Summer project
Bioinformatics Specialization · Cohort 2024
GWAS of Cystic Fibrosis Lung Disease Using a Variable Number of Tandem Repeats Called from Long-Read Sequencing
Cystic fibrosis (CF) is a genetic disease affecting 70,000-100,000 individuals worldwide.1 It is caused by variations in the CFTR gene, impacting multiple organs, particularly the lungs. A recent genome-wide association study (GWAS) identified possible genetic links to lung function in CF, including a region near the SLC9A3 gene on chromosome 5.2. This region contains repetitive genetic sequences, and whether these repeats contribute to the observed genetic associations is unclear.2 This study aims to use HiFi technology from Pacific Biosciences (PacBio) to explore the association between repeat lengths genome-wide, particularly in the SLC9A3 region, and lung function in CF patients. Subjects with CF were recruited into the Canadian Cystic Fibrosis Gene Modifier Study (CGMS). High-molecular-weight DNA was sequenced using PacBio whole-genome long-read HiFi sequencing (30X). The Tandem Repeat Genotyping Tool (TRGT)3 and its repeat catalog were used to genotype repeats. The subjects' ancestry was inferred, and significant PCs from PCA were included as covariates.
With KAUST Academy
- Cohort 2024
University of Toronto · Bioinformatics Summer Program
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