MIP4IBD: An Easy and Rapid Genotyping-by-Sequencing Assay for the Inflammatory Bowel Diseases Risk Loci

Area of Science:

• Genetics
• Genomics
• Bioinformatics

Background:

• Inflammatory bowel diseases (IBD) are polygenic, influenced by numerous genetic variants.
• Accurate genotyping and polygenic risk scores (PRS) are crucial for translational and functional IBD research.
• Existing methods may lack the flexibility or cost-effectiveness required for large-scale genetic studies.

Purpose of the Study:

• To develop and validate MIP4IBD, a flexible and cost-effective genotyping-by-sequencing assay for IBD risk variants.
• To establish an integrated bioinformatics pipeline for processing sequencing data and calculating PRS.
• To assess the clinical utility of MIP4IBD in distinguishing IBD patients from controls and identifying risk factors.

Main Methods:

• Developed MIP4IBD assay targeting 463 IBD risk variants and 77 additional relevant variants.
• Optimized molecular inversion probe (MIP) capture and library preparation using IBD DNA samples.
• Created a custom GitHub pipeline for data processing, performance testing, and genotype calling.
• Validated the assay on 149 IBD patients and 104 controls, with post hoc quality control.

Main Results:

• MIP4IBD demonstrated a 3.5-day turnaround time at €15 per sample with high throughput.
• Achieved 92.6% variant capture success and high genotype concordance (99.3%-99.6%) with established platforms.
• Calculated PRS significantly higher in IBD patients (0.42 vs -0.49, P=1.95E-11).
• Highest PRS quartile associated with 15.7-fold increased IBD risk and earlier age of onset (26 vs 37 years).

Conclusions:

• MIP4IBD is a validated, scalable, and cost-effective genotyping assay for IBD risk loci.
• The integrated bioinformatics pipeline facilitates genotype and PRS calculation.
• MIP4IBD is suitable for translational and clinical applications due to its cost-effectiveness and flexibility.