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Abstract
BackgroundAnalysing variant antigen gene families on a population scale is a difficult challenge for conventional methods of read mapping and variant calling due to the great variability in sequence, copy number, and genomic loci. In African trypanosomes, hemoparasites of humans and animals, this is complicated by variant antigen repertoires containing hundreds of genes subject to various degrees of sequence recombination.FindingsWe introduce Variant Antigen Profiler (VAPPER), a tool that allows automated analysis of the variant surface glycoprotein repertoires of the most prevalent livestock African trypanosomes. VAPPER produces variant antigen profiles for any isolate of the veterinary pathogens Trypanosoma congolense and Trypanosoma vivax from genomic and transcriptomic sequencing data and delivers publication-ready figures that show how the queried isolate compares with a database of existing strains. VAPPER is implemented in Python. It can be installed to a local Galaxy instance from the ToolShed (https://toolshed.g2.bx.psu.edu/) or locally on a Linux platform via the command line (https://github.com/PGB-LIV/VAPPER). The documentation, requirements, examples, and test data are provided in the Github repository.ConclusionBy establishing two different, yet comparable methodologies, our approach is the first to allow large-scale analysis of African trypanosome variant antigens, large multi-copy gene families that are otherwise refractory to high-throughput analysis.
Highlights
Analysing variant antigen gene families on a population scale is a difficult challenge for conventional methods of read mapping and variant calling due to the great variability in sequence, copy number, and genomic loci
We introduce Variant Antigen Profiler (VAPPER), a tool that allows automated analysis of the variant surface glycoprotein repertoires of the most prevalent livestock African trypanosomes
We briefly present how VAPPER can be used to further our knowledge of antigenic diversity and variation
Summary
Advances in next-generation sequencing have enabled researchers to produce high-throughput genomic data for diverse pathogens. Analysing multi-copy, contingency gene families remains challenging due to their abundance, high mutation and recombination rates, and unstable gene loci [1]. These gene families are often involved in many processes of pathogenesis, including antigenic variation, virulence, host use, and immune modulation in a multitude of pathogens [2,3,4]. African trypanosomes are extracellular hemoparasites that cause human sleeping sickness and animal African trypanosomiasis (AAT) Their genomes contain up to 2,500 VSG genes [6, 7] dispersed through specialized, hemizygous chromosomal regions called subtelomeres, smaller chromosomes, and Received: 3 December 2018; Revised: 17 June 2019; Accepted: 9 July 2019.
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