Base Genomics: A novel method for single-step, ultra-sensitive, combined DNA methylation and mutation detection of cancer from liquid biopsies using WGS

10万基因组计划和其他类似的努力清楚地表明，包括癌症在内的许多疾病过程是由称为DNA的组织遗传物质的后天变化引起的。有许多不同类型的DNA变化，如“DNA突变”和“DNA甲基化”。然而，目前可用的测序方法都不能可靠地在同一实验中的任何时间检测到所有这些DNA变化。因此，从同一组织中同时识别获得的DNA突变以及DNA甲基化被认为是癌症诊断和学术研究的“圣杯”。现有的检测DNA甲基化的方法，如被称为“亚硫酸氢盐测序”(BS)的方法，会破坏大部分DNA。这意味着这些方法不是很敏感，结果往往仍然不确定，而且测序过程非常昂贵。重要的是，这也意味着这些方法需要更多的DNA作为初始材料，而这些材料往往很难获得，特别是来自小型癌症活检的临床组织。这对于分析所谓的“液体活组织检查”来说是一个特别的挑战，所谓的“液体活组织检查”是通过简单的抽血获得的，含有少量循环中的肿瘤DNA。液体活组织检查是一种非侵入性的方法，将来可能被用来更早地诊断癌症，并监测癌症患者是否对治疗有反应。与癌症组织活组织检查相反，液体活组织检查可以很容易地重复多次。基础基因组学已经开发出一种全新的方法，即同时检测DNA突变和DNA甲基化，不破坏DNA，因此允许在一次测序实验中从少量DNA中灵敏地检测到获得性DNA变化。与现有的方法相比，TAPS还能以更低的测序成本提供更准确的结果。在这里，我们将使用来自基因组学英国癌症试点的样本和WGS数据。在第一组实验中，我们专门使用早期癌症患者的液体活检将TAP与现有方法进行比较，以测试TAP是否在检测特定于癌症组织的液体活检的DNA突变和DNA甲基化变化方面具有优势。如果是这样的话，我们将继续在更大的队列中测试TAPs是否可以正确地从液体活检中识别癌症患者。同时，这些实验将证明TAPS是一种非常有前途的学术研究和临床癌症诊断工具。

The 100,000 Genome Project and other similar efforts have clearly demonstrated that many disease processes including cancer, are caused by acquired changes in the genetic material of tissue called DNA. There are many different types of DNA changes such as "DNA mutations" and "DNA methylation". However, none of the currently available sequencing methods reliably detects all of these DNA changes at any one time in the same experiment. The combined and simultaneous identification of acquired DNA mutations together with DNA methylation from the same tissue is therefore considered as the "holy grail" of cancer diagnostics and academic research.Existing methods to detect DNA methylation such as a method called "bisulfite sequencing (BS)" destroy most of the DNA. It means that these methods are not very sensitive, results remain often uncertain and the sequencing process is very expensive. Importantly, it also means that these methods require more DNA as starting material which is often difficult to obtain, especially from clinical tissue that comes from small cancer biopsies. This is a particular challenge for the analysis of so called "liquid biopsies" that are obtained from a simple blood draw and that contain small amounts of circulating tumour DNA. Liquid biopsies are a non-invasive method that might be used in future to diagnose cancer much earlier and also to monitor whether patients with cancer respond to therapy as -contrary to cancer tissue biopsies- liquid biopsies can be repeated easily many times.Base Genomics have developed a completely novel method called "TAPS" that simultaneously detects DNA mutations and DNA methylation, does not destroy DNA and that therefore allows sensitive detection of acquired DNA changes in a single sequencing experiments from low amounts of DNA. Compared to existing methods, TAPS also provides more precise results at lower sequencing costs.Here, we will make use of samples and WGS data from the Genomics England Cancer Pilot. In the first set of experiments, we specifically compare TAPS to existing methods using liquid biopsies from patients with early stage cancer to test whether TAPS is superior in detecting both DNA mutations and DNA methylation changes from liquid biopsies that are specific to cancer tissue. If this is the case, we will go on to test in a larger cohort, whether TAPS can correctly identify patients with cancer from liquid biopsies.Together, these experiments will demonstrate TAPS as a highly promising tool for academic research and clinical cancer diagnostics.