A novel instrument for high efficiency extraction of circulating nucleic acids

描述(申请人提供)：如果在存在健康细胞的背景DNA以及血清、尿液和粪便样本中固有的污染物的情况下，在体液中能够以足够低的丰度检测到来自垂死肿瘤细胞的循环核酸，则可能产生癌症的早期迹象。能够从体液中富集少量部分完整的肿瘤DNA，同时排除健康细胞中的污染物和背景DNA的方法将是一个很大的优势。如果DNA可以富含发出癌基因激活信号或其他与肿瘤相关的序列特征的序列突变，情况就尤其如此。 我们开发了一种DNA浓缩和提取方法(SCoda)，在其最简单的形式下，承诺增加从体液中提取的DNA的数量和纯度，同时减少处理步骤和成本。SCoda将允许从尿液、粪便或血清等样本中方便地提取核酸生物标记物，用于非侵入性癌症检测和癌症基因组研究。SCoda提供了一种高效浓缩低丰度DNA的方法，同时具有高度的污染物排斥作用。这项技术在法医学和基因组学研究中的应用正在商业化，其价值在这两个领域都得到了证明。 我们的目标是将SCoda技术应用于从血清到粪便的体液中提取循环DNA。我们希望它出色的效率和对污染物的排斥，正如我们的取证工作所证明的那样，将在生物标记物提取方面产生好处。此外，我们计划对SCoda进行修改，以允许对特定的低丰度DNA序列进行浓缩。这将通过改变浓缩机制来实现，这样只会浓缩包含与肿瘤细胞相关的特定序列的DNA片段。这有望提供一种预浓缩工具，能够异常灵敏地检测体液中的肿瘤DNA生物标记物。

DESCRIPTION (provided by applicant): Circulating nucleic acids from dying tumor cells may yield an early indication of cancer if they could be detected at sufficiently low abundance in body fluids in the presence of background DNA from healthy cells as well as contaminants inherent to blood serum, urine, and stool samples. Methods capable of enriching for small quantities of partially intact tumor DNA from body fluids while rejecting contaminants and background DNA from healthy cells would be a great advantage. This would be particularly true, if the DNA could be enriched for sequence mutations that signal oncogene activation or other tumor related sequence signatures. We have developed a method of DNA concentration and extraction (SCODA) that, in its simplest form, promises to increase the amount and purity of DNA extracted from body fluids, while reducing the amount of processing steps and cost. SCODA will allow facile extraction of nucleic acid biomarkers from samples such as urine, stool, or blood serum for non-invasive cancer detection, and for genomic studies of cancer. SCODA provides a means for high efficiency concentration of low abundance DNA with a high degree of contaminant rejection. Applications of this technology to forensics and genomics research are being commercialized, and its value has been proven in both fields. We aim to apply SCODA technology to extraction of circulating DNA from body fluids ranging from blood serum to stool. We expect that its outstanding efficiency and rejection of contaminants, as proven in our forensics work, will yield benefits in biomarker extractions. Furthermore, we plan to make modifications to SCODA that will allow enrichment for specific low abundance DNA sequences. This will be done by altering the concentration mechanism, such that only DNA fragments containing specific sequences relating to tumor cells will be concentrated. This promises to provide a pre-concentration tool that would enable exceptionally sensitive detection of tumor DNA biomarkers in body fluids.