Commercialization of a highly-sensitive, scalable and low-input compatible kit-based solution for discovery of translocations from FFPE tumor biopsies

将高度灵敏、可扩展且低输入兼容的基于试剂盒的解决方案商业化，用于从 FFPE 肿瘤活检中发现易位

• 批准号: 9910099
• 负责人: Siddarth Selvaraj
• 金额: $ 99.93万
• 依托单位: ARIMA GENOMICS, INC.
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2022-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9910099
• 关键词: 3-Dimensional; Address; Adoption; Advanced Malignant Neoplasm; Age; Bar Codes; Benchmarking; Bioinformatics; Biological Assay; Biopsy; Cause of Death; Cells; Clinical; Collaborations; Communities; Coupled; DNA; DNA sequencing; Data; Detection; Development; Diagnosis; Dimensions; Disease; Economics; Ensure; Epigenetic Process; Evaluation; Fine needle aspiration biopsy; Formalin; Freezing; Funding; Genes; Genome; Genomic Instability; Genomics; Individual; Informatics; Infrastructure; Knowledge; Lead; Malignant Neoplasms; Manuals; Marketing; Measures; Methods; Molecular Conformation; Molecular Weight; Mutation; Nature; Paraffin Embedding; Patients; Performance; Phase; Precision therapeutics; Procedures; Protocols documentation; Reagent; Research; Sales; Sampling; Science; Shipping; Spectral Karyotyping; Speed; Sum; Technology; Testing; Time; TimeLine; Translocation Breakpoint; Validation; anticancer research; base; cancer diagnosis; cancer genomics; cancer type; chromosome conformation capture; cloud based; commercialization; cost; design; experience; experimental study; gene panel; genetic information; genetic profiling; genome-wide; improved; innovation; insight; new technology; novel; precision oncology; preservation; product development; prognostic; programs; prototype; research and development; success; technology development; tool; tumor

Commercialization of a highly-sensitive, scalable and low-input compatible kit-based solution for discovery of translocations from FFPE tumor biopsies Arima Genomics Project Summary/Abstract Despite decades of research, cancer takes the lives of nearly 600,000 people every year in the US. The cancer research community has made key advancements towards improving the precision of cancer diagnosis and recently substantial efforts have been put forth into the genetic profiling of tumors. Specifically, efforts have been focused on developing methods to profile genetic alterations such as translocations that are prognostic in cancer. Knowledge of an individual's translocation profile can be used to uncover the mechanistic basis of cancer, accelerating cancer research towards development of new precision therapies. Current standard, including NGS, are limited in their ability to characterize translocations. This is because for NGS (WGS or gene panel seq.) to profile translocations, breakpoint-spanning reads are needed and NGS does not enrich for such reads. FISH enriches for breakpoint info by capturing spatial conformation of the genome within cells and but it has limited utility due to its low-throughput nature and its requirement of apriori info of the translocation partners. Spectral Karyotyping (SKY) needs living cells and cannot be performed on FFPE samples, which is a major sample type for cancer samples. Altogether, a method that is (a) high-throughput along the lines of NGS; (b) enriches translocations along the lines of FISH; (c) not requiring apriori indo of translocating partners to enable promiscuous translocation detection; and (d) compatible with FFPE samples – would result in a highly sensitive and scalable solution for translocation discovery. We satisfy the unmet need via a leapfrog solution. We use HiC to capture conformation on the lines of FISH and couple it with NGS (HiC-Seq) to detect translocations at high sensitivity, high precision, high PPV and low FP. Our team has unmatchable expertise in the science of HiC and its commercialization. Specifically, we commercialized Arima-HiC kits in 2018 for studying conformation in the context of Epigenetics research and generated $1.2M in revenue in the 1st year of commercialization with 200+ customers, all from 1 sales executive. However, these kits are not compatible to FFPE, is manual, labor- and time-intensive and cannot handle batches of >10-20 samples at a time – to enable broad adoption toward cancer research, we have shown the development a boxed kit, the “T-Seq Kit”, based on enhanced HiC optimized for performance, speed, ease of use that is compatible to low-input FFPE, fresh and frozen samples. We validate the technology development from sample to insight in a patient-derived FFPE GIST biopsy and demonstrate that we can sensitively profile translocations even from low tumor purity samples (or low MAF). As part of this direct-2-phase II program, we propose to further develop our technology into a robust kit-based “T-Seq Solution”, comprising same day 8hr sample to sequencing, full 96-plate automated and versatile HiC protocols (to all sample types) that is compatible with existing NGS (ILMN) workflow for customer convenience and bundled with cloud-based push-button bioinformatics equipped with tools for sensitive genome-wide and targeted translocation discovery. We also propose rigorous and essential product development experiments, to ensure commercialization of a robust, premium-performance kit-based product. Upon successful completion of the technical and commercial developments in Aims 1 & 2, we propose to benchmark and validate the sample-to-insight T-Seq Solution through collaboration and prototype (beta) kit and bioinformatics evaluations with key opinion leaders (KOLs) across customer segments of large sequencing centers, academic labs, and pharma.

高灵敏度、可扩展和低输入兼容的基于试剂盒的解决方案的商业化， FFPE肿瘤活检发现易位 Arima Genomics 项目总结/摘要 尽管经过数十年的研究，癌症在美国每年夺走近60万人的生命。癌症 研究界在提高癌症诊断精度方面取得了关键进展， 最近，在肿瘤的遗传谱方面已经投入了大量的努力。具体而言， 一直专注于开发方法来分析遗传改变，如易位，这是预后， 癌个体易位谱的知识可用于揭示易位的机制基础。 癌症，加速癌症研究，以开发新的精确疗法。现行标准， 包括NGS，在它们表征易位的能力方面是有限的。这是因为对于NGS（WGS或基因 panel seq.）为了分析易位，需要跨越断点的读段，而NGS并不富集这种读段。 阅读。FISH通过捕获细胞内基因组的空间构象来富集断裂点信息，但它 由于其低通量性质和其需要易位的先验信息， 伙伴光谱核型分析（SKY）需要活细胞，不能在FFPE样本上进行，这是一个非常困难的方法。 癌症样本的主要样本类型。总之，一种方法是（a）高通量沿着NGS路线; (b)丰富了沿着FISH路线的易位;（c）不需要易位伴侣的先验插入， 能够进行混杂易位检测;以及（d）与FFPE样品相容-将导致高度的 敏感且可扩展的易位发现解决方案。我们通过蛙跳式解决方案满足未满足的需求。 我们使用HiC捕获FISH线上的构象，并将其与NGS（HiC-Seq）偶联以检测 在高灵敏度、高精度、高PPV和低FP下检测易位。我们的团队拥有无与伦比的专业知识， HiC科学及其商业化。具体来说，我们在2018年将Arima-HiC试剂盒商业化， 在表观遗传学研究的背景下研究构象，并在第一年产生了120万美元的收入。 商业化与200+客户，所有从1销售主管.然而，这些套件不兼容 FFPE是手动的，劳动力和时间密集型的，并且不能一次处理>10-20个样品的批次-以使 广泛采用对癌症研究，我们已经显示了发展的盒装试剂盒，“T-Seq试剂盒”，基于 基于针对性能、速度、易用性进行优化的增强型HiC，兼容低输入FFPE、新鲜 冷冻样品。我们在患者源性FFPE中验证了从样本到洞察力的技术发展 GIST活检，并证明我们可以敏感地分析易位，即使是从低肿瘤纯度样本 (or低MAF）。作为这个直接-2-阶段II计划的一部分，我们建议进一步发展我们的技术， 稳健的基于试剂盒的“T-Seq解决方案”，包括同一天8小时样品测序，全96板自动化， 通用HiC协议（适用于所有样品类型），与客户现有的NGS（ILMN）工作流程兼容 方便，并与基于云的按钮生物信息学捆绑，配备了敏感的 全基因组和靶向易位发现。我们还提出了严格和必要的产品 开发实验，以确保一个强大的，优质性能的试剂盒为基础的产品的商业化。 在目标1和目标2的技术和商业发展顺利完成后，我们建议 通过协作和原型（beta）套件对样本到洞察的T-Seq解决方案进行基准测试和验证 与大型测序客户群中的关键意见领袖（KOL）进行生物信息学评估 中心、学术实验室和制药公司。