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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
Genes to diseases (G2D) computational method to identify asthma candidate genes
Karine Tremblay1, Mathieu Lemire, Camille Potvin
1Department of Medicine, Laval University, Québec, Quebec, Canada.
Plos One
|August 7, 2008
Summary
A novel method using the Genes to Diseases tool identified potential asthma genes. A protective association for PTPRE rs7081735 with allergic asthma was found in one cohort but not replicated.
Area of Science:
- Genetics
- Computational Biology
- Asthma Research
Background:
- Asthma is a complex genetic and environmental trait.
- Identifying predisposing factors requires robust methodologies.
- Novel approaches are needed for candidate gene selection in genetic association studies.
Purpose of the Study:
- To describe a new methodological approach for selecting candidate genes for asthma.
- To utilize the Genes to Diseases (G2D) tool combined with genome-wide scan data.
- To identify and test candidate genes in specific chromosomal loci linked to asthma and atopy.
Main Methods:
- Employed the Genes to Diseases (G2D) tool for data mining of public databases.
- Integrated G2D analysis with genome-wide scan data from the Saguenay-Lac-St-Jean (SLSJ) asthmatic familial collection.
- Selected ten candidate genes and genotyped 91 single nucleotide polymorphisms (SNPs) in a larger SLSJ sample (n=1167) using family-based association tests.
Main Results:
- Identified a suggestive protective association between PTPRE rs7081735 and allergic asthma in the SLSJ sample (p = 0.000463).
- This association was not replicated in the Childhood Asthma Management Program (CAMP) cohort.
- Further sequencing and genotyping around the significant SNP did not reveal new associations.
Conclusions:
- The Genes to Diseases (G2D) tool is effective for selecting candidate genes in chromosomal regions linked to complex traits like asthma.
- The study highlights the challenges in replicating genetic associations for complex diseases across different cohorts.
- Further research is needed to validate the role of identified candidate genes in asthma pathogenesis.
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