Functional genomic analyses of emerging Cryptococcus subtypes in North America

描述（由申请人提供）：最近在北美出现了临床和流行病学上新颖的加蒂隐球菌种群。现在，研究加蒂弓形虫亚型的“种群基因组”以确定与其表型差异的基因组关联是可行的，也是必要的。本提案所描述的计划是通过对北美加蒂c主要类群和亚类群进行大规模全基因组测序和表达比较，阐明临床疾病、结局和其他差异的基因组原因。尽管最近的一些研究已经发现了明显的基因表达变异，这可能有助于解释一些表型差异，但结果并不一致，这可能是由于在目标亚型中分析的分离株数量有限。所述方法的第一部分是对200个加蒂杆菌基因组（约18Mb基因组）进行测序，包括所有已知的新北美菌株（VGIIc）分离株，以及北美和世界各地其他VGII种群的高度多样化样本，为比较分析提供比以前更多的数据。此外，我们将在不同的生长条件下对每个基因型进行转录组分析。这种基于生物信息学的分析方法将包括群体内部和群体之间的基因组成分比较、目标基因序列变异、重组分析、系统发育和表达分析。这将允许在这些种群中识别泛基因组，包括稳定（核心）基因组以及可能更易变且易于重组的塑料（附属）基因组。具有测序分离株的综合元数据集的可用性将允许对基因组变化与临床和流行病学特征之间的关联进行统计分析。这种基因组-转录组-流行病学方法可以基于基因组含量提供改进的临床结果预测。除了设计之外，该提案的主要优势在于它汇集了世界一流的基因组学、生物信息学、真菌学、临床和流行病学专业知识。此外，利用具有相关临床和流行病学元数据的综合菌株库将有助于对这一新出现的健康问题采取进一步有针对性和探索性的办法。这些是将基因组信息转化为诊断和治疗行动所必需的基础研究。

DESCRIPTION (provided by applicant): Clinically and epidemiologically novel populations of Cryptococcus gattii have recently emerged in North America. It is now feasible, and necessary, to examine the "population genome" of C. gattii subtypes to identify genomic associations with its phenotypic differences. The plan described in this proposal is to elucidate genomic causes of clinical disease, outcome and other differences by conducting large-scale whole genome sequence and expression comparisons among the major groups and subgroups of C. gattii in North America. Although some recent studies have identified apparent gene expression variation that may help explain some phenotypic differences, there have been inconsistent results, perhaps due to the limited number of isolates analyzed within the targeted subtypes. The first part of the described approach is to sequence 200 genomes of C. gattii (~18Mb genome), including all known isolates of the new North American strain (VGIIc), and highly diverse samples of the other VGII populations in North America and from around the world, providing more data than previously available for comparative analysis. In addition, we will conduct transcriptome analysis of each genotype under various growth conditions. This bioinformatic-based analytical approach will include genomic component comparisons within and between populations, targeted gene sequence variations, recombination analysis, phylogenetics, and expression analysis. This will permit the identification of the pan genome within these populations, including the stable (core) genome as well as the plastic (accessory) genome which maybe more mutable and prone to recombination. The availability of comprehensive metadata sets with the sequenced isolates will allow for statistical analyses of the association between genomic changes and clinical and epidemiological features. This genomic-transcriptomic-epidemiologic approach can provide improved clinical outcome prediction based on genome content. Beyond the design, a major strength of this proposal is that it brings together world-class genomics, bioinformatics, mycological, clinical and epidemiological expertise. In addition, access to comprehensive strain repositories with associated clinical and epidemiological metadata will allow for further targeted and exploratory approaches to this emerging health problem. These are foundational studies essential for translating genomic information into diagnostics and therapeutic actions. PUBLIC HEALTH RELEVANCE: The recent emergence of new populations of the fungus Cryptococcus gattii in northwestern North America has caused outbreaks of differing disease types and outcomes than previously seen. The approach described here is to comprehensively explore the genomes of entire populations of these new strain types in order to identify clinically and epidemiologically important genomic changes that may help predict patient outcome and health impacts on the affected local population.