Automated and Guided Workflows for Clinical Testing Using NGS Assays

使用 NGS 检测进行临床测试的自动化和引导式工作流程

• 批准号: 9894817
• 负责人: Andreas Scherer
• 金额: $ 64.97万
• 依托单位: GOLDEN HELIX, INC.
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-03-15 至 2021-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9894817
• 关键词: Accountability; Adopted; Adoption; Algorithms; American; Appropriateness Review; Automation; Benchmarking; Bioinformatics; Biological Assay; Classification; Clinical; Clinical Laboratory Improvement Amendments; Clinical assessments; Collaborations; Communication; Competence; Complex; Complex Analysis; Computer software; Copy Number Polymorphism; Data; Data Sources; Decision Support Systems; Dependence; Detection; Development; Diagnosis; Elements; Ensure; Environment; Future; Genetic; Genetic Screening; Genetic Services; Genomics; Government; Guidelines; Hand; Hereditary Disease; Human Resources; Individual; Industry; Industry Standard; Informatics; Inherited; Institution; Judgment; Knowledge; Laboratories; Malignant Neoplasms; Medical; Medical Genetics; Mutation; Newborn Infant; Nucleotides; Outcome; Output; Patient-Focused Outcomes; Patients; Personal Satisfaction; Phase; Positioning Attribute; Privatization; Procedures; Process; Rare Diseases; Reporting; Resources; Risk Assessment; Running; Sampling; Single Nucleotide Polymorphism; Small Business Innovation Research Grant; Source; Specialist; System; Talents; Testing; Time; Training; Variant; Work; analysis pipeline; base; blind; cost; data hosting; data integration; data warehouse; design; disease diagnosis; genetic association; genetic testing; genetic variant; genomic data; genomic variation; improved; in silico; medical schools; molecular pathology; next generation sequencing; precision medicine; pressure; prototype; reproductive; research clinical testing; secondary analysis; success; testing services; tool; tumor; web app

The work done in a genetic laboratory to process a sample requires many detailed-oriented steps and a wealth of individual and institutional knowledge. The output of this process often has a significant impact on a patient’s outcome and wellbeing. At the same time, the work is repetitive and requires the handling of large test volumes under the time pressures inherent in medical procedures. This is particularly the case with next-generation sequencing (NGS) based tests, which are increasingly used to diagnose rare diseases, analyze mutation profiles of tumors, offer reproductive genetic services and perform newborn genetic screening. Existing software solution in this space have taken steps to make the overall work for a clinician simpler. Still, the efforts have not addressed the dependency on expert judgment and the following of detailed and often complex procedures to complete a genetic test. This environment lends itself to the application of workflow automation capabilities. The key benefits for the clinical users are the following: 1. Minimizing the potential for error: Workflow automation ensures essential and necessary tasks from going unnoticed. With tasks and the personnel that perform them being compressively tracked, workflow automation saves labs from far reaching and potentially very costly expenses associated with lab personnel errors. 2. Reducing costs and increasing throughput: Integrating internal communication into the workflow platform reduces the overhead required to conduct clinical work and stay compliant. The result is more work can be done with the same personnel. 3. Creating accountability and reducing subjectivity: As the complex rules and institutional knowledge of a laboratory gets codified into a workflow, every analytical step can be assigned and attributed to individual lab personnel while reducing the amount of choices made outside the system also reduces variance of outcomes attributed to operator subjectivity. In this project, we bring all elements of the clinical workflow for next-generation sequencing together. This includes the detection of single nucleotide variations and copy number variations, the annotation and clinical assessment of those variants, the storing of the finalized report and all associated data in a genetic data warehouse. This project will also cover the automation of the informatics that enable a decision support system capable of implementing variant classification guidelines such as those by the American College of Medical Genetics, Association of Molecular Pathology and other leading industry bodies.

在基因实验室中完成的处理样本的工作需要许多详细的步骤和大量的财富 个人和机构的知识。这一过程的结果通常对患者的 结果和幸福。同时，这项工作是重复性的，需要处理大量的测试 在医疗程序固有的时间压力下。下一代的情况尤其如此 基于测序(NGS)的测试越来越多地被用于诊断罕见疾病、分析突变图谱 提供生殖遗传服务，并进行新生儿基因筛查。现有软件解决方案 在这一领域已经采取措施，使临床医生的整体工作变得更简单。尽管如此，这些努力还没有解决 对专家判断的依赖，以及完成一项详细且往往复杂的程序的后续步骤 基因测试。这种环境适合工作流自动化功能的应用。主要优势 供临床用户使用的产品如下： 1.将出错的可能性降至最低：工作流自动化确保从 没有被注意到。通过压缩跟踪任务和执行任务的人员，工作流 自动化使实验室避免了与实验室相关的影响深远且可能非常昂贵的费用 人员失误。 2.降低成本和提高吞吐量：将内部沟通整合到工作流程中 平台减少了进行临床工作并保持合规性所需的管理费用。结果是更多 工作可以用同样的人员来完成。 3.创造问责和减少主观性：作为复杂的规则和制度知识 实验室的每一个分析步骤都可以被分配和归因于 个别实验室人员在减少系统外做出的选择数量的同时，也减少了 结果的差异归因于操作员的主观性。 在这个项目中，我们将下一代测序的临床工作流程的所有要素结合在一起。这 包括单核苷酸变异和拷贝数变异的检测、注释和临床 评估这些变异，将最终报告和所有相关数据存储在基因数据中 仓库。该项目还将涵盖实现决策支持系统的信息学自动化 能够执行不同的分类指南，如美国医学院的分类指南 遗传学、分子病理学协会和其他领先的行业组织。