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

将高度敏感、可扩展且低投入兼容的基于套件的解决方案商业化 从FFPE肿瘤活检中发现易位 ARIMA基因组学 项目摘要/摘要 尽管进行了数十年的研究，但在美国，癌症每年夺去近60万人的生命。癌症 研究界在提高癌症诊断和治疗的精确度方面取得了重大进展 最近，人们在肿瘤的基因图谱方面进行了大量的努力。具体地说，已经做出了努力 一直专注于开发方法来描述基因改变，如可预测预后的易位 癌症。对个体易位特征的了解可以用来揭示 癌症，加速癌症研究向新的精确疗法的发展。现行标准， 包括NGS在内，它们表征易位的能力有限。这是因为对于NGS(WGS或基因 面板顺序。)要分析易位，需要跨越断点的读取，而NGS不会对此进行丰富 阅读。FISH通过捕捉细胞内基因组的空间构象丰富了断点信息，但它 由于其低吞吐量的性质以及其对移位的先验信息的要求，其实用性有限 合伙人。光谱核型分析(Sky)需要活细胞，不能在FFPE样本上进行，这是一种 癌症样本的主要样本类型。总而言之，这是一种方法，即(A)沿着NGS的路线进行高吞吐量； (B)丰富了沿鱼线的易位；(C)不需要先验的印度支那将伙伴转移到 启用混杂易位检测；以及(D)与FFPE样本兼容-将导致高度 用于移位发现的敏感且可扩展的解决方案。我们通过越级解决方案满足了未得到满足的需求。 我们使用HIC来捕获鱼的线条上的构象，并将其与NGS(HIC-Seq)相耦合来检测 高灵敏度、高精度、高PPV和低FP的易位。我们的团队在以下方面拥有无与伦比的专业知识 HIC的科学及其商业化。具体地说，我们在2018年将ARIMA-HIC套件商业化 在表观遗传学研究的背景下研究构象，并在年第1年创造了120万美元的收入 拥有200名客户的商业化，全部由一名销售主管完成。但是，这些工具包与 FFPE是人工、劳力和时间密集型的，并且不能一次处理10-20批次的样品-以实现 广泛采用癌症研究，我们已经展示了一个盒装试剂盒，“T-Seq试剂盒”，基于 增强型HIC针对性能、速度和易用性进行了优化，兼容低输入FFPE、Fresh 和冰冻的样本。我们在患者衍生的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的样本 (或低MAF)。作为DIRECT-2-阶段II计划的一部分，我们建议将我们的技术进一步开发为 强大的套件为基础的“T-Seq解决方案”，包括当天8小时样本到测序，全96版自动化和 与客户现有NGS(ILMN)工作流程兼容的多功能HIC协议(适用于所有样本类型) 方便，并捆绑了基于云的按钮生物信息学配备的敏感工具 全基因组和定向易位发现。我们还提出了严谨和必要的产品 开发实验，以确保基于强大、高性能套件的产品的商业化。 在成功完成目标1及2的技术及商业发展后，我们建议 通过协作和原型(测试版)套件对样本到洞察力T-Seq解决方案进行基准测试和验证 以及与关键意见领袖(KOL)对大型排序客户群进行生物信息学评估 中心、学术实验室和制药公司。

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.