Liquid Biopsies: A Technical Dive into Biology and Innovations

Travis J. Yates, PhD
Field Applications Scientist

Liquid Biopsies: A Technical Dive into Biology and Innovations

If you've been following our series thus far, you've learned that while new and innovative strategies to combat the progression of malignant disease continue to evolve, the field has an unmet need. The reality is that a large number of cancer patients will experience recurrence in the form of metastatic disease within a short period of time following primary tumor treatment. Recent clinical studies show that adjuvant therapeutic intervention following treatment of the primary tumor or once recurrent disease has been identified can provide a greater benefit when caught early (Steeg, 2016). The need for better diagnostic tools to detect molecular residual disease (MRD) and other biological signals in an earlier, non-invasive manner is essential, and Personalis is committed to solving the technological challenges required to develop these tools.

One of these challenges is limitations naturally inherent to the sample format. While liquid biopsy provides a less invasive and possibly more highly compliant method for monitoring patients, the levels of ctDNA present in a given sample may be incredibly low. This could be due to a number of factors, such as tumor indication, as not all malignancies shed DNA at the same rate (Kilgour et al., 2020). Vascularity, location, and other factors have been suggested as reasonings for the differences in shedding potential (Bronkhorst et al., 2019). To accommodate this biological reality, sequencing platforms need to be highly sensitive for utilization in a liquid biopsy approach. One approach that has been taken is advancing bioinformatic pipelines to reduce noise and increase error suppression (Newman et al., 2014 & 2016). Another methodology that is being exploited is the obvious difference in fragment length for ctDNA vs. other fragments of DNA derived from healthy tissues/cells (Underhill et al., 2016). It's exciting to note that not only are sequence mutations being assessed but other biomarker strategies which include assessing methylation, structural alterations, and fragmentation are being explored.

Another point of consideration is the need for genetic evaluation of the patient's primary tumor. In some cases, the primary tumor may not be available due to the indication or sample procurement restrictions. To date, the majority of liquid biopsy assays for MRD utilize a tumor-informed approach. While these tumor informed approaches have been shown to increase sensitivity (the need for which was described earlier) this does require having access to an initial tumor biopsy for analysis. This initial sequencing of the tumor tissue is used to determine a variant profile that will be used to identify the ctDNA within the sample and indicate the presence of MRD (Abbosh et al., 2017; Magbanua et al., 2021; Wan et al., 2020; & Zviran et al., 2020). Therefore, work is being done to develop a tumor agnostic approach that retains the high sensitivity of a tumor informed approach, currently considered the state-of-the-art in ctDNA analysis. A tumor agnostic assay relies on input material (ctDNA) from the plasma only and employs a standard set of alterations. Tumor agnostic approaches may incorporate some of the additional signatures discussed earlier, such epigenomics, to facilitate ctDNA detection (Parikh et al., 2021).

Personalis understands that as precision medicine continues to advance, liquid biopsies will increasingly be utilized in translational research and clinical studies. This is why we have focused our R&D efforts on offering two impactful solutions for the field. First, NeXT Liquid Biopsy™ leverages our proprietary exome-wide sequencing coverage to complement our tissue-based ImmunoID NeXT^® platform for solid tumors. Together, these two assays provide a comprehensive overview of the complexities of tumor dynamics that influences aspects of therapeutic resistance and disease progression (Figure 1).

A final challenge to be addressed for liquid biopsy solutions for MRD is the heterogeneity found within a tumor. This topic is specifically tied to the exact number of variants needed for proper detection of ctDNA within a sample (Pantel et al, 2021). Current applications have a varied number of alterations used to detect the presence of ctDNA within a patient sample, but the number of variants has traditionally been quite low. These variants can also be tumor informed or captured as standard panels (Abbosh et al., 2017; Magbanua et al., 2021; Wan et al., 2020; Zviran et al., 2020; & Parikh et al., 2021). As the field matures, various solutions will become more appropriate for particular situations. Strong efforts in the field from groups like, the Friends of Cancer Research and BloodPAC, have been implemented to try to address particular challenges. These challenges include the ones mentioned previously, which include pre-analytical variables, validation, and standardization on reporting.

What's more, Personalis continues to innovate and address the needs of the oncology community in detecting disease recurrence and making informed treatment decisions. NeXT Personal^TM is a tumor-informed, ultra sensitive assay that allows for a personalized approach to MRD and variant tracking. This liquid biopsy solution for MRD is a multi-modal assay and can be the answer in a multitude of clinical settings.

Contact us to learn more about NeXT Personal and NeXT Liquid Biopsy.

All products described here are for Research Use Only and not for use in diagnostic procedures (except as specifically noted).