IDENTIFYING HETEROGENEOUS TRANSGENERATIONAL DNA METHYLATION SITES VIA CLUSTERING IN BETA REGRESSION

• 成果类型: Article
• 署名作者: Han, Shengtong; Zhang, Hongmei; Lockett, Gabrielle A.; Mukherjee, Nandini; Holloway, John W.; Karmaus, Wilfried
• 署名单位: University of Memphis; University of Southampton; University of Southampton
• 刊物名称: ANNALS OF APPLIED STATISTICS
• ISSN/ISSBN: 1932-6157
• DOI: 10.1214/15-AOAS865
• 发表日期: 2015
• 页码: 2052-2072
• 关键词: paternal alcohol exposure; asthma; algorithm; regions; sex

摘要

This paper explores the transgenerational DNA methylation pattern ( DNA methylation transmitted from one generation to the next) via a clustering approach. Beta regression is employed to model the transmission pattern from parents to their offsprings at the population level. To facilitate this goal, an expectation maximization algorithm for parameter estimation along with a BIC criterion to determine the number of clusters is proposed. Applying our method to the DNA methylation data composed of 4063 CpG sites of 41 mother-father-infant triads, we identified a set of CpG sites in which DNA methylation transmission is dominated by fathers, while at a large number of CpG sites, DNA methylation is mainly maternally transmitted to the offspring.