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Detecting sequence variants in clinically important protozoan parasites.
International Journal for Parasitology ( IF 3.7 ) Pub Date : 2019-12-16 , DOI: 10.1016/j.ijpara.2019.10.004
Larissa Calarco 1 , Joel Barratt 1 , John Ellis 1
Affiliation  

Second and third generation sequencing methods are crucial for population genetic studies, and variant detection is a popular approach for exploiting this sequence data. While mini- and microsatellites are historically useful markers for studying important Protozoa such as Toxoplasma and Plasmodium spp., detecting non-repetitive variants such as those found in genes can be fundamental to investigating a pathogen's biology. These variants, namely single nucleotide polymorphisms and insertions and deletions, can help elucidate the genetic basis of an organism's pathogenicity, identify selective pressures, and resolve phylogenetic relationships. They also have the added benefit of possessing a comparatively low mutation rate, which contributes to their stability. However, there is a plethora of variant analysis tools with nuanced pipelines and conflicting recommendations for best practise, which can be confounding. This lack of standardisation means that variant analysis requires careful parameter optimisation, an understanding of its limitations, and the availability of high quality data. This review explores the value of variant detection when applied to non-model organisms such as clinically important protozoan pathogens. The limitations of current methods are discussed, including special considerations that require the end-users' attention to ensure that the results generated are reproducible, and the biological conclusions drawn are valid.

中文翻译:

检测临床上重要的原生动物寄生虫的序列变异。

第二代和第三代测序方法对于种群遗传学研究至关重要,而变异检测是利用该序列数据的一种流行方法。尽管微型卫星和微型卫星在历史上是研究重要原生动物(如弓形虫和疟原虫)的有用标记,但检测非重复性变体(如基因中发现的变体)可能是调查病原体生物学的基础。这些变异,即单核苷酸多态性以及插入和缺失,可以帮助阐明生物体致病性的遗传基础,确定选择性压力并解决系统发育关系。它们还具有具有较低突变率的额外好处,这有助于其稳定性。然而,有大量的变体分析工具,这些工具具有细微差别的流水线和最佳实践的相互矛盾的建议,这可能会造成混淆。缺乏标准化意味着变量分析需要仔细的参数优化,了解其局限性以及高质量数据的可用性。这篇综述探讨了将变体检测应用于非模型生物(如临床上重要的原生动物病原体)时的价值。讨论了当前方法的局限性,包括需要最终用户注意的特殊考虑因素,以确保生成的结果可重现,并且得出的生物学结论是有效的。缺乏标准化意味着变量分析需要仔细的参数优化,了解其局限性以及高质量数据的可用性。这篇综述探讨了将变体检测应用于非模型生物(如临床上重要的原生动物病原体)时的价值。讨论了当前方法的局限性,包括需要最终用户注意的特殊考虑因素,以确保产生的结果是可重现的,并且得出的生物学结论是有效的。缺乏标准化意味着变量分析需要仔细的参数优化,了解其局限性以及高质量数据的可用性。这篇综述探讨了将变体检测应用于非模型生物(如临床上重要的原生动物病原体)时的价值。讨论了当前方法的局限性,包括需要最终用户注意的特殊考虑因素,以确保产生的结果是可重现的,并且得出的生物学结论是有效的。
更新日期:2019-12-17
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