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A Novel Trio-based Bayesian Method to Identify Rare Variants for Birth Defects

一种新的基于三重奏的贝叶斯方法来识别出生缺陷的罕见变异

基本信息

批准号：
9249077
负责人：
MICHAEL D SWARTZ
金额：
$ 7.7万
依托单位：
UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-06-01 至 2019-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9249077
关键词：
Affect Algorithms Automobile Driving Bayesian Method Bayesian Modeling Benchmarking Biological Candidate Disease Gene Child Child health care Childhood Clinical Congenital Abnormality Congenital Heart Defects Couples Data Data Set Disease Etiology Evolution Family Foundations Gene Frequency Genes Genetic Genetic Counseling Genetic Models Genetic Variation Genotype Healthcare Hereditary Disease Heritability Human Individual Infant Mortality Intervention Logistic Regressions Measures Methodology Methods Minor Mission Modeling Morbidity - disease rate National Heart, Lung, and Blood Institute Newborn Infant Parents Pediatric Cardiac Genomics Consortium Performance Population Prevalence Prevention strategy Property Public Health Research Research Personnel Risk Sampling Sequence Analysis Speed Structure Sum Techniques Testing United States United States National Institutes of Health Validation Variant base case control congenital heart disorder cost database of Genotypes and Phenotypes design disability disorder risk expectation genetic analysis genetic variant genome-wide high risk improved innovation novel population stratification public health relevance rare variant screening tool treatment strategy validation studies

项目摘要

DESCRIPTION (provided by applicant): Although advances in genome wide and candidate gene association studies continue to identify common genetic variants contributing to birth defects (a leading cause of infant mortality [54]), recent evidence indicates that discovered loci only account for a small fraction of risk. As a result, researchers are shifting focus to investigae rare variants that could be responsible for this missing heritability of birth defects. The trio design (genotyping the affected child and both parents) is preferred for such association studies because it is robust to population substructure and only requires sequencing three people, rather than larger families. However established methods for analyzing common variants using trio data are hindered by reduced power when analyzing rare variants using sequence data. Thus, there is a critical need to develop methods that jointly test for common and rare variants using the trio design to comprehensively model the genetic factors associated with birth defects in order to identify the genetic variants driving the association with disease risk. Current methods for analyzing rare variants primarily focus on pooling the rare variants in a region and performing a global test for that region. To further increase power, some methods include common variants in the model as covariates. Of the few most recent methods that can statistically identify rare variants that drive the association, all are based on the case control design, which requires birth defect researchers who have been collecting trio data to find an external set of controls. This is less than ideal. There is a strong need for methods that can jointly analyze common and rare variants using trio data in such a way that can statistically identify the genetic variants (rare and common) that drive association with birth defects. We propose to fulfill this need with the following aims: (1) Develop a Bayesian stochastic search variable selection method for common and rare variant analysis using trio data that can identify the variants driving the association; and (2) Compare the performance of the global component to existing global tests for trio data using both simulated and real data for congenital heart defects. To achieve these aims, we will develop a novel Bayesian model for trio data, using the Expectation-Maximization algorithm to quickly compute the modes of the Bayesian posterior distribution as estimates for genetic regions as well as specific variants (rare and common). The proposed research is innovative because it will develop new and powerful statistical methodology. The proposed research is significant because it will produce a new powerful and widely applicable method for uncovering the genetic basis for birth defects and other childhood diseases. Ultimately, the new methods will improve birth defects research, and the application to real data can improve our understanding of the etiology of congenital heart defects, potentially improving genetic counseling and prevention strategies for congenital heart defects.