cfDNA Assay Emerges as Viable Option for MSI Detection

Cell-free DNA-based detection of microsatellite instability status was found to be highly concordant with tissue-based MSI testing.

Martina Lefterova, MD, PhD

Cell-free DNA (cfDNA)-based detection of microsatellite instability (MSI) status was found to be highly concordant with tissue-based MSI testing, according to results of an analysis recently published in Clinical Cancer Research.1,2

Findings showed that incorporating MSI detection into the 74-gene panel liquid biopsy assay Guardant360 demonstrated high concordance in approximately 1145 cfDNA samples for which MSI status based on standard tissue testing was available.

“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,” study co-author Martina Lefterova, MD, PhD, laboratory director and medical director at Guardant Health, stated in a press release. “The addition of MSI detection increases the utility of the assay to direct clinicians beyond targeted therapies to include immunotherapies.”

The National Comprehensive Cancer Network’s clinical practice guidelines recommend MSI as a biomarker in at least 9 malignancies: esophageal/esophagogastric cancer, cervical cancer, pancreatic cancer, ovarian cancer, colorectal cancer (CRC), prostate cancer, gastric cancer, cervical cancer, and cholangiocarcinoma.

MSI status is generally tested via standard tissue biopsy; yet, MSI testing is underutilized in clinical practice due to lack of viable tissue, the inherent invasive nature of tissue-based biopsies, and a lack of routine testing. If detected, MSI-high (MSI-H) status is a predictive marker to receive treatment with immunotherapy.

Currently, pembrolizumab (Keytruda) is approved for the treatment of adult and pediatric patients with unresectable or metastatic, MSI-H or mismatch repair deficient (dMMR) solid tumors that have progressed after prior treatment and who have no satisfactory alternative treatment options, as well as for patients with MSI-H or dMMR CRC following progression on a fluoropyrimidine, oxaliplatin, and irinotecan.

The combination of nivolumab (Opdivo) and ipilimumab (Yervoy) is also indicated for the treatment of adult and pediatric patients ≥12 years with MSI-H or dMMR metastatic CRC following progression on a fluoropyrimidine, oxaliplatin, and irinotecan.

To develop a pan-cancer MSI detection panel, investigators identified 90 relevant microsatellite loci to include in the Guardant360 panel. Archived cfDNA or plasma samples from patients with available tissue-based MSI testing results were evaluated using a circulating tumor DNA MSI algorithm. Tissue-based methods included immunohistochemistry (IHC), polymerase chain reaction (PCR), and next-generation sequencing (NGS).

Results showed that cfDNA MSI evaluation was linked with high specificity, precision, and sensitivity, with a limit of detection of 0.1% tumor content. In the 949 unique evaluable patients, cfDNA testing accurately detected 87% of patients reported as having MSI-H tumors, and 99.5% of those having microsatellite stable disease, leading to an overall accuracy rate of 98.4%; the positive predictive value was 95%.

Moreover, compared with IHC, concordance of cfDNA MSI with PCR and NGS was significantly higher.

Researchers also evaluated MSI status using the Guardant360 in 28,459 consecutive samples from patients with advanced cancer. The prevalence of MSI-H in this cohort was assessed across 16 cancer types: bladder carcinoma, breast carcinoma, cholangiocarcinoma, colon adenocarcinoma, cancer of unknown primary, head and neck squamous cell carcinoma, hepatocellular carcinoma, lung adenocarcinoma, lung cancer not otherwise specified, lung squamous cell carcinoma, pancreatic adenocarcinoma, prostate adenocarcinoma, stomach adenocarcinoma, uterine endometrial carcinoma, and "other" cancer diagnosis.

In this cohort, investigators noted 278 samples spanning tumors that had prevalent MSI-H status: endometrial cancers, gastric cancers, and CRC. MSI-H prevalence was low in head and neck cancers, lung cancer, and bladder cancer, demonstrating similarity with existing tissue-based sample data.

Additionally, investigators analyzed the activity in patients with gastric cancer whose tumors were MSI-H and were treated with either pembrolizumab (n = 15) or nivolumab (n = 1) after receiving chemotherapy in a phase II trial (NCT02589496). Results showed that the objective response rate was 63% (95% CI, 36%-84%). Three patients had a complete response and 7 patients had a partial response (n = 7) with sustained clinical benefit, via RECIST 1.1 criteria. An additional 3 patients had stable disease and the disease control rate was 81% (95% CI, 54%-95%).

“Following the tissue-agnostic approval of pembrolizumab for patients with MSI-high tumors, a barrier to improved outcomes for many patients is the awareness and testing of MSI status,” study co-author Scott Kopetz, MD, PhD, associate professor of Gastrointestinal Medical Oncology at The University of Texas MD Anderson Cancer Center and co-author of the study, stated in the press release. “By adding MSI testing into a noninvasive screening panel, clinicians can routinely scan for this prognostic factor without ordering a separate test.”

The study authors concluded that this assay enables highly accurate detection of MSI status that is concurrent with comprehensive genomic profiling, and expands immunotherapy access for those with advanced disease.


  1. Willis J, Lefterova MI, Artyomenko A, et al. Validation of microsatellite instability detection using a comprehensive plasma-based genotyping panel [published online ahead of print August 4, 2019]. Clin Can Res. doi: 10.1158/1078-0432.CCR-19-1324.
  2. Microsatellite Instability Detection Via Liquid Biopsy Test Shows High Concordance With Results From Tissue Samples. American Association for Cancer Research. Published August 5, 2019. Accessed August 5, 2019.