Molecular Kits and Software for Lymphoid Malignancy Work-ups

项目总结 项目名称：淋巴系恶性肿瘤的分子试剂盒和软件 组织：GigaGen Inc. 派：大卫·S·约翰逊，博士。 这项第二阶段SBIR建议的具体目标是开发四个仅供研究使用(RUO)多路传输 用于全面淋巴系统恶性肿瘤病理检查的分子试剂盒。 与下一代测序(NGS)相结合的多路扩增在以下方面有很大的等待市场 淋巴系恶性肿瘤的病理，与当前相比，显著降低了材料和劳动力成本 方法：Kerschmann，Zehnder和Negrin los博士)。例如，目前对白血病的研究 寡克隆需要费力的定制，每个对象的成本高达5000美元，周转时间为 几个星期。每年大约有175,000例新的淋巴系统恶性肿瘤，每次检查需要1000美元，我们 据估计，仅在美国，我们的套件的年市场就达到1.75亿美元。由此带来的技术创新 来自第一阶段SBIR项目(Johnson等人，2012年)的是一个生物信息学系统，用于“清洁” 困扰多重剧目扩增的非代表性扩增(Robins等人，2012年)。这个 这一拟议的SBIR二期项目带来的市场创新将提供更快和更便宜的 使用免疫谱系分析的淋巴恶性肿瘤检查系统(“GigaMune(R)hemeOnc”)。 在第二阶段，我们将采取以下步骤开发GigaMune(R)hemeOnc：(I)制造四个原始的 设备制造商(OEM)分子试剂盒，包括扩增母体混合物、扩增引物、 清理试剂和阳性对照混合物；(Ii)实施基于网络的分析、QC和QA软件 四个分子试剂盒；以及(Iii)使用来自美国病理学家学会(CAP)的参考样本 量化试剂盒和软件的分析有效性。如果我们能做到这一点，我们的二期工程就会成功。 实现以下里程碑：(I)在GigaGen的10次重复运行中，OEM试剂盒应该扩增出质粒 阳性对照混合使得克隆类型低至0.1%具有平均变异系数 (CV)20%(功率=0.8，？=0.05)，并且在接收器操作员特性曲线(AUC)下有面积 大于0.8(功率=0.8，？=0.05)；以及(Ii)在三个测试点的15次重复运行中，OEM套件 应该放大参考样本，使克隆类型低至0.1%的平均变异系数为20% (功率=0.8，？=0.05)，AUC大于0.8(功率=0.8，？=0.05)，故障率&2%。 在第二阶段完成后，我们将向病理实验室销售Ruo GigaMune(R)HemeOnc试剂盒和软件 全世界。这些试剂盒和软件将是同类中最好的，并有助于临床研究和开发 CLIA实验室开发的测试(LDT)。在未来，我们将探索构建GigaMune(R)的优势 进入FDA批准的体外诊断(IVD)试剂盒。目前，IVD路线是不可能的，因为 目前还没有FDA批准的NGS系统可以与GigaMune(R)一起使用 HeameOnc.

PROJECT SUMMARY Project Title: Molecular Kits and Software for Lymphoid Malignancy Work-ups Organization: GigaGen Inc. PI: David S. Johnson, Ph.D. The Specific Aim of this Phase II SBIR proposal is to develop four research use only (RUO) multiplexed molecular kits for comprehensive lymphoid malignancy pathology work-ups. Multiplexed amplification coupled with next generation sequencing (NGS) has a large awaiting market for pathology of lymphoid malignancy, significantly decreasing material and labor costs compared with current methods (Drs. Kerschmann, Zehnder, & Negrin LOS). For example, current work-ups for leukemia oligoclonality require laborious customization, cost up to ~$5000 per subject, and have a turnaround time of several weeks. With around 175,000 new lymphoid malignancies per year, and $1000 per work-up, we estimate that the annual market for our kits in the US alone is ~$175 million. The technical innovation resulting from the Phase I SBIR project (Johnson et al., 2012) was a bioinformatics system for "cleaning" the nonrepresentative amplification that plagues multiplexed repertoire amplification (Robins et al., 2012). The market innovation resulting from this proposed Phase II SBIR project would be to provide a faster and cheaper system for lymphoid malignancy work-ups that use immune repertoire analysis ("GigaMune(R) HemeOnc"). In Phase II, we will take the following steps to develop GigaMune(R) HemeOnc: (i) manufacture four original equipment manufacturer (OEM) molecular kits that include amplification master mix, amplification primers, clean-up reagents, and positive control mixes; (ii) implement web-based analysis, QC, and QA software for the four molecular kits; and (iii) use reference samples from the College of American Pathologists (CAP) to quantify the analytical validity of the kits and software. We will be successful in our Phase II project if we achieve the following milestones: (i) across 10 replicate runs at GigaGen, the OEM kits should amplify plasmid positive control mixes such that clonotypes present as low as 0.1% have an average coefficient of variation (CV) of <20% (power=0.8, ¿=0.05) and with an area under the receiver operator characteristic curve (AUC) greater than 0.8 (power=0.8, ¿=0.05); and (ii) across 15 replicate runs at three testing sites, the OEM kits should amplify reference samples such that clonotypes present as low as 0.1% have an average CV of <20% (power=0.8, ¿=0.05) and with an AUC greater than 0.8 (power=0.8, ¿=0.05) and a failure rate <2%. After Phase II is complete, we will market the RUO GigaMune(R) HemeOnc kits and software to pathology labs worldwide. These kits and software will be best in class and facilitate clinical research and development of CLIA laboratory-developed tests (LDTs). In the future, we will explore the advantages of building GigaMune(R) HemeOnc into an FDA-cleared in vitro diagnostic (IVD) kit. For now, the IVD route is not possible, because there are currently no FDA-cleared NGS systems that could be used in conjunction with GigaMune(R) HemeOnc.