A next-generation method for cytogenomics using Hi-C proximity ligation sequencing

使用 Hi-C 邻近连接测序的下一代细胞基因组学方法

• 批准号: 10397703
• 负责人: Stephen Matthew Eacker
• 金额: $ 83.79万
• 依托单位: PHASE GENOMICS, INC.
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-05-01 至 2023-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10397703
• 关键词: Accounting; Address; Affect; Aneuploidy; Animals; Benchmarking; Cell Line; Child; Chromosome abnormality; Chromosomes; Clinical; Collection; Computer software; Conceptions; Couples; Cytogenetic Analysis; Cytogenetics; DNA Ligation; DNA Sequence Rearrangement; DNA sequencing; Data; Data Set; Decision Making; Detection; Diagnosis; Diagnostic; Diagnostic Procedure; Event; Fetal Viability; Fluorescent in Situ Hybridization; Funding; Future; Gametogenesis; Genetic; Genome; Genomics; Goals; Grant; Hi-C; Industry Standard; Infertility; Karyotype; Karyotype determination procedure; Laboratories; Lead; Length; Lesion; Letters; Ligation; Manuals; Methodology; Methods; Molecular Biology; Mosaicism; Mutation; Online Systems; Outcome; Performance; Phase; Plants; Pregnancy loss; Process; Protocols documentation; Reagent; Reporting; Reproducibility; Reproduction; Reproductive Medicine; Research; Resolution; Sampling; Sensitivity and Specificity; Series; Services; Single Nucleotide Polymorphism; Small Business Innovation Research Grant; Software Tools; Study Section; System; Technology; Testing; Time; United States; Variant; clinically relevant; cloud based; cohort; computational platform; cost; design; feasibility testing; genetic testing; improved; large datasets; meetings; next generation; novel strategies; precision medicine; reproductive; scaffold; tool

ABSTRACT Reproductive genetic tests are a disparate collection of methodologies with identify specific classes of mutations known to interfere with gametogenesis, conception and fetal viability. The number and variety of tests addressing this clinical need reflect the scale of genetic lesions that are relevant to reproductive medicine, ranging from whole chromosome aneuploidy to single nucleotide variants. In this proposal, we describe a highly scalable reproductive genetic test that can deliver results that span this scale at high resolution, lower cost, and faster turnaround time than current tests. Our approach uses a proximity ligation DNA sequencing method called Hi-C, which captures ultra-long-range genomic contiguity information using ubiquitious short-read sequencing and benchtop molecular biology. We have demonstrated extensively that Hi-C data can be used to order and orient genome assemblies, reconstructing end-to-end chromosome sequences. This method also identifies structural genomic rearrangements including balanced translocations, inversions, and other aberrations not detectable by typical sequencing approaches. We propose to apply high-throughput proximity ligation as a cytogenomic method to detect the breadth of chromosomal aberrations at high resolution and low cost. This proposal outlines a path to a commercially available product and service, which will establish a highly validated method for use in research and eventually in a diagnostic setting. This will be accomplished by 1) designing an easy to use Hi-C protocol amenable to multiwell plate handling, 2) building a robust computational platform to reproducibly call chromosome aberrations from Hi-C data, and 3) proving the validity and reproducibility of these methods on real world samples. The resulting kit and software product will be a new cytogenomic method called Karyotyping by SequencingTM (KBS) that we will deploy as a Precision Medicine test for the reproductive testing market.

抽象的 生殖基因测试是一组不同的方法，用于识别特定类别的突变 已知会干扰配子发生、受孕和胎儿活力。测试的数量和种类 这种临床需求反映了与生殖医学相关的遗传病变的规模，范围从 全染色体非整倍体到单核苷酸变异。在这个提案中，我们描述了一个高度可扩展的 生殖基因测试可以以高分辨率、更低的成本和更快的速度提供跨越这种规模的结果 比当前测试的周转时间。 我们的方法使用称为 Hi-C 的邻近连接 DNA 测序方法，该方法可捕获超长距离 使用普遍存在的短读长测序和台式分子生物学获得基因组连续性信息。我们 已广泛证明 Hi-C 数据可用于排序和定向基因组组装， 重建端到端染色体序列。该方法还可以识别结构基因组 重排，包括平衡易位、倒位和其他典型无法检测到的畸变 测序方法。 我们建议应用高通量邻近连接作为一种细胞基因组方法来检测 高分辨率和低成本的染色体畸变。该提案概述了一条商业化之路 可用的产品和服务，这将建立一种高度验证的方法用于研究并最终 在诊断环境中。这将通过 1) 设计一个易于使用的 Hi-C 协议来实现 多孔板处理，2) 构建强大的计算平台以可重复地调用染色体畸变 来自 Hi-C 数据，以及 3) 证明这些方法在现实世界样本上的有效性和可重复性。这 由此产生的试剂盒和软件产品将是一种新的细胞基因组学方法，称为 Karyotyping by SequencingTM (KBS) 我们将把它部署为生殖检测市场的精准医学测试。