Enabling precision medicine via standard communication of HTS provenance, analysis, and results
Enabling precision medicine via standard communication of HTS provenance, analysis, and results
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DOI：
10.1371/journal.pbio.3000099
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发表时间：
2018-12-01
期刊：
影响因子：
9.8
通讯作者：
Mazumder, Raja
中科院分区：
文献类型：
--
作者：
Alterovitz, Gil;Dean, Dennis;Mazumder, Raja
基于患者或病原体独特基因组序列的个性化方法是精准医疗的基础。基因组研究结果必须是可靠的和可重复的，实验数据采集应遵循可发现、可访问、可互操作和可重复使用（FAIR）的指导原则。此外，有效的精准医疗需要标准化的报告，从湿实验室程序扩展到计算方法。BioCompute框架（https：//w3id.org/biocompute/1.3.0）支持基因组序列数据来源的标准化报告，包括来源域、可用性域、执行域、验证工具包和错误域。该框架促进了通信并促进了互操作性。采用BioCompute框架的生物信息学计算实例很容易被科学家、监管机构、测试开发人员和临床医生中继、重复（如果需要）和比较。减轻执行上述任务的负担大大扩展了实际应用的范围。大型临床试验、精准医学和监管提交需要一套商定的标准，以确保基因组分析的有效沟通和记录。BioCompute范式和由此产生的BioCompute Objects（BCOs）提供了该标准，并可作为GitHub组织（https：//github.com/biocompute-objects）免费访问，遵循“Open-Stand.org协作开放标准开发原则”。“随着高通量测序（HTS）研究使用BCO进行交流，监管机构（例如，美国食品药品监督管理局（FDA）、诊断测试开发人员、研究人员和临床医生可以扩大合作，推动精准医学的创新，从而可能减少与下一代测序工作流程交换、报告和监管审查相关的时间和成本。
A personalized approach based on a patient's or pathogen's unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the "Open-Stand.org principles for collaborative open standards development." With high-throughput sequencing (HTS) studies communicated using a BCO, regulatory agencies (e.g., Food and Drug Administration [FDA]), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next-generation sequencing workflow exchange, reporting, and regulatory reviews.