PopPAnTe: population and pedigree association testing for quantitative data.
PopPAnTe: population and pedigree association testing for quantitative data.
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DOI：
10.1186/s12864-017-3527-7
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发表时间：
2017-02-10
期刊：
影响因子：
4.4
通讯作者：
Falchi M
中科院分区：
文献类型：
--
作者：
Visconti A;Al-Shafai M;Al Muftah WA;Zaghlool SB;Mangino M;Suhre K;Falchi M
以家系为基础的设计，从双生子研究到具有复杂系谱数据的孤立群体，是遗传分子生物标志物遗传研究的宝贵资源。用于基于家族的研究的现有软件主要集中于促进反应表型和遗传标记之间的关联，并且目前没有用户友好的工具可用于将相关样品中的关联研究直接扩展到通用定量数据的大数据集，如由当前组学技术产生的那些。我们开发了PopPAnTe，一个用户友好的Java程序，它评估了相关样品中定量数据的关联。此外，PopPAnTe还实现了数据预处理和后处理，基于区域的测试以及关联的经验评估。PopPAnTe是一个集成和灵活的框架，用于在具有大量预测因子和响应变量的相关样本中进行成对关联检验。它可以处理任何规模和复杂性的家族数据，或者当家谱信息未知时，它使用个体之间的遗传相似性信息，如从全基因组遗传数据推断的信息。因此，当大量的系谱信息缺失时，它在促进使用来自群体分离株的生物库数据收集方面特别有用。
Family-based designs, from twin studies to isolated populations with their complex genealogical data, are a valuable resource for genetic studies of heritable molecular biomarkers. Existing software for family-based studies have mainly focused on facilitating association between response phenotypes and genetic markers, and no user-friendly tools are at present available to straightforwardly extend association studies in related samples to large datasets of generic quantitative data, as those generated by current -omics technologies. We developed PopPAnTe, a user-friendly Java program, which evaluates the association of quantitative data in related samples. Additionally, PopPAnTe implements data pre and post processing, region based testing, and empirical assessment of associations. PopPAnTe is an integrated and flexible framework for pairwise association testing in related samples with a large number of predictors and response variables. It works either with family data of any size and complexity, or, when the genealogical information is unknown, it uses genetic similarity information between individuals as those inferred from genome-wide genetic data. It can therefore be particularly useful in facilitating usage of biobank data collections from population isolates when extensive genealogical information is missing.