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

“10万人基因组计划”和其他类似的努力已经清楚地表明，包括癌症在内的许多疾病过程都是由被称为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无法在同一实验中在任何时间可靠地检测到所有这些DNA变化。因此，将获得性DNA突变与来自同一组织的DNA甲基化结合起来同时进行鉴定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，比如一种叫做亚硫酸氢盐测序（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，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作为起始材料，而这些材料通常很难获得，尤其是从来自小型癌症活检的临床组织中。这对于所谓的“液体活组织检查”的分析来说是一个特别的挑战，这种检查是从简单的抽血中获得的，含有少量循环肿瘤DNA。液体活检是一种非侵入性的方法，将来可能用于更早地诊断癌症，并监测癌症患者是否对治疗有反应。与癌症组织活检相反，液体活检可以很容易地重复多次。Base Genomics开发了一种名为“TAPS”的全新方法，可以同时检测DNA突变和DNA甲基化，不会破坏DNA，因此可以在单次测序实验中从少量DNA中灵敏地检测获得的DNA变化。与现有方法相比，TAPS还能以更低的测序成本提供更精确的结果。在这里，我们将利用基因组学英国癌症试点的样本和WGS数据。在第一组实验中，我们专门将TAPS与现有的早期癌症患者液体活检方法进行比较，以测试TAPS在检测癌症组织特异性液体活检的DNA突变和DNA甲基化变化方面是否更优越。如果是这样的话，我们将在更大的队列中进行测试，看看TAPS是否能通过液体活检正确识别癌症患者。总之，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.