PopPAnTe: population and pedigree association testing for quantitative data

BMC Genomics

Software

Wadha A. Al Muftah¹  Mashael Al-Shafai²  Karsten Suhre³  Shaza B. Zaghlool³  Alessia Visconti⁴  Mario Falchi⁴  Massimo Mangino⁵ 

[1] Department of Genomics of Common Diseases, Imperial College London, London, UK;Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar;Research Division, Qatar Science Leadership Program, Qatar Foundation, Doha, Qatar;Department of Genomics of Common Diseases, Imperial College London, London, UK;Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar;Research Division, Qatar Science Leadership Program, Qatar Foundation, Doha, Qatar;Department of Biomedical Sciences, College of Health Sciences at Qatar University, Doha, Qatar;Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar;Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK;Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK;NIHR Biomedical Research Centre at Guy’s and St Thomas’ Foundation Trust, London, UK;

关键词: Association studies;    Heritability;    -omics;    Family data;    Isolated population;    Population genetics;   

DOI  :  10.1186/s12864-017-3527-7

 received in 2015-10-30, accepted in 2017-01-31,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundFamily-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.ResultsWe 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.ConclusionsPopPAnTe 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.

【 授权许可】

CC BY   
© The Author(s) 2017

【 图 表 】

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