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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
Candidate genes detected in transcriptome studies are strongly dependent on genetic background
Pernille Sarup1, Jesper G Sørensen, Torsten N Kristensen
1Department of Biological Sciences, Aarhus University, Aarhus, Denmark. pernille.sarup@biology.au.dk
Plos One
|February 2, 2011
Summary
Whole genome transcriptomic studies identify candidate genes, but findings vary significantly across studies. Candidate gene importance requires validation, as results are highly sensitive to genetic background, impacting trait analysis.
Area of Science:
- Genomics and Transcriptomics
- Drosophila melanogaster research
- Quantitative Trait Gene discovery
Background:
- Whole genome transcriptomic studies are powerful tools for identifying candidate genes associated with organismal traits.
- However, the functional validation and cross-study reproducibility of these candidate genes remain significant challenges in the field.
- Understanding the influence of genetic background on transcriptomic study outcomes is crucial for accurate gene discovery.
Purpose of the Study:
- To analyze the overlap of candidate genes identified from independent gene expression studies in Drosophila melanogaster.
- To investigate the sensitivity of transcriptomic candidate gene identification to genetic background and experimental conditions.
- To provide recommendations for improving the reliability and validation of candidate genes from transcriptomic analyses.
Main Methods:
- Comparative analysis of candidate genes identified from multiple whole genome transcriptomic studies.
- Focus on studies utilizing similar technical platforms for gene expression analysis in Drosophila melanogaster.
- Examination of gene overlap across different traits and sexes within consistent genetic backgrounds.
Main Results:
- Little overlap was observed in candidate genes for the same traits within the same sex across independent studies.
- A high degree of overlap was found between different traits and sexes when analyzing data from the same genetic backgrounds.
- Transcriptomic candidate gene identification demonstrated significant sensitivity to genetic background, potentially masking or overriding treatment effects.
Conclusions:
- Candidate genes identified through transcriptomics are highly influenced by genetic background, necessitating careful interpretation.
- Functional validation through additional experiments is essential to confirm the importance of putative candidate genes.
- Future transcriptomic studies should prioritize analyzing genes, networks, and pathways that consistently affect traits across diverse genetic backgrounds.
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