Development of a novel whole genome amplification method that mimics nature

描述（由申请人提供）：BioHogs是哈佛医学院的Stanley塔博尔博士和Charles Richardson博士发明的一种新型的、基于引物的全基因组扩增（pWGA）技术的独家许可方。该pWGA系统利用多种复制蛋白，包括引发酶/解旋酶、DNA聚合酶、单链DNA结合蛋白和几种其它辅助蛋白，以实现快速和灵敏的全基因组扩增。因此，将这项新技术从大学实验室推向市场是一项具有挑战性的任务。在第一阶段，我们评估了这项技术的性能，并成功地在大规模生产中纯化了所有必要的蛋白质。我们成功地推出了第一代Rapisome pWGA试剂盒，据我们所知，这是第一个从细胞复制体重建的商业化DNA扩增系统。我们还发现了pWGA平台的其他有利特征。首先，我们已经证明pWGA平台可以实时检测痕量DNA（100 fg）。此外，我们已经证明，与另一种市售WGA产品（来自GE Healthcare的GenomiPhi）相比，pWGA平台在从低拷贝数（100个拷贝）的输入扩增（108倍）环状DNA方面特别有效。二期研究的总体目标是：1）通过优化关键组件和微调每个组件，继续提高pWGA系统的性能（如果成功，将推出具有更低扩增偏倚和更高保真度的第二代pWGA试剂盒）; 2）在上述一期研究的基础上，探索pWGA在生物医学研究和临床诊断中的新应用。基于第一阶段的数据，pWGA的应用可能会扩展到两个新的领域。一个是作为通用DNA检测系统，将开发用于检测生物样品或药物产品中的痕量DNA污染。第二个新应用涉及环状DNA扩增，基于第一阶段的观察，即pWGA可以以极高的效率扩增环状DNA（从100个拷贝到超过1010个拷贝）。我们建议开发pWGA作为靶向环状DNA病毒（如人乳头瘤病毒（HPV））的临床研究和诊断应用的工具。我们将使用pWGA扩增含有HPV的样本，随后使用Luminex系统确定HPV基因型。公共卫生相关性：全基因组扩增（WGA）技术是癌症和遗传研究的有用工具。扩增整个基因组使研究人员能够对给定的样本进行更多的测试。另外两种类型的WGA已经商业化用于研究应用：1）源自聚合酶链反应的方法和2）多重置换扩增（MDA）。Rubicon Genomics公司开发了一种基于PCR的WGA平台Genometics”研究用试剂盒，可通过Sigma-Aldrich获得。通用电气医疗公司以GenomiPhi”的名称销售MDA技术，而Qiagen以RESID-g（R）的名称销售MDA套件。这两种技术都有一定的局限性。基因组测序系统产生短的PCR扩增子，这限制了其在下游应用如RELP、DNA测序和克隆中的使用。此外，它需要多步反应装置。MDA还经常需要在等温DNA扩增之前进行热变性步骤以促进引物退火，这增加了反应设置的复杂性并且可能将突变引入模板中。此外，在MDA中使用随机引物使得其即使在不存在输入模板的情况下也易于非特异性DNA扩增。基于引物的全基因组扩增（pWGA）平台是细胞复制体的体外重建。它进行简单的一步等温全基因组扩增，无需添加引物。pWGA反应比PCR或MDA反应更快。该扩增对输入的DNA模板具有高度的灵敏度和特异性。最小量（100 fg）的输入DNA的扩增可以与背景区分开，这具有被开发成用于检测和定量给定样品中不想要的DNA污染的快速通用DNA检测工具的潜力。与MDA相比，pWGA在扩增环状DNA方面效率高100倍，特别是当输入量有限（100个拷贝）时。我们相信，pWGA的这一特性可用于开发一种高灵敏度的多重检测方法，用于检测和基因分型广谱环状DNA病毒，如人乳头瘤病毒（HPV）和单纯疱疹病毒（HSV）。

DESCRIPTION (provided by applicant): BioHelix is the exclusive licensee for a novel, primase-based Whole Genome Amplification (pWGA) technology invented by Drs. Stanley Tabor and Charles Richardson at Harvard Medical School. This pWGA system utilizes multiple replication proteins including a primase/helicase, a DNA polymerase, a single-stranded DNA binding protein, and several other accessory proteins to achieve rapid and sensitive whole genome amplification. As such, bringing this novel technology from the university laboratory to the market place is a challenging task. During Phase I, we evaluated the performance of this technology and successfully purified all necessary proteins in large production scale. We successfully launched the first generation Rapisome" pWGA kit, which is, to our knowledge, the first commercially available DNA amplification system reconstructed from a cellular replisome. We have also discovered additional advantageous features of the pWGA platform. First, we have shown that the pWGA platform can perform real-time detection of trace amounts of DNA (100 fg). In addition, we have demonstrated that in comparison with another commercially available WGA product (GenomiPhi from GE Healthcare) the pWGA platform is particularly efficient in amplifying (by 108 fold) circular DNA from low copy numbers (100 copies) of input. The overall goal of the Phase II research will be: 1) To continue to improve the performance of the pWGA system by optimizing the key components and fine-tuning each component (if successful, a second-generation pWGA kit with lower amplification bias and higher fidelity will be launched); 2) To explore new applications for pWGA in biomedical research and clinical diagnostics based on the aforementioned studies in Phase I. Based on the phase I data, the applications of pWGA may be expanded into two new areas. One is as a universal DNA detection system, which will be developed for the detection of trace amounts of DNA contamination in biological samples or pharmaceutical products. The second new application is related to circular DNA amplification, based upon the phase I observation that pWGA can amplify circular DNA with extremely high efficiency (from 100 copies to over 1010). We propose to develop pWGA as a tool for clinical research and diagnostic applications targeting circular DNA viruses such as human Papillomavirus (HPV). We will use pWGA to amplify samples containing HPV and subsequently determine the HPV genotype using the Luminex system. PUBLIC HEALTH RELEVANCE: Whole Genome Amplification (WGA) technologies are useful tools for cancer and genetic research. Amplifying the entire genome enables researchers to perform more tests on a given sample than would otherwise be possible. Two other types of WGA have been commercialized for research applications: 1) methods derived from the polymerase chain reaction and 2) multiple displacement amplification (MDA). Rubicon Genomics has developed a PCR-based WGA platform GenomePlex" Kits for Research Use, available through Sigma-Aldrich. GE Healthcare markets the MDA technology under the name GenomiPhi" while Qiagen sells MDA kits under the name REPLI-g(R). Both of these technologies have some limitations. The GenomePlex" system generates short PCR amplicons, which limits its use in downstream applications such as RELP, DNA sequencing, and cloning. In addition, it requires a multiple-step reaction setup. MDA also often requires a heat-denaturation step before isothermal DNA amplification to facilitate primer annealing, which increases the complexity of the reaction setup and may introduce mutations into the template. In addition, the use of random primers in MDA makes it prone to non-specific DNA amplification even in the absence of an input template. The primase-base Whole Genome Amplification (pWGA) platform is an in vitro reconstruction of a cellular replisome. It performs a simple, one-step isothermal whole genome amplification without added primers. The pWGA reaction is more rapid than either PCR or MDA. The amplification is highly sensitive and specific for input DNA template. Amplification of a minimal amount (100 fg) of input DNA can be distinguished from background, which has a potential of being developed into a fast universal DNA detection tool for detection and quantification of unwanted DNA contamination in a given sample. In comparison with MDA, pWGA is 100-times more efficient in amplifying circular DNA, especially when the amount of input is limited (100 copies). We believe that this feature of pWGA can be used to develop a highly sensitive multiplex assay for the detection and genotyping of a broad spectrum of circular DNA viruses, such as human Papillomavirus (HPV) and Herpes Simplex Virus (HSV).