分析具有部分缺失儿童基因型的病例-母亲-对照-母亲设计下基因-环境相互作用的方法和软件。

IF 1.1 4区 生物学 Q4 GENETICS & HEREDITY Human Heredity Pub Date : 2023-01-01 Epub Date: 2023-04-26 DOI:10.1159/000529559
Alexandre Bureau, Yuang Tian, Patrick Levallois, Yves Giguère, Jinbo Chen, Hong Zhang
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引用次数: 0

摘要

简介通过病例-母亲-对照-母亲的设计,可以研究胎儿和母亲的遗传因素以及环境暴露对生命早期结果的影响。儿童基因型与环境因素之间的孟德尔约束和条件独立性使得半参数似然法能够比标准逻辑回归更有效地估计逻辑模型。由于收集儿童基因型存在困难,因此需要处理缺失儿童基因型的方法:我们回顾了一种分层回顾似然法和两种半参数似然法:一种前瞻性似然法和一种改进的回顾性似然法,后者将母体基因型建模为协变量的函数或不指定其联合分布(稳健型)。我们还回顾了实现这些建模方法的软件,在模拟研究中比较了它们的统计特性,并以基因-环境交互作用和部分缺失的儿童基因型为重点,说明了它们的应用:结果:稳健回溯似然法提供的估计值基本无偏,其标准误差仅略大于根据暴露建立母体基因型模型时的标准误差。前瞻性似然法遇到了最大化问题。在应用 CYP2E1 和饮用水消毒副产物与小妊高症婴儿的关系时,回顾性似然法允许使用所有的协变量,而前瞻性似然法仅限于少数几个协变量:结论:我们推荐使用稳健版的改良追溯似然法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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Methods and Software to Analyze Gene-Environment Interactions under a Case-Mother-Control-Mother Design with Partially Missing Child Genotype.

Introduction: The case-mother-control-mother design allows to study fetal and maternal genetic factors together with environmental exposures on early life outcomes. Mendelian constraints and conditional independence between child genotype and environmental factors enabled semiparametric likelihood methods to estimate logistic models with greater efficiency than standard logistic regression. Difficulties in child genotype collection require methods handling missing child genotype.

Methods: We review a stratified retrospective likelihood and two semiparametric likelihood approaches: a prospective one and a modified retrospective one, the latter either modeling the maternal genotype as a function of covariates or leaving their joint distribution unspecified (robust version). We also review software implementing these modeling alternatives, compare their statistical properties in a simulation study, and illustrate their application, focusing on gene-environment interactions and partially missing child genotype.

Results: The robust retrospective likelihood provides generally unbiased estimates, with standard errors only slightly larger than when modeling maternal genotype based on exposure. The prospective likelihood encounters maximization problems. In the application to the association of small-for-gestational-age babies with CYP2E1 and drinking water disinfection by-products, the retrospective likelihood allowed a full array of covariates, while the prospective likelihood was limited to few covariates.

Conclusion: We recommend the robust version of the modified retrospective likelihood.

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来源期刊
Human Heredity
Human Heredity 生物-遗传学
CiteScore
2.50
自引率
0.00%
发文量
12
审稿时长
>12 weeks
期刊介绍: Gathering original research reports and short communications from all over the world, ''Human Heredity'' is devoted to methodological and applied research on the genetics of human populations, association and linkage analysis, genetic mechanisms of disease, and new methods for statistical genetics, for example, analysis of rare variants and results from next generation sequencing. The value of this information to many branches of medicine is shown by the number of citations the journal receives in fields ranging from immunology and hematology to epidemiology and public health planning, and the fact that at least 50% of all ''Human Heredity'' papers are still cited more than 8 years after publication (according to ISI Journal Citation Reports). Special issues on methodological topics (such as ‘Consanguinity and Genomics’ in 2014; ‘Analyzing Rare Variants in Complex Diseases’ in 2012) or reviews of advances in particular fields (‘Genetic Diversity in European Populations: Evolutionary Evidence and Medical Implications’ in 2014; ‘Genes and the Environment in Obesity’ in 2013) are published every year. Renowned experts in the field are invited to contribute to these special issues.
期刊最新文献
Place of concordance-discordance model in evaluating NGS performance. Implications of the Co-Dominance Model for Hardy-Weinberg Testing in Genetic Association Studies. Joint Linkage and Association Analysis Using GENEHUNTER-MODSCORE with an Application to Familial Pancreatic Cancer. Investigation of Recessive Effects of Coding Variants on Common Clinical Phenotypes in Exome-Sequenced UK Biobank Participants. comorbidPGS: An R Package Assessing Shared Predisposition between Phenotypes Using Polygenic Scores.
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