A new liquid biopsy test could help determine which patients are likely to respond to immune checkpoint inhibitors, according to a paper published today in Clinical Cancer Research by researchers at Personal Genome Diagnostics and Johns Hopkins.
Keytruda, an immune checkpoint inhibitor, has been approved for patients with unresectable or metastatic tumors that tested high for microsatellite instability (MSI-H or MSI-high) or mismatch repair deficiency (dMMR). However, detecting MSI-H and dMMR status is often challenging. Currently, MSI is detected using tissue biopsies and technologies such as PCR-based amplification or next-generation sequencing. These processes are complicated and have sensitivity limitations, and certain tumor samples lack enough tissue for accurate testing, explained the study's lead author Andrew Georgiadis.
"A liquid biopsy test assessing MSI could reach a larger subset of patients, such as those where tissue is limited or where there are safety concerns around additional surgical intervention," he added.
To evaluate the sensitivity and specificity of a liquid biopsy approach developed by Personal Genome Diagnostics, the team developed a 98 kb pan-cancer 58-gene panel, then employed a multifactorial error-correction method and a novel peak-finding algorithm to identify MSI frameshift alleles in cell-free DNA (cfDNA). The study was based on 61 patients with advanced cancer and 163 plasma samples from healthy individuals.
The authors explained that MSI can be detected by measuring the length of altered microsatellite sequences in tumor DNA as compared with normal DNA. In this study, the researchers flagged certain sequence data for error correction, then subjected the data to a peak-finding algorithm that identified instability in the loci. If 20 percent or more of the loci were determined to have MSI, the samples were classified as MSI-high.
For tumor mutational burden, NGS data were processed, and variants were identified using the VariantDx software. The researchers set five mutations in the targeted plasma panel as the threshold for identifying tumors as having exceptionally high mutational burden.
For MSI, the test produced a specificity of greater than 99 percent, and a sensitivity of 78 percent. For TMB, the test produced a specificity of greater than 99 percent, and a sensitivity of 67 percent.
The researchers also obtained plasma from 29 patients with metastatic cancers, including colorectal, ampullary, small intestine, endometrial, gastric, and thyroid. Among these, archival tissue-based analysis classified 23 cases as MSI-high and six cases as microsatellite stable. The VariantDx test detected high MSI in 18 of the 23 MSI-high patients (78.3 percent), and correctly identified the six microsatellite stable cases.
The researchers found that direct detection of MSI in baseline cfDNA was associated with progression-free survival of patients who were being treated with immune checkpoint blockade. Improvements in overall survival were not statistically significant.