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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
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Detecting disease variants in case-parent trio studies using the bioconductor software package trio
Holger Schwender1, Qing Li, Christoph Neumann
1Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany.
Genetic Epidemiology
|July 23, 2014
Summary
This study introduces a reproducible workflow for analyzing genetic case-parent trio data using the open-source Bioconductor trio package. It enables comprehensive genome-wide association studies for complex diseases.
Area of Science:
- Genetics
- Bioinformatics
- Computational Biology
Background:
- Case-parent trio studies are crucial for identifying genetic variants linked to complex diseases.
- Existing software packages may lack flexibility and reproducibility features for genomic data analysis.
Purpose of the Study:
- To present a reproducible genome-wide analysis workflow for case-parent trio data.
- To demonstrate the functionality of the open-source Bioconductor trio package.
Main Methods:
- Utilized a software vignette with step-by-step instructions and examples.
- Employed data from previous genetic trio studies.
- Applied functions for association tests, parent-of-origin effects, and power calculations.
Main Results:
- Illustrated marginal association tests and parent-of-origin effect assessments.
- Demonstrated power and sample size calculations.
- Showcased detection of gene-gene and gene-environment interactions.
Conclusions:
- The Bioconductor trio package provides a reproducible framework for analyzing case-parent trio data.
- This workflow supports comprehensive genetic analyses, including complex interaction detection.
Keywords:
case-parent triosgene-environment interactionsparent-of-origin effectssoftwaretransmission disequilibrium testsMore Related Videos
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