量，并开发一种考虑模型不确定性的综合方法。 这些不同的方法将说明和对比纯粹的探索性方法使用的数据来自结肠癌家族登记（C-CFR）叶酸研究，腺瘤病例对照研究，和随机腺瘤预防试验。2.扩展此框架，利用生物标志物测量的中间代谢物浓度和酶活性率的子样本的主题。我们将开发分析方法，并探索最佳的抽样方案分层的疾病，暴露和基因型的各种组合，可在整个研究人群。这些方法将说明与腺瘤病例对照，额外的生物标志物，将在一个悬而未决的C-CFR拨款申请，和两个纵向研究中测量的同型半胱氨酸水平已经可用的数据。3.将叶酸途径的生物学知识组织成一个正式的本体。我们将开发系统的方法，从本体中提取先验协变量，用于我们的分层建模框架，并将探讨如何将信息纳入跨物种的途径进化。4.将这种候选途径方法扩展到全基因组范围。我们将探索从全基因组数据推断途径的方法，并使用全基因组关联数据为基于途径的分析提供信息。这些方法将应用于正在进行的C-CFR GWAS的数据。 我们提出的四个示例数据集被部分选择来说明一系列设计，包括基于家庭的，基于人群的病例对照，纵向和随机试验。

DESCRIPTION (provided by applicant): An important challenge in the field of molecular epidemiology is to develop methods for studying multiple gene and multiple environmental factors as interacting factors contributing to disease. The overall goal of this proposal is to develop novel approaches to this problem, using folate metabolism as an important candidate pathway in colorectal carcinogenesis and as a prototype for other candidate biochemical and metabolic pathways, and to apply them to several datasets on colorectal cancer and colorectal adenomas. We have the following specific aims: 1. Develop a modeling framework incorporating biological understanding about the structure of a complex pathway, illustrated by folate metabolism. This will involve extensions to our differential equations model for folate metabolism, using the predictions of this in silico model to derive prior covariates for our hierarchical modeling framework, and developing an integrated approach allowing for model uncertainty. These various methods will be illustrated and contrasted with purely exploratory methods using data from the Colon Cancer Family Registry (C-CFR) folate study, an adenoma case-control study, and a randomized adenoma prevention trial. 2. Extend this framework to exploit biomarker measurements of intermediate metabolite concentrations and enzyme activity rates on a subsample of subjects. We will develop analytical methods and explore optimal sampling schemes stratifying on various combinations of disease, exposure, and genotypes that are available on an entire study population. These approaches will be illustrated with already available data on homocysteine levels in the adenoma case-control, additional biomarkers that will be measured in a pending C-CFR grant application, and two longitudinal studies. 3. Organize biological knowledge for the folate pathway into a formal ontology. We will develop systematic methods for extracting prior covariates from an ontology for use in our hierarchical modeling framework, and will explore ways of incorporating information on evolution of pathways across species. 4. Extend this candidate pathway approach to the genome-wide scale. We will explore methods for inferring pathways from genome-wide data and for using genome-wide association data to inform pathway-based analyses. These methods will be applied to data from the ongoing C-CFR GWAS. The four example datasets we propose were chosen in part to illustrate a range of designs, including family-based, population-based case-control, longitudinal, and randomized trial.