Precise Length and 5-Methylcytosine Assessments of Repeat Sequences

重复序列的精确长度和 5-甲基胞嘧啶评估

• 批准号: 10254007
• 负责人: Anna Schibel
• 金额: $ 27.19万
• 依托单位: ELECTRONIC BIOSCIENCES, INC.
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-05-10 至 2023-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10254007
• 关键词: Achievement; Amyotrophic Lateral Sclerosis; Automation; Back; Biological; Biological Assay; Biological Sciences; Biopsy; Biotin; Buffers; Capillary Electrophoresis; Cells; Clinical; Code; Consensus Sequence; Consumption; DNA; DNA Repeat Expansion; DNA Restriction Enzymes; DNA Sequence; Development; Diagnostic; Disease; Epigenetic Process; Foundations; Fragile X Syndrome; Friedreich Ataxia; G-Quartets; GTP-Binding Protein alpha Subunits, Gs; Genetic; Genetic Diseases; Genome; Genomic Segment; Genomics; Genotype; Goals; Gold; Guanine; Hemolysin; Human; Huntington Disease; Immobilization; Length; Libraries; Methodology; Methods; Methylation; Microsatellite Repeats; Minisatellite Repeats; Motor; Mutation; Myotonic Dystrophy; Nucleotides; Patients; Pattern; Phase; Polymerase; Population; Preparation; Process; Reader; Reading; Resolution; Role; Sampling; Satellite DNA; Severities; Small Business Innovation Research Grant; Spinocerebellar Ataxias; Streptavidin; Structure; System; Tandem Repeat Sequences; Technology; Third Generation Sequencing; Time; base; disease diagnosis; ds-DNA; genome sequencing; illness length; improved; insertion/deletion mutation; nanopore; next generation sequencing; patient population; personalized care; point-of-care diagnostics; population health; prognostic; prognostic assays; prognostic value; programs; screening panel; single molecule; synthetic construct; whole genome

Project Summary During this program, Electronic BioSciences, Inc. (EBS) will develop and demonstrate a complete, end-to-end, universal methodology for repeat sequence characterization, including precise length and methylation (5- methylcytosine or 5mC) assessments. This technology will be enabled by the development and demonstration of a sequence-targeted sample and library preparation that will enable the isolation and enrichment of any repeat sequence with a known sequential context or loci for disease-specific diagnostics. Specifically, satellite DNA is comprised of sequence repeats that occur in tandem 5 or more times. Among this DNA, microsatellites have a 1–10 nucleotide (nt) repeat pattern and minisatellites have a >10-nt long repeat pattern. A specific type of satellite DNA found in coding regions of the genome are repeat expansions. Increases in repeat sequence length and epigenetic 5mC status have been correlated to a number of diseases, including Myotonic Dystrophy, Huntington’s Disease, Friedreich’s Ataxia, Fragile X, Fragile XE, Amyotrophic Lateral Sclerosis or ALS, etc., and the targeted characterization of these regions would represent a direct approach (relative to whole genome sequencing) towards clinical and point-of-care diagnostics. However, there is no technology presently available that is ideally suited for characterizing these repeat sequences as a result of read length (associated with next generation sequencing approaches) or accuracy (associated with third generation sequencing approaches), which has significantly limited the understanding of the role repeat sequences have in disease states, their diagnostic/prognostic utility, and the development of associated assays. During this Phase I SBIR program, EBS will develop and demonstrate a technology that will allow these regions to be efficiently assessed for disease state diagnostics.

项目摘要 在此计划中，电子生物科学公司（EBS）将开发并展示完整的端到端， 重复序列表征的通用方法，包括精度长度和甲基化（5- 甲基胞嘧啶或5MC）评估。该技术将由开发和演示启用 以序列为目标的样品和库制备的准备，该样品将使任何重复的隔离和丰富 具有已知顺序上下文或疾病特异性诊断区域的序列。具体而言，卫星DNA是 完成在5次或更多次中发生的序列重复序列完成。在此DNA中，微卫星具有 1-10核苷酸（NT）重复模式，而迷你卫星具有> 10-nt的长重复模式。特定类型的卫星 在基因组的编码区域中发现的DNA是重复扩展。重复序列长度增加，并且 表观遗传5MC状态已与多种疾病相关，包括肌发育症， 亨廷顿氏病，弗里德里希的共济失调，脆弱的X，脆弱的XE，肌萎缩性侧面硬化症或ALS等，以及 这些区域的目标表征将代表一种直接的方法（相对于整个基因组 测序）进行临床和护理点诊断。但是，目前尚无技术 理想情况下适合表征由于读取长度而表征这些重复序列（与下一个相关 生成测序方法）或准确性（与第三代测序方法相关）， 这极大地限制了对重复序列在疾病状态的作用的理解， 诊断/预后效用以及相关评估的发展。在此阶段I SBIR计划中，EBS 将开发并展示一种将使这些地区有效评估疾病的技术 状态诊断。