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使用全基因组测序数据分析白念珠菌的拷贝数变异和等位基因比。

Copy Number Variation and Allele Ratio Analysis in Candida albicans Using Whole Genome Sequencing Data.

机构信息

Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA.

出版信息

Methods Mol Biol. 2023;2658:105-125. doi: 10.1007/978-1-0716-3155-3_8.

Abstract

Whole genome sequencing of human fungal pathogens has revolutionized the speed and accuracy in which sequence variants that cause antifungal resistance can be identified. Genome rearrangements resulting in copy number variation (CNV) are a significant source of acquired antifungal drug resistance across diverse fungal species. Some CNVs are transient in nature, while other CNVs are stable and well tolerated even in the absence of antifungal drugs. By visualizing whole genome sequencing read depth as a function of genomic location, CNVs and CNV breakpoints (genomic positions where the copy number changes occur relative to the rest of the genome) are rapidly identified. A similar analysis can be used to visualize allele ratio changes that occur across the genomes of heterozygous fungal species, both in the presence and absence of CNVs. This protocol walks through the bioinformatic analysis of CNVs and allele ratios utilizing free, open-source visualization tools. We provide code to use with an example dataset (matched antifungal drug-sensitive and drug-resistant Candida albicans isolates) and notes on how to expand this protocol to other fungal genomes.

摘要

全基因组测序技术的发展极大地提高了鉴定导致抗真菌药物耐药性的序列变异的速度和准确性。基因组重排导致的拷贝数变异(CNV)是不同真菌物种获得抗真菌药物耐药性的重要来源。一些 CNV 是瞬时的,而其他 CNV 则是稳定的,即使在没有抗真菌药物的情况下也能很好地耐受。通过将全基因组测序读深度可视化作为基因组位置的函数,可以快速识别 CNV 和 CNV 断点(相对于基因组其余部分,发生拷贝数变化的基因组位置)。类似的分析可用于可视化杂合真菌物种基因组中发生的等位基因比值变化,包括 CNV 存在和不存在的情况。本方案介绍了利用免费的开源可视化工具对 CNV 和等位基因比值进行生物信息学分析的方法。我们提供了一个示例数据集(配对的抗真菌药物敏感和耐药性白色念珠菌分离株)的代码,并介绍了如何将该方案扩展到其他真菌基因组。

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