人群高原习服相关复杂性状的基因组变异解析

High altitude acclimatization (HAA) is a process involving the change of a series of physiological traits during subjects reaching a higher altitude. Delineating the genetic architecture of such a process poses a great challenge, given the complexity of such involving multiple complex traits and their longitudinal changes. Previous studies failed to reach a consensus association between individual traits and genetic variants. However, our preliminary analyses showed that (1) factor analysis could convert a large number of complex traits into several composite phenotypes, each of which encompassing multiple correlated traits demonstrates a specific physiological function (e.g. red blood cell volume); (2) the change of composite phenotypes during HAA were found to be associated genetic variants in hypoxia related genes; (3) different hypoxia related genes may play different roles in acute and chronic phases of HAA. Based on aforementioned observations, we hypothesize that HAA traits manifest as several composite phenotypes, each of which is influenced by multiple genes including hypoxia related genes, respectively. To test this hypothesis, in this proposed study, we plan to collect 1,000 soldiers with longitudinal HAA traits at lowland, acute phase (3 days after the arrival of high altitude), and chronic phase (3 months after). The HAA traits will be converted into composite phenotypes for subsequent analyses. The genetic variants associated with HAA will be identified in the exomes of the samples with extreme composite phenotypes as qualitative traits, and validated in all samples as quantitative traits. Furthermore, the genes with altered expression during HAA, especially those under the regulation of hypoxia related genes, will be identified through RNA sequencing in a sample with extreme composite phenotypes, and validated in all samples using qPCR. The integration of the aforementioned results is expected to reveal a preliminary picture of the genetic architecture as well as a network of gene expressions of HAA traits. This proposed study may help with the development of an effective strategy to delineate the genetic architecture of complex and longitudinal traits.

高原习服是指平原世居者在高原地区的低氧等因素刺激下发生的一系列复杂生理性状的变化过程。涉及多个复杂性状及其纵向变化的遗传学研究极为复杂，尚无成功范例可循。我们前期研究发现，高原习服相关性状的变化无法与遗传变异建立明确关联，但通过表型因子分析可提取出若干复合表型因子，每个复合表型因子不仅分别对应明确的生理功能（如红细胞体积），且若干复合表型因子的变化与低氧调控基因显著关联。我们还发现，不同低氧调控基因在习服急性期和慢性期的作用差异明显。据此我们假设，高原习服呈现多个复合表型因子，这些因子与低氧调控基因密切相关。本研究拟根据纵向研究设计采集样本，针对从平原到高原的急慢性适应的表型变化，用全外显子测序寻找与高原习服性状相关的基因组变异，用转录组测序寻找高原习服中的差异表达基因，通过大样本验证，初步揭示高原习服中的基因调控网络。本研究有助于探索复杂性状遗传学分析的新方法和新策略。

高原习服是指平原世居者进入高原或高原世居者进入更高海拔地区时在高原低氧等因素刺激下发生的一系列复杂生理性状的变化过程。这类涉及多个复杂性状及其纵向变化的遗传学研究极为复杂，尚无成功范例可循。我们通过全基因组和全外显子测序技术，探索了个体遗传变异与高原习服相关表型之间的关联，发现EPHX2基因CDS区域突变与高原习服慢性期心率之间存在显著关联，发现NOS3基因与MTHFR基因CDS区域突变与高原急性期头痛之间存在显著关联，同时发现TMPRSS6基因与EGLN1基因突变与高原习服慢性期红细胞相关表型变化之间具显著关联，且两个基因之间存在交互作用。此外，我们发展了一套表型因子分析策略，可通过谱分解联合偏最小二乘路径模型从30余个生理及生化表型中提取出代表重要生理功能的14个复合表型因子，基于复合表型的模型拟合度显著优于基于单表型的模型，大幅降低了数据维度和数据噪音。我们还发现高原习服平原期及急性期人体血清尿素氮水平与急性高原头痛之间存在显著关联，且多种分析方法均显示其效应独立于血氧饱和度而存在，提示人体氮代谢与高原不良反应之间密切相关。此外，我们基于此次高原习服数据建立了多种大数据处理与遗传分析方法，包括基因-表型连续方差分析方法, 用于大数据建模的随机比特森林建模方法，稀疏性函数型结构方程模型算法，以及用于纵向数据降维的中央平均子空间估计方程算法等。综上，通过本研究，我们发展了一套复杂性状的分析方法，探索了个体急慢性高原习服表型异质性的遗传特征，发现了经典低氧调控相关基因及其他基因与高原习服急性期和慢性期表型之间的关联。我们所发现的与高原习服不良事件相关的基因及生理生化表型可为高原医学和其他缺氧相关疾病的研究和发展提供基础和帮助。更重要的是，我们的工作成果为极端环境下人类复杂性状的遗传学研究提供了宝贵的理论与实践经验。