Genotyping Panel Accurately Identifies Biomarkers for Solid Cancers in Plasma

By Will Boggs MD

August 13, 2019

NEW YORK (Reuters Health) - A highly sensitive cell-free DNA (cfDNA) sequencing-based method allows simultaneous determination of microsatellite instability (MSI) status and genomic biomarkers for solid cancers in plasma, researchers report.

National Comprehensive Cancer Network clinical practice guidelines recommend MSI as a biomarker for at least nine cancer types. MSI testing is most commonly performed via polymerase chain reaction (PCR) and/or immunohistochemistry (IHC) analysis of tumor-tissue specimens, but recently next-generation sequencing (NGS) has also been shown to accurately characterize MSI status in tumors.

Dr. Martina I. Lefterova from Guardant Health, in Redwood City, California, and colleagues describe the design and validation of MSI assessment on a cell-free circulating-tumor DNA platform (Guardant360) that also includes a previously validated 74-gene panel.

In analytical sensitivity studies, the 95% limit of MSI detection was determined to be 0.4% at 5 ng input and 0.1% at 30 ng input, the team reports in Clinical Cancer Research, online August 4.

In evaluable patients, the platform accurately detected 87% of tissues with high MSI status and 99.5% of tissues that were microsatellite stable, for an overall accuracy of 98.4% (934/949 samples) and a positive predictive value of 95% (71/75 samples).

Concordance between platform results and tissue MSI status was higher with NGS (239/244, 98.0%) and PCR (450/462, 97.4%) than with IHC (93/112, 83.0%).

When the researchers applied their MSI algorithm to more than 28,000 consecutive advanced-cancer patients' clinical samples tested in their laboratory, 278 samples comprising 16 different tumor types were identified as having high MSI status, which is similar to the overall prevalence of around 1% previously reported for tissues.

MSI status by circulating cfDNA also predicted immunotherapy response. Ten of 16 patients with metastatic gastric cancer who tested MSI-high achieved either complete (three patients) or partial (seven patients) objective responses, with three additional patients with stable disease, after treatment with pembrolizumab or nivolumab after the failure of standard of care chemotherapy. These responses were durable during a median duration of treatment of 39 weeks.

"In summary, we have developed and validated a cfDNA-based targeted NGS panel that accurately assesses MSI status while also providing comprehensive tumor genotyping, allowing pan-solid tumor guideline-complete testing from a single peripheral blood draw with high sensitivity, specificity and precision," the researchers conclude. "Such simultaneous characterization of MSI status and tumor genotype from a simple peripheral blood draw has the potential to expand access to both targeted therapy and immunotherapies to all advanced cancer patients including those for whom current tissue-based testing paradigms are inadequate."

Dr. Sameek Roychowdhury of The Ohio State University, in Columbus, who recently evaluated an NGS-based method for the rapid detection of pan-cancer MSI, told Reuters Health by email, "This is an exciting study showing the potential application of non-invasive liquid biopsy to detect a clinically relevant pattern called MSIH (MSI-high) in patients with advanced cancer. Patients who are positive for this marker can benefit substantially from immune system-boosting therapies."

"In some instances, it's not feasible to test a patient's tumor sample or block of tissue; in these situations, a liquid biopsy can prove helpful," said Dr. Roychowdhury, who was not involved in the study. "One caveat is that the current sensitivity demonstrated in this study is not 100% - 87% of cases (71/82) were correctly identified. Patients who are 'negative for MSIH' by blood test should have a tumor biopsy to make sure they don't have this marker. It's a marker we absolutely don't want to miss."

Dr. Lefterova did not respond to a request for comments.


Clin Cancer Res 2019.