Advancements in minimal residual disease (MRD) detection have led to more sensitive cell-free DNA assays applicable across lymphoma subtypes, according to Reid W. Merryman, MD, instructor in medicine at Harvard Medical School and an attending physician at Dana-Farber Cancer Institute.
Evolution of MRD Assays in Lymphoma
Merryman noted that while MRD assays like flow cytometry and PCR have been used for decades in lymphoma subtypes with circulating components or chromosomal rearrangements, high throughput sequencing has broadened the use of circulating tumor DNA (ctDNA) across all lymphoma subtypes. The key to this development has been increasing the number of tumor reporters to improve sensitivity.
Using diffuse large B-cell lymphoma (DLBCL) as a focal point, Merryman discussed three categories of MRD assays: immunoglobulin high throughput sequencing (IgHTS), panel-based assays, and emerging assays.
IgHTS Assays
IgHTS assays track 1 to 5 tumor reporters, identifying tumor-specific clonotypes. Studies in DLBCL have shown that ctDNA assessments using this approach are associated with disease bulk, and dynamic changes over time correlate with PET response and progression-free survival. However, IgHTS has a modest lead time of just under 4 months, which may limit its utility in guiding therapy.
Panel-Based Assays
Panel-based assays, such as cancer personalized profiling by deep sequencing (CAPP-seq), track dozens of tumor reporters. These disease-specific panels of mutations offer improved sensitivity compared to IgHTS. A study comparing CAPP-Seq with immunoglobulin sequencing in DLBCL showed that CAPP-Seq had a higher likelihood of identifying a tumor genotype, pretreatment ctDNA, and ctDNA at relapse. Another study demonstrated that pretreatment ctDNA levels were prognostic of patient outcomes. However, an analysis using plasma samples from the phase 3 POLARIX trial showed that the prognostic value of these assays was best at the end of the trial, which is not ideal for affecting treatment decisions early on. In this study, 3-year PFS rates were modestly better in patients with negative ctDNA (81%) compared to those with positive ctDNA (51%).
Emerging Assays
Newer assays maximize tumor reporters by using phased variants or whole genome sequencing (WGS), tracking hundreds or even thousands of tumor reporters to maximize sensitivity. PhasED-seq, a newer ctDNA assay, takes advantage of phase variants, where multiple mutations occur on a single DNA molecule in close proximity. Research has shown that PhasED-seq has improved sensitivity compared with CAPP-Seq. Another novel MRD assay is the whole-genome sequencing MAESTRO assay, which uses short allele-specific probes to enrich thousands of prespecified mutations and enable their detection using Duplex Sequencing with up to 100-fold fewer sequencing reads. A pilot study has shown high sensitivity of MAESTRO as a marker of relapse in patients with DLBCL.
Clinical Implications
Merryman concluded that novel assays have improved the sensitivity of ctDNA detection in lymphoma, leading to clinical trials that adapt therapy based on ctDNA results.
