Roadmap for development of diagnostic tests for helminths

What are we trying to achieve and why? What is the problem we are trying to solve?

Improve parasite genomic, transcriptomic, proteomic and metabolomic resources and methodologies to underpin the identification of biomarkers for infection intensity and genetic markers for anthelmintic resistance diagnostics.

What are the scientific and technological challenges (knowledge gaps needing to be addressed)?

• Helminths have complex genomes and high levels of genetic variation which makes genome assembly, annotation and analysis challenging.
• Incentive for researchers to continue to improve genome assemblies and annotations beyond first published drafts is low since publication impact is low for “genome improvement papers”.
• Ongoing curation of reference genomes, genomic data and associated informatic resources and tools is dependant on individual researcher interest/goodwill.
• Relatively few resources or research to date for novel helminth biomarker discovery (microRNA, metabolites etc)

What approaches could/should be taken to address the research question?

• Continued Improvement of current reference genome assemblies and using short read and long-read technologies
• Generate reference genomes for those helminth species lacking such a resource, eg some of the cattle and sheep GIN species.
• Continual improvement of annotations for the major parasite species of interest.
• Provide web-based publically available curated databases and associated tools for the reference genomes.
• Develop platforms to allow continued improvement of gene annotation and information by the helminth research community eg. WebApollo.
• Undertake population genomic and genome-wide approaches to investigate and define genetic variation in relevant helminth species and identify anthelmintic drug resistance loci.
• Undertake more discovery research on cell-free DNA, microRNA, proteomics, metabolics for biomarker and resistance marker discovery.

What else needs to be done before we can solve this need?

Expansion and improvement of current draft genome assemblies for livestock helmith species and sustainable systems for data curation.

Existing knowledge including successes and failures

• Many draft reference genomes now available for an increasing number of livestock nematode and trematode species. However, still a number of species without such respources.
  Most of the current draft genome genomes are not sufficiently complete ( both in terms of assembly and annotation) to allow genetic mapping/population genomic approaches to identify anthelmintic resistance loci or to allow truly comprehensive whole genome approaches. Haemonchus contortus is still the only chromosomal level reference genome assembly to date
• Chromosomal level genome assemblies are needed for genetic mapping and population genomic approaches to identify genetic loci for drug resistance markers.
• Many labs working on helminth diagnostics do not always have access to ppecialist bioionformatic expertise needed to mine and use genomic data.