PopPAnTe

Population and pedigree association testing for quantitative data

Alessia Visconti, Mashael Al-Shafai, Wadha A. Al Muftah, Shaza Zaghlool, Massimo Mangino, Karsten Suhre, Mario Falchi

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background: 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. Results: 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. Conclusions: 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.

Original languageEnglish
Article number150
JournalBMC Genomics
Volume18
Issue number1
DOIs
Publication statusPublished - 10 Feb 2017

Fingerprint

Pedigree
Twin Studies
Genetic Markers
Population
Software
Biomarkers
Genome
Technology
Phenotype
Datasets

Keywords

  • -omics data
  • Association studies
  • Family data
  • Heritability
  • Isolated population
  • Population genetics

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

PopPAnTe : Population and pedigree association testing for quantitative data. / Visconti, Alessia; Al-Shafai, Mashael; Al Muftah, Wadha A.; Zaghlool, Shaza; Mangino, Massimo; Suhre, Karsten; Falchi, Mario.

In: BMC Genomics, Vol. 18, No. 1, 150, 10.02.2017.

Research output: Contribution to journalArticle

Visconti, Alessia ; Al-Shafai, Mashael ; Al Muftah, Wadha A. ; Zaghlool, Shaza ; Mangino, Massimo ; Suhre, Karsten ; Falchi, Mario. / PopPAnTe : Population and pedigree association testing for quantitative data. In: BMC Genomics. 2017 ; Vol. 18, No. 1.
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