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，INSVAST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。
本文通过分享5篇已发表文章来介绍Sentieon在药企科研项目中的应用。
Amgen Inc.
药物毒性可引起基因组不稳定，染色体重排，产生额外副作用
标题：Biomarkers of Genome Instability in Normal Mammalian Genomes Following Drug-induced Replication Stress
发表期刊：Environmental and Molecular Mutagenesis
发表日期：2020年2月20日
主要作者单位：Amgen Research, Amgen Inc.
使用Sentieon模块：Sentieon BWA, TNseq, TNscope
We show that drug-induced replication stress leads to increased genome instability in vitro using proliferating primary human cells as well as in vivo in rat bone marrow and duodenum. We studied the in vivo genomic consequences of drug-induced replication stress in rats treated with 10 mg/kg of cyclophosphamide for up to fourteen days followed by PCR-free whole genome sequencing (30X coverage) of bone marrow and duodenum cells. Cyclophosphamide induced chromosomal structural rearrangements at an average of 90 genes, including 40 inter-intra chromosomal translocations and following even two days of treatment.
PROTACs耐药抗性产生是由于其E3连接酶复合物核心区基因突变
标题：Acquired Resistance to BET-PROTACs (Proteolysis-Targeting Chimeras) Caused by Genomic Alterations in Core Components of E3 Ligase Complexes
发表期刊：Molecular Cancer Therapeutics
发表日期：2019年7月18日
主要作者单位：Oncology Discovery, Genomic Research Center, AbbVie Inc.
使用Sentieon模块：Sentieon BWA, TNscope, joint-calling
Proteolysis-targeting chimeras (PROTAC) are bifunctional molecules that hijack endogenous E3 ubiquitin ligases to induce ubiquitination and subsequent degradation of protein of interest. Using BET-PROTACs as a model system, we demonstrate that resistance to both VHL- and CRBN-based PROTACs can occur in cancer cells following chronic treatment. Acquired resistance to both VHL- and CRBN-based BET-PROTACs was primarily caused by genomic alterations that compromise core components of the relevant E3 ligase complexes.
全外显子测序评估肿瘤突变负荷（TMB）的生信分析方法
标题：Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non‐Small‐Cell Lung Cancer
发表期刊：Molecular Diagnosis and Therapy
发表日期：2019年6月27日
主要作者单位：Translational Medicine, Global Biometric Sciences, Bristol-Myers Squibb
使用Sentieon模块：Sentieon TNseq
Here we describe the in-depth evaluation of bioinformatic TMB analysis by whole exome sequencing (WES) in formalin-fixed, paraffin-embedded samples from a phase III clinical trial. TMB scores from CheckMate 026 samples including missense mutations only were similar to those generated from data in The Cancer Genome Atlas, but those including all mutations were generally higher. Using databases for germline subtraction (instead of matched
controls) showed a trend for race-dependent increases in TMB scores. Parameter variation can impact TMB calculations, highlighting the need for standardization.
药物抗体发生突变的检测和原因探究
标题：Early Identification of Unusually Clustered Mutations and a Root Cause in Therapeutic Antibody Development
发表期刊：Biotechnology and Bioengineering
发表日期：2018年5月19日
主要作者单位：Product Development, Research and Development, Bristol-Myers Squibb
使用Sentieon模块：Sentieon DNAseq
This study reports findings of an unusual cluster of mutations spanning 22 base pairs in a monoclonal antibody (mAb) expression vector. It was identified by two orthogonal methods: mass spectrometry on expressed protein and next-generation sequencing (NGS) on the plasmid DNA. The finding highlights the necessity of rigorous examination on expression vector design and early monitoring of molecule integrity at both DNA and protein levels to prevent clones from having sequence variants during cell line development.
剪切体亚基变异影响药物分子结合，产生耐药抗性
标题：Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A–SF3b complex
发表期刊：Nature Communications
发表日期：2017年5月25日
主要作者单位：H3 Biomedicine Inc.
使用Sentieon模块：Sentieon TNseq
Pladienolide, herboxidiene and spliceostatin have been identified as splicing modulators that target SF3B1 in the SF3b subcomplex. Here we report that PHF5A, another component of this subcomplex, is also targeted by these compounds. Mutations in PHF5A-Y36, SF3B1-K1071, SF3B1-R1074 and SF3B1-V1078 confer resistance to these modulators, suggesting a common interaction site. RNA-seq analysis reveals that PHF5A-Y36C has minimal effect on basal splicing but inhibits the global action of splicing modulators. Collectively, we propose that PHF5A–SF3B1 forms a central node for binding to these splicing modulators.
除了本文中精选的五篇发表文献之外，Sentieon在全球几十家大中小型制药企业中被广泛应用，无论是临床前科研还是临床研究团队均能从Sentieon软件中获益。从我们和用户的沟通中了解到，和科研机构相比，制药企业对于技术的选择有自己的偏好：相对于技术的前沿性，更加关心技术的成熟度，稳定性以及监管机构的态度。具体到Sentieon软件的使用，大多数药企选择我们和GATK/Mutect2结果匹配的版本，倾向于固定在某一个版本号长期使用。
针对药企团队的特殊需求，Sentieon团队积极提供专业技术支持，针对药企使用的版本可进行分支版本补丁升级，在修复bug的同时避免其他改动。另外Sentieon团队和药企临床部门配合，为分析流程的FDA申请提供完善的文档支持。
