Serret-Larmande Arnaud, Kaltman Jonathan R, Avillach Paul
Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts, USA.
JAMIA Open. 2022 Jan 14;5(1):ooac001. doi: 10.1093/jamiaopen/ooac001. eCollection 2022 Apr.
Reproducibility in medical research has been a long-standing issue. More recently, the COVID-19 pandemic has publicly underlined this fact as the retraction of several studies reached out to general media audiences. A significant number of these retractions occurred after in-depth scrutiny of the methodology and results by the scientific community. Consequently, these retractions have undermined confidence in the peer-review process, which is not considered sufficiently reliable to generate trust in the published results. This partly stems from opacity in published results, the practical implementation of the statistical analysis often remaining undisclosed. We present a workflow that uses a combination of informatics tools to foster statistical reproducibility: an open-source programming language, Jupyter Notebook, cloud-based data repository, and an application programming interface can streamline an analysis and help to kick-start new analyses. We illustrate this principle by (1) reproducing the results of the ORCHID clinical trial, which evaluated the efficacy of hydroxychloroquine in COVID-19 patients, and (2) expanding on the analyses conducted in the original trial by investigating the association of premedication with biological laboratory results. Such workflows will be encouraged for future publications from National Heart, Lung, and Blood Institute-funded studies.
医学研究中的可重复性一直是个长期存在的问题。最近，新冠疫情使这一事实广为人知，因为多项研究的撤稿引起了大众媒体的关注。其中大量撤稿事件是在科学界对研究方法和结果进行深入审查之后发生的。因此，这些撤稿事件削弱了人们对同行评审过程的信心，因为该过程被认为不足以可靠到让人对已发表的结果产生信任。这部分源于已发表结果的不透明性，统计分析的实际操作往往未被披露。我们提出了一种工作流程，它结合了多种信息学工具来促进统计可重复性：一种开源编程语言、Jupyter Notebook、基于云的数据存储库以及一个应用程序编程接口，这些可以简化分析并有助于启动新的分析。我们通过以下方式阐述这一原则：（1）重现ORCHID临床试验的结果，该试验评估了羟氯喹对新冠患者的疗效；（2）通过研究用药前情况与生物实验室结果之间的关联，对原始试验中的分析进行扩展。美国国立心肺血液研究所资助的研究在未来发表时应鼓励采用这样的工作流程。
