MhGeneS: An Analytical Pipeline to Allow for Robust Microhaplotype Genotyping

Area of Science:

• Genomics
• Bioinformatics
• Population Genetics

Background:

• Microhaplotypes, small linked SNP sets, offer higher polymorphism than SNPs.
• Applications span forensics, wildlife monitoring, and genomic epidemiology.
• Targeting exonic regions requires careful amplicon design to capture functional sites and minimize indels.

Purpose of the Study:

• To develop and validate a bioinformatics pipeline (MhGeneS) for accurate microhaplotype genotyping in coding gene regions.
• To assess the impact of sequencing quality metrics on microhaplotype calling accuracy.
• To establish robust quality control for microhaplotype data.

Main Methods:

• Developed the MhGeneS pipeline, integrated with Seq2Sat, for microhaplotype validation.
• Genotyped microhaplotype regions in Zfx, Zfy, and Prnp genes of caribou (Rangifer tarandus) using Illumina paired-end sequencing.
• Analyzed sequencing error profiles, read depth, and amplicon trimming effects on genotyping accuracy.

Main Results:

• Identified sequencing error rate profiles and read depth as critical quality metrics for microhaplotype calling.
• Achieved confident microhaplotype genotyping for the Prnp gene by optimizing amplicon trimming and setting a minimum read depth of 20.
• Demonstrated the broader applicability of MhGeneS to various microhaplotype profiling tasks.

Conclusions:

• MhGeneS pipeline enhances the reliability of microhaplotype genotyping, particularly in coding regions.
• Read depth and sequence trimming parameters are crucial and may be locus-specific, requiring validation.
• Accurate microhaplotype data is essential for reliable genetic marker applications.