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PhenoMIP: High-Throughput Phenotyping of Diverse Caenorhabditis elegans Populations via Molecular Inversion Probes.
G3: Genes, Genomes, Genetics ( IF 2.6 ) Pub Date : 2020-10-27 , DOI: 10.1534/g3.120.401656
Calvin Mok 1 , Gabriella Belmarez 2 , Mark L Edgley 3 , Donald G Moerman 3 , Robert H Waterston 2
Affiliation  

Whether generated within a lab setting or isolated from the wild, variant alleles continue to be an important resource for decoding gene function in model organisms such as Caenorhabditis elegans. With advances in massively parallel sequencing, multiple whole-genome sequenced (WGS) strain collections are now available to the research community. The Million Mutation Project (MMP) for instance, analyzed 2007 N2-derived, mutagenized strains. Individually, each strain averages ~400 single nucleotide variants amounting to ~80 protein-coding variants. The effects of these variants, however, remain largely uncharacterized and querying the breadth of these strains for phenotypic changes requires a method amenable to rapid and sensitive high-throughput analysis. Here we present a pooled competitive fitness approach to quantitatively phenotype subpopulations of sequenced collections via molecular inversion probes (PhenoMIP). We phenotyped the relative fitness of 217 mutant strains on multiple food sources and classified these into five categories. We also demonstrate on a subset of these strains, that their fitness defects can be genetically mapped. Overall, our results suggest that approximately 80% of MMP mutant strains may have a decreased fitness relative to the lab reference, N2. The costs of generating this form of analysis through WGS methods would be prohibitive while PhenoMIP analysis in this manner is accomplished at less than one-tenth of projected WGS costs. We propose methods for applying PhenoMIP to a broad range of population selection experiments in a cost-efficient manner that would be useful to the community at large.



中文翻译:

PhenoMIP:通过分子倒置探针对多种秀丽隐杆线虫种群进行高通量表型分析。

无论是在实验室环境中产生还是从野外分离,变异等位基因仍然是在模式生物(如秀丽隐杆线虫)中解码基因功能的重要资源. 随着大规模平行测序的进步,研究界现在可以使用多个全基因组测序 (WGS) 菌株集合。例如,百万突变项目 (MMP) 分析了 2007 年 N2 衍生的诱变菌株。单独地,每个菌株平均约 400 个单核苷酸变体,相当于约 80 个蛋白质编码变体。然而,这些变体的影响在很大程度上仍未得到表征,并且查询这些菌株的表型变化的广度需要一种适合快速和敏感的高通量分析的方法。在这里,我们提出了一种汇总的竞争健身方法来定量现象通过类型排序集合的子群 分子 一世反转 p长袍(PhenoMIP)。我们对 217 个突变菌株在多种食物来源上的相对适应性进行了表型分析,并将其分为五类。我们还证明了这些菌株的一个子集,它们的适应性缺陷可以通过基因映射。总体而言,我们的结果表明,相对于实验室参考,大约 80% 的 MMP 突变菌株可能具有降低的适应度,N2。通过 WGS 方法生成这种形式的分析的成本将令人望而却步,而以这种方式进行 PhenoMIP 分析的成本不到 WGS 预计成本的十分之一。我们提出了以经济高效的方式将 PhenoMIP 应用于广泛的种群选择实验的方法,这将对整个社区有用。

更新日期:2020-11-06
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