Cell-Free DNA Sequencing Highly Concordant With Tissue-Based Testing in the Detection of Microsatellite Instability Status


Key Points

  • Incorporation of pan-cancer MSI detection into the 74-gene panel Guardant360 liquid biopsy assay showed high concordance with matched tissue samples in nearly 1,000 patients.
  • The study results show that a liquid biopsy test has the potential to expand access to both targeted therapy and immunotherapies to patients with advanced cancer, including for those patients in whom current tissue-based testing paradigms are inadequate

Microsatellite instability (MSI) is an important predictive biomarker of response to immune checkpoint blockade in solid cancers. However, despite recommendations by clinical practice guidelines, MSI is often not assessed, usually due to tissue insufficiency, unavailability, or infeasibility. Although noninvasive blood-based methods have been developed to detect MSI, they have had limited sensitivity in detecting MSI.

A study by Willis et al published in Clinical Cancer Research investigated the accuracy of MSI detection using the 74-gene panel Guardant360 liquid biopsy assay in comparison to standard-of-care tissue-based testing among patients with advanced cancer. Results showed that the liquid biopsy assay was highly concordant with tissue-based testing in nearly 1,000 patients. The study results show that liquid biopsy has the potential to expand access to both targeted therapy and immunotherapies to patients with advanced cancer.

Study Methodology

To develop a pan-cancer MSI detection panel, the researchers identified 90 relevant microsatellite loci to include in the Guardant360 panel. The assay was analytically validated according to established guidelines, and clinically validated using 1,145 cell-free DNA (cfDNA) samples for which tissue MSI status based on standard-of-care tissue testing was available. The landscape of cfDNA-based MSI across solid tumor types was investigated in a cohort of 28,459 clinical plasma samples.

In addition, the researchers evaluated the clinical outcomes of 16 patients with metastatic gastric cancer that had previously progressed following standard of care chemotherapy. The patients had MSI-high tumors that were detected using liquid biopsy and were treated with either pembrolizumab (15 patients) or nivolumab (1 patient).


The researchers found that cfDNA MSI evaluation was shown to have high specificity, precision, and sensitivity, with a limit of detection of 0.1% tumor content. In evaluable patients, cfDNA testing accurately detected 87% (71 of 82 samples) of MSI-high tissue and 99.5% of microsatellite-stable tissue (863 of 867), for an overall accuracy of 98.4% (934 of 949) and a positive predictive value of 95% (71 of 75). Concordance of cfDNA MSI with tissue polymerase chain reaction and next-generation sequencing was significantly higher than immunohistochemistry. Prevalence of cfDNA MSI for major cancer types was consistent with those reported for tissue-based testing. Robust clinical activity of immunotherapy treatment was seen in patients with advanced gastric cancer positive for MSI as detected by cfDNA, with 63% (10 of 16) of patients achieving complete or partial remission with sustained clinical benefit.

Clinical Relevance

“The results from our study show that Guardant360, a liquid biopsy test, can deliver valid MSI-high results that can be used to guide treatment planning for patients with advanced cancer,” said study author Martina I. Lefterova, MD, PhD, Medical Director and Clinical Laboratory Director of Guardant Health, in a statement. “The addition of MSI detection increases the utility of the assay to direct clinicians beyond targeted therapies to include immunotherapies…our results show that MSI detection in blood samples is not only possible, but valid and informative for immunotherapy selection in patients with a wide range of advanced solid tumors.”

Disclosure: Funding for this study was provided by Guardant Health. For full disclosures of the study authors, visit

The content in this post has not been reviewed by the American Society of Clinical Oncology, Inc. (ASCO®) and does not necessarily reflect the ideas and opinions of ASCO®.