Sentieon 软件应用之公共卫生机构
Sentieon 致力于解决生物信息数据分析中的速度与准确度瓶颈，通过算法的深度优化和企业级的软件工程，大幅度提升 NGS 数据处理的效率、准确度和可靠性。自 2015 年的初始版本开始，Sentieon 推出了包括比对到变异检测在内的完整二次分析的解决方案，可用于胚系突变检测和体细胞突变检测。
多年来，Sentieon 软件被业内的制药企业，科研院所，临床医学，农业基因组等领域的用户广泛采用。为了让更多用户了解 Sentieon 在自己工作的领域的应用案例，INSVAT 从已发表的项目中精选一些有代表性文章作为案例分享给大家。
本期我们介绍 FDA 采购 Sentieon 的情况，以及另外 4 篇近期发表的文章来介绍 Sentieon 软件在全球范围内的公共卫生机构中的应用情况。
01 / FDA
FDA 公开招标采购 Sentieon 软件，整合进入 FDA 自用分析平台
标题：Request for Quote – Sentieon Software – FDA-RFQ-21-1242676
公示平台：sam.gov
招标日期：2021 年 6 月 11 日
招标单位：美国药监局 FDA CBER 办公室
The FDA CBER Office of Biostatistics and Epidemiology is seeking Sentieon software or equal for the HIVE (High-performance Integrated Virtual Environment). Enterprise level products such as HIVE require software to provide uninterrupted stability and functionality. The Sentieon software will be integrated into the HIVE platform to facilitate use for researchers and reviewers across the FDA. The Contractor shall provide Sentieon Software or equal that is or supports the HIVE by providing an additional suite of bioinformatics secondary analysis tools that process genomics data with high computing efficiency, fast turnaround time, exceptional accuracy, and 100% consistency.
02 /中国食品药品检定研究院
基于全外显子以及 panel 测序的低肿瘤含量样本中 TMB 的检测方式系统化评估
标题：Influence of low tumor content on tumor mutational burden estimation by whole-exome sequencing and targeted panel sequencing.
发表期刊：Clinical and Translational Medicine
发表日期：2021 年 5 月 6 日
主要作者单位：National Institutes for Food And Drug Control 中国食品药品检定研究院
Hereditary spherocytosis (HS) is a hereditary disease of hemolytic anemia that occurs due to the erythrocyte membrane defects. Dubin–Johnson syndrome (DJS), which commonly results in jaundice, is a benign hereditary disorder of bilirubin clearance that occurs only rarely. The co-occurrence of HS and DJS is extremely rare. A 21-year-old female patient presented to our department because of severe jaundice, severe splenomegaly, and mild anemia since birth. We eventually confirmed the
diagnosis of co-occurring DJS and HS by next generation sequencing (NGS). The treatment of ursodeoxycholic acid in combination with phenobarbital successfully increased hemoglobin and reduced total bilirubin and direct bilirubin.
03 / 澳大利亚新南威尔士卫生部
新型 CAR T-cell 疗法导致的 2 例淋巴癌患者的基因分析
标题：Investigation of product derived lymphoma following infusion of piggy-Bac modified CD19 chimeric antigen receptor T-cells.
发表日期：2021 年 5 月 11 日
主要作者单位：NSW Health 澳大利亚新南威尔士卫生部
We performed a Phase I clinical trial of donor derived CD19-specific chimeric antigen receptor T-cells (CAR T-cells) for B-cell malignancy that relapsed or persisted after matched related allogeneic hemopoietic stem cell transplant. Following CAR T-cell infusion, one patient developed a gradually enlarging retroperitoneal tumor due to a CAR expressing CD4+ T-cell lymphoma. Screening of other patients led to the detection of a second CAR T-cell tumor in thoracic para-aortic lymph nodes in an asymptomatic patient. Analysis of the first lymphoma showed a high transgene copy number, but no insertion into typical oncogenes. There were also structural changes such as altered genomic copy number and point mutations unrelated to the insertion sites. Although CAR T-cells have an enviable record of safety to date, our results emphasize the need for caution and regular follow up of CAR T recipients, especially when novel methods of gene transfer are used to create genetically modified immune therapies.
04 / 英国盖伊和圣托马斯国民保健信托基金会
基于 panel 测序的分子检测在侏儒症诊断方面效用的评估
标题：Diagnostic Utility of Next-Generation Sequencing-Based Panel Testing in 543 Patients with Suspected Skeletal Dysplasia
发表期刊：Journal of the American College of Cardiology
发表日期：2021 年 8 月 3 日
主要作者单位：Guy’s and St. Thomas’ NHS Trust 英国盖伊和圣托马斯国民保健信托基金会
Skeletal dysplasia is typically diagnosed using a combination of radiographic imaging, clinical examinations, and molecular testing. In this study, we retrospectively reviewed patient reports to assess the diagnostic yield, reported variant characteristics, impact of copy number variation, and performance in prenatal diagnostics of panel tests for variants in genes associated with skeletal dysplasia and growth disorders. These findings demonstrate the utility of panel testing for individuals with a suspected skeletal dysplasia or growth disorder, with a particularly high diagnostic yield seen in prenatal cases. Pursuing comprehensive panel testing with high-resolution CNV analysis can provide a diagnostic benefit, given the considerable phenotype overlap amongst skeletal dysplasia conditions.
05 / 美国农业部
棉花野生种系关键功能基因的研究
标题：The Gossypium stocksii genome as a novel resource for cotton improvement
发表期刊：G3 Genes|Genomes|Genetics
发表日期：2021 年 4 月 19 日
主要作者单位：USDA 美国农业部
Gossypium stocksii is a wild cotton species native to Africa, which is part of a clade of vastly understudied species. Most of what is known about this species comes from pest resistance surveys and/or breeding efforts, which suggests that G. stocksii could be a valuable reservoir of natural pest resistance. Here, we present a high-quality de novo genome sequence for G. stocksii. We compare the G. stocksii genome with resequencing data from a closely related, understudied species (Gossypium somalense) to generate insight into the relatedness of these cotton species.
总结
除了本文中精选的五篇公开文档之外，Sentieon 在全球超过一千家商业公司与学术机构中被广泛应用。可以看出，不同于学术与商业机构，政府部门的科研项目一般着重于以下几类：1）具有行业标杆意义的标准化评估项目；2）重要临床应用的效能评估项目；3）临床实验的效果以及不良反应的评估；4）遗传资源的相关评估。这些科研项目通常会对行业乃至整个社会的发展产生重要的推动作用。相对来说此类项目并不追求最新颖的技术方法，但是对成熟度和可靠性有重要的要求。同时，被政府部门使用的这些方法也会推动业内其他用户的接受，从而在将来的产品注册等环节进一步降低风险。我们很高兴看到 Sentieon 软件今年在政府部门使用有了大量的公开案例，为业界技术方向的选择提供了参考！
最后需要说明的是，Sentieon 软件作为数据分析软件，不涉及到数据的存储以及传输流程，可在断网环境下本地化部署，完全符合各国对于本国遗传资源保护的相关条例。
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