SBIR Phase I: High-Throughput Multi-Analyte ChIP Assay Development

该小企业创新研究（SBIR）一期项目旨在开发一种高通量、多分析物染色质免疫沉淀（ChIP）系统。ChIP是一种广泛应用于生命科学和生物医学研究的技术，用于绘制DNA结合蛋白结合的特定DNA序列。它的应用范围从单基因分析到使用下一代测序（NGS）技术作为读出的全基因组应用。正如设想的那样，所提出的技术将把冗长而繁琐的多日芯片转变为高通量兼容的单日实验。该技术将导致将含有NGS平台兼容标签和“条形码”序列的寡核苷酸插入与免疫沉淀抗体相关的DNA片段中。每个抗体将与一个独特的条形码相关联，也可用于直接DNA测序或PCR分析。该方法的可行性将通过系统地确定将含有寡核苷酸的条形码插入染色质的最佳条件，然后与抗体偶联的寡核苷酸结合来实现。最终验证将在基因组尺度上使用NGS进行，将新方法产生的文库的基因组表示与传统ChIP的基因组表示进行比较。这个项目的广泛影响/商业潜力是深远的。生命科学研究工具市场目前估计为420亿美元，由于研究人员购买商业表观遗传产品而不是花费时间和精力在内部开发它们，以及NGS的进步，加速了全基因组表观遗传分析，表观遗传领域正在经历高速增长。高通量、多分析物芯片的成功开发将对生命科学和生物医学研究领域的科学和商业产生重大影响。在推出后不到五年的时间里，它预计将取代传统的ChIP，后者占表观遗传学研究工具市场的20-25%，预计2010年市场规模为1.75 - 2.45亿美元。这种方法的发展将通过消除技术障碍，并通过显着减少与传统ChIP相关的样本量要求，包括单细胞分析的潜力，向几乎所有研究人员开放表观遗传分析。这项技术的发展将刺激其他新技术的创造，如用于高通量筛选的均质ChIP，多分析物ChIP，并为环境，营养和毒理学学科打开大门，以在基因组范围内研究任何真核生物的表观遗传谱。

This Small Business Innovation Research (SBIR) Phase I project proposes to develop a high-throughput, multi-analyte chromatin immunoprecipitation (ChIP) system. ChIP is a widely used technique among life science and biomedical researchers seeking map the specific DNA sequences that are bound by a DNA binding protein. Its use ranges from single gene analysis through to genome-wide applications that use next generation sequencing (NGS) technologies as readout. As envisioned, the proposed technology will transform the lengthy and cumbersome multi-day ChIP into a high throughput compatible single-day experiment. The technology will result in the insertion of oligonucleotides containing NGS platform-compatible tags and "bar-code" sequences into DNA fragments associated with the immunoprecipitating antibodies. Each antibody will be associated with a unique barcode that can also be used for direct DNA sequencing or PCR analysis. Feasibility of this approach will be achieved by systematic identification of optimal conditions for insertion of the bar-code containing oligonucleotides into chromatin, and then, with antibody-coupled oligonucleotides. Final validation will be performed at the genome scale using NGS to compare the genomic representation of the library produced by the novel method with that of traditional ChIP. The broader impact/commercial potential of this project is far reaching. The life sciences research tools market is currently estimated at $42 billion, with the epigenetic sector experiencing high growth fueled by researchers purchasing commercial epigenetic products rather than spending the time and effort to develop them in-house, and by advances in NGS, which has accelerated genome-wide epigenetic analyses. Successful development of the high-throughput, multi-analyte ChIP will have significant impact scientifically and commercially in the life sciences and biomedical research arenas. In less than five years post-launch, it is projected to replace traditional ChIP, which represents 20-25% of the epigenetic research tools market estimated at $175-245M in 2010. The development of this method will open epigenetic analysis to virtually all researchers by eliminating technical barriers, and by significantly reducing sample size requirements associated with traditional ChIP, including a potential for single cell analysis. Development of this technology will spur the creation of additional novel technologies such as homogeneous ChIP for high throughput screening, multi-analyte ChIP, and open the door for environmental, nutrition, and toxicology disciplines to study the epigenetic profiles of any eukaryotic organism on a genome wide scale.