Making genotyping cheaper and easier

让基因分型变得更便宜、更容易

• 批准号: 2290744
• 金额: --
• 依托单位: University of Nottingham
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2290744
• 关键词: Making; genotyping; cheaper; easier

BackgroundThe opportunity to capture the full spectrum of genetic variants in any given species is crucial, as this allows accurate classification of individuals and the more accurate linkage of causal variants to phenotypes. There are now a plethora of tools and techniques that allow differential profiling of variant types, from single nucleotide polymorphisms, to DNA base modifications. The challenge is to develop approaches that are easier to execute and analyse. ObjectivesThis studentship will aim to develop both laboratory and bioinformatics techniques to capture the full spectrum of genetic variants using a variety of biological models with modifications of agronomic importance that require the development of specific tests to study non-standard genetic modifications. ApproachesThe research work will be divided into upto four workpackages (WPs), each with clear deliverables. These may include:WP1: SNP panel construction- work to identify a low cost method for SNP evaluation using single molecule sequencing WP2: Epi-allele identification using single molecule sequencing- using Phytophthora fragariae as a model of epiallelic variationWP3: Structural variant tracking- using Fusarium formae specialis structural rearrangements to identify dynamic genomic rearrangementsWP4: k-mer and signature based identification- reference free approaches of tracking allelic variation using single molecule sequencing. Benefit to the industryThe research outcome from this work will enable the development of novel genotyping technologies that can be used in breeding, varietal characterization and molecular diagnostics.

捕捉任何给定物种的全谱遗传变异的机会是至关重要的，因为这允许对个体进行准确的分类，并更准确地将因果变异与表型联系起来。现在有大量的工具和技术允许对变异类型进行差异分析，从单核苷酸多态性到DNA碱基修饰。挑战在于开发更容易执行和分析的方法。该项目旨在开发实验室和生物信息学技术，利用各种生物模型捕获遗传变异的全谱，这些模型具有重要的农艺修饰，需要开发特定的测试来研究非标准的遗传修饰。研究工作将分为多达四个工作包（wp），每个工作包都有明确的可交付成果。这些可能包括：WP1: SNP面板构建-使用单分子测序确定低成本的SNP评估方法；WP2：使用单分子测序进行外显等位基因鉴定-使用fragariae疫霉菌作为外显等位基因变异模型；wp3：结构变异跟踪-使用镰刀菌特殊结构重排确定动态基因组重排；利用单分子测序追踪等位基因变异的K-mer和基于签名的无参考鉴定方法。这项工作的研究成果将有助于开发新的基因分型技术，可用于育种、品种鉴定和分子诊断。