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pleioR: A powerful and fast test and software for the study of pleiotropy in systems involving many traits with biobank-sized data

pleioR：一个强大而快速的测试和软件，用于研究涉及生物库大小数据的许多性状的系统中的多效性

基本信息

批准号：
10424541
负责人：
Gustavo de los Campos
金额：
$ 7.83万
依托单位：
MICHIGAN STATE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-06-15 至 2023-05-31
项目状态：
已结题

项目摘要

Pleiotropy (i.e., variants that confer risk to multiple characters) leads to the genetic correlation between traits and underlies the development of many syndromes. The identification of variants with pleiotropic effects on health- related traits can improve the biological understanding of gene action and disease etiology, and can help to advance disease-risk prediction. However, mapping pleiotropic risk loci is statistically and computationally challenging. Schaid et al. (Genetics, 2016) proposed an intersection-union sequential test that addresses the statistical challenges emerging in multi-trait genome-wide association analyses. Schaid’s sequential Likelihood Ratio Test (sLRT) is powerful, provides adequate error control, and leads to easy-to-interpret results. However, the adoption of the methodology remains limited because the proposed test and the existing software do not scale to big data (hundreds of thousands of individuals, millions of SNPs, many traits). Therefore, we propose to develop an alternative to the sLRT that achieves the same power but involves computations that scale to big data. Our approach adopts the intersection-union sequential testing framework but uses a Wald test and an approximation that substantially reduces the computational burden. Preliminary results presented in this grant show that the proposed test, and the beta C++ implementation we developed, has the power and error-control performance of the sLRT, it is considerably faster (by a factor of about 300), and scales to big data. In this project, we will (Aim 1) conduct extensive simulations to assess the statistical properties of the proposed test. (Aim 2) We will integrate memory mapping with optimized in-memory computations to develop open-source software that will implement the proposed test within the R environment, in a software package that will scale to big-data analysis. (Aim 3) Finally, we will use the methods and software developed in Aim 3, together with data from the UK-Biobank, to study the genetic underpinnings of Metabolic Syndrome. The advent of biobank data has opened unprecedented opportunities for mapping genetic loci affecting complex biological networks. However, more efficient data analysis tools are needed to unleash the potential of modern biobanks. This proposal will: (i) Develop novel methods for mapping risk loci affecting systems of traits. (ii) Develop and share with the research community software that can be used to analyze multidimensional phenotypes with big data. (iii) Advance knowledge of the genetic basis of Metabolic Syndrome.

多效性(即赋予多个性状风险的变异)导致性状和基因之间的遗传相关性是许多证候发展的基础。对健康具有多效性影响的变异体的鉴定相关性状可以提高对基因作用和疾病病因的生物学理解，并有助于推动疾病风险预测。然而，绘制多效性风险基因座在统计和计算上都是具有挑战性的。Schaid等人。(《遗传学》，2016) 提出了一种交并序贯检验方法，解决了多性状的统计难题全基因组关联分析。Schaid的序贯似然比检验(SLRT)是强大的，提供了足够的错误控制，并导致易于解释的结果。然而，该方法的采用仍然有限。因为建议的测试和现有软件不能扩展到大数据(数十万人，数以百万计的SNPs，许多特征)。因此，我们建议开发一种替代轻便铁路的方案，以达到同样的效果。强大，但涉及可扩展到大数据的计算。我们的方法采用了交集-并序测试框架，但使用了Wald测试和近似这大大减少了计算负担。这项拨款的初步结果显示，建议的测试，以及我们开发的测试版C++实现，具有 SLRT的速度要快得多(提高了约300倍)，并且可以扩展到大数据。在这个项目中，我们将(目标1)进行广泛的模拟来评估拟议测试的统计特性。 (目标2)我们将把内存映射与优化的内存计算相结合，以开发开源将在R环境中实施建议测试的软件，在可扩展到大数据分析。(目标3)最后，我们将使用目标3中开发的方法和软件，以及来自英国生物库，研究代谢综合征的遗传基础。生物库数据的出现为绘制影响复合体的遗传基因座提供了前所未有的机会生物网络。然而，需要更高效的数据分析工具来释放现代数据的潜力生物库。这一建议将：(I)开发新的方法来定位影响性状系统的风险基因座。(Ii)发展并与研究社区分享可用于分析大样本多维表型的软件数据。(Iii)对代谢综合征的遗传基础有深入的了解。