HOOKSNIP: A BROWSER TOOL FOR DESIGNING ALLELE-SPECIFIC PCR PRIMERS IN HOOKWORM

Area of Science:

• Parasitology
• Molecular Biology
• Bioinformatics

Background:

• Anthelmintic resistance in hookworms necessitates cost-effective, field-deployable genotyping methods.
• Allele-specific PCR (AS-PCR) offers rapid detection of drug-resistance markers from parasite eggs or larvae without sequencing.
• Single-nucleotide polymorphisms (SNPs) are key markers for anthelmintic resistance.

Purpose of the Study:

• To develop a user-friendly, browser-based application for designing allele-specific PCR primers for hookworm genotyping.
• To facilitate the identification of anthelmintic resistance markers in Ancylostoma species.
• To reduce practical barriers in SNP validation for large-scale resistance monitoring.

Main Methods:

• Development of hookSNiP, a web application for designing allele-specific primer pairs.
• Integration of curated reference genomes and variant call format (VCF) validation.
• Implementation of strand-aware primer orientation and tiered rescue modes for design constraints.

Main Results:

• hookSNiP provides validated primer designs for Ancylostoma species.
• The tool ensures compatibility with genome sequences and gene annotations.
• It incorporates features to overcome strict primer design limitations.

Conclusions:

• hookSNiP simplifies SNP validation and AS-PCR primer design for hookworm genotyping.
• The application enhances the feasibility of large-scale surveillance for anthelmintic resistance.
• This tool supports global efforts to combat drug-resistant parasitic infections.