Statistical and Computational Methods for Large-Scale Sequencing Studies

大规模测序研究的统计和计算方法

• 批准号: 9013897
• 负责人: Han Chen
• 金额: $ 10.37万
• 依托单位: HARVARD SCHOOL OF PUBLIC HEALTH
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-12-15 至 2016-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9013897
• 关键词: Accounting; Acute Lung Injury; Address; Adult Respiratory Distress Syndrome; Affect; African American; Architecture; Asthma; Atherosclerosis; Award; Biological; Biometry; Cardiovascular system; Complex; Computing Methodologies; Coronary heart disease; Data; Data Analyses; Disease; Educational workshop; Ethnic group; European; Family; Family Study; Frequencies; Functional disorder; Future; Genetic; Genetic Heterogeneity; Genetic Research; Genetic screening method; Genomics; Goals; Heterogeneity; Hispanic Americans; Hispanic Community Health Study/Study of Latinos; Human; Individual; Joints; Knowledge; Large-Scale Sequencing; Learning; Mentors; Meta-Analysis; Metabolic; Metabolic Diseases; Methods; Minority; Modeling; Morbidity - disease rate; Mutation; Non-Insulin-Dependent Diabetes Mellitus; Obstructive Sleep Apnea; Participant; Phase; Phenotype; Population; Population Genetics; Public Health; Public Health Schools; Research; Research Design; Research Personnel; Sampling; Statistical Methods; Statistical Models; Stratification; Structure; Study of Latinos; Supervision; Testing; United States; Variant; base; career development; computer science; cost; design; disorder risk; exome sequencing; gene environment interaction; genetic association; genetic variant; genome wide association study; human disease; hypertensive heart disease; insight; interest; next generation sequencing; novel; personalized medicine; population based; prevent; respiratory; semiparametric; skills; study population; targeted sequencing; technology development; trait; user friendly software

 DESCRIPTION (provided by applicant): The primary goal of this proposal is to support Dr. Han Chen's career development in transition from a trainee into an independent researcher in statistical genetics and genomics with expertise in large-scale sequencing association studies for complex diseases and traits, such as cardiovascular, respiratory, metabolic diseases, including Coronary Heart Disease (CHD), hypertension, asthma, Acute Lung Injury / Acute Respiratory Distress Syndrome (ALI/ARDS), Obstructive Sleep Apnea (OSA) and Type 2 Diabetes (T2D). Dr. Chen is currently a postdoctoral research fellow in the Department of Biostatistics at Harvard T. H. Chan School of Public Health, and he has developed statistical methods for genome-wide association studies (GWAS), sequencing association studies and meta-analysis. Minority ethnic groups in the United States such as African- Americans and Hispanic-Americans have previously been underrepresented in genetic association studies. There is an increasingly pressing need to design and conduct GWAS and sequencing studies to better understand, prevent and treat complex diseases in these ethnic groups. To achieve this goal, it is important to develop advanced statistical and computational methods to address the challenges in analyzing these data. Specifically, the applicant proposes to develop statistical and computational methods to 1) account for population structure and relatedness in sequencing studies; and 2) test for genetic heterogeneity and test for gene-environment interaction accounting for heterogeneous environmental effects in trans-ethnic sequencing studies. This will provide new insights into biological functional studies, more accurate disease risk prediction, and advance personalized medicine. The proposed methods will be applied to ongoing sequencing studies for OSA, a condition that affects more than 10% of the population in the United States, especially African- Americans and Hispanic-Americans, and is associated with profound cardio-metabolic morbidity. During the mentored period, the applicant will learn more about modern statistical models for correlated data analysis such as advanced parametric, semiparametric, and additive mixed models, and develop the new statistical frameworks for the proposed research under the guidance of Dr. Xihong Lin (primary mentor). The applicant will also expand knowledge on complex human diseases under the guidance of Dr. Susan Redline (co-mentor), and broaden his background in population genetics and computer science through coursework, workshops and seminars. With skills acquired in the mentored period, the applicant will adapt the statistical models to different data and research questions, and apply them in sequencing association studies to better understand the genetic architecture of complex human diseases. Upon the completion of this award, the applicant will have become a productive and independent researcher in statistical genetics and genomics with expertise in large- scale sequencing studies with applications to complex human disease research.

 描述（申请人提供）：该提案的主要目标是支持Han Chen博士的职业发展，从实习生转变为统计遗传学和基因组学的独立研究员，具有复杂疾病和特征的大规模测序关联研究的专业知识，如心血管，呼吸系统，代谢疾病，包括冠心病（CHD），高血压，哮喘，急性肺损伤/急性呼吸窘迫综合征（ALI/ARDS）、阻塞性睡眠呼吸暂停（OSA）和2型糖尿病（T2 D）。陈博士目前是哈佛T.生物统计学系的博士后研究员。H.陈博士是公共卫生学院的教授，他开发了全基因组关联研究（GWAS），测序关联研究和荟萃分析的统计方法。美国的少数民族群体，如非洲裔美国人和西班牙裔美国人，以前在遗传关联研究中代表性不足。越来越迫切需要设计和进行GWAS和测序研究，以更好地了解，预防和治疗这些种族群体的复杂疾病。为了实现这一目标，重要的是要开发先进的统计和计算方法，以解决分析这些数据的挑战。具体而言，申请人提出开发统计和计算方法，以1）解释测序研究中的群体结构和相关性;以及2）测试遗传异质性和测试跨种族测序研究中解释异质环境效应的基因-环境相互作用。这将为生物功能研究提供新的见解，更准确的疾病风险预测，并推进个性化医疗。所提出的方法将应用于正在进行的OSA的测序研究，OSA是一种影响美国超过10%的人口，特别是非洲裔美国人和西班牙裔美国人的病症，并且与严重的心脏代谢发病率相关。在指导期间，申请人将学习更多关于相关数据分析的现代统计模型，如先进的参数，半参数和加法混合模型，并在Xihong Lin博士（主要导师）的指导下为拟议的研究开发新的统计框架。申请人还将在Susan Redline博士（共同导师）的指导下扩大对复杂人类疾病的知识，并通过课程，研讨会和研讨会扩大他在人口遗传学和计算机科学方面的背景。凭借在指导期间获得的技能，申请人将使统计模型适应不同的数据和研究问题，并将其应用于测序关联研究，以更好地了解复杂人类疾病的遗传结构。完成该奖项后，申请人将成为统计遗传学和基因组学方面富有成效的独立研究人员，拥有大规模测序研究的专业知识，并应用于复杂的人类疾病研究。