Department of Internal Medicine, University Center of Autoimmunity, University Medical Center Mainz, Mainz, Germany
Monte Rosa Therapeutics, Basel, Switzerland.
RMD Open. 2021 Jan;7(1). doi: 10.1136/rmdopen-2020-001324.
Here, we assess the usage of high throughput sequencing (HTS) in rheumatic research and the availability of public HTS data of rheumatic samples.
We performed a semiautomated literature review on PubMed, consisting of an R-script and manual curation as well as a manual search on the Sequence Read Archive for public available HTS data.
Of the 699 identified articles, rheumatoid arthritis (n=182 publications, 26%), systemic lupus erythematous (n=161, 23%) and osteoarthritis (n=152, 22%) are among the rheumatic diseases with the most reported use of HTS assays. The most represented assay is RNA-Seq (n=457, 65%) for the identification of biomarkers in blood or synovial tissue. We also find, that the quality of accompanying clinical characterisation of the sequenced patients differs dramatically and we propose a minimal set of clinical data necessary to accompany rheumatological-relevant HTS data.
HTS allows the analysis of a broad spectrum of molecular features in many samples at the same time. It offers enormous potential in novel personalised diagnosis and treatment strategies for patients with rheumatic diseases. Being established in cancer research and in the field of Mendelian diseases, rheumatic diseases are about to become the third disease domain for HTS, especially the RNA-Seq assay. However, we need to start a discussion about reporting of clinical characterisation accompany rheumatological-relevant HTS data to make clinical meaningful use of this data.
在此，我们评估高通量测序（HTS）在风湿研究中的应用以及风湿样本的公共 HTS 数据的可用性。
我们在 PubMed 上进行了半自动化文献综述，该综述由 R 脚本和手动策展以及对公共可用 HTS 数据的 Sequence Read Archive 的手动搜索组成。
在 699 篇已确定的文章中，类风湿关节炎（n=182 篇出版物，26%）、系统性红斑狼疮（n=161 篇，23%）和骨关节炎（n=152 篇，22%）是报告使用 HTS 检测最多的风湿疾病。最具代表性的检测方法是 RNA-Seq（n=457，65%），用于鉴定血液或滑膜组织中的生物标志物。我们还发现，伴随测序患者的临床特征的质量差异很大，我们提出了一套伴随风湿相关 HTS 数据所需的最小临床数据。
HTS 允许同时分析许多样本中的广泛分子特征。它为风湿疾病患者的新型个性化诊断和治疗策略提供了巨大的潜力。在癌症研究和孟德尔疾病领域已经确立的 HTS，即将成为风湿疾病的第三个疾病领域，特别是 RNA-Seq 检测。然而，我们需要开始讨论报告伴随风湿相关 HTS 数据的临床特征，以使其能够对临床有意义地使用该数据。
