Combining variant detection and fragment length analysis improves detection of minimal residual disease in postsurgery circulating tumour DNA of stage II–IIIA NSCLC patients

Abstract

Stage II–IIIA nonsmall cell lung cancer (NSCLC) patients receive adjuvant chemotherapy after surgery as standard‐of‐care treatment, even though only approximately 5.8% of patients will benefit. Identifying patients with minimal residual disease (MRD) after surgery using tissue‐informed testing of postoperative plasma circulating cell‐free tumour DNA (ctDNA) may allow adjuvant therapy to be withheld from patients without MRD. However, the detection of MRD in the postoperative setting is challenging, and more sensitive methods are urgently needed. We developed a method that combines variant calling and a novel ctDNA fragment length analysis using hybrid capture sequencing data. Among 36 stage II–IIIA NSCLC patients, this method distinguished patients with and without recurrence of disease in a 20 times repeated 10‐fold cross validation with 75% accuracy (P = 0.0029). In contrast, using only variant calling or only fragment length analysis, no signification distinction between patients was shown (P = 0.24 and P = 0.074 respectively). In addition, a variant‐level fragmentation score was developed that was able to classify variants detected in plasma cfDNA into tumour‐derived or white‐blood‐cell‐derived variants with 84% accuracy. The findings in this study may help drive the integration of various types of information from the same data, eventually leading to cheaper and more sensitive techniques to be used in this challenging clinical setting.

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

“…Additionally, the analysis of ctDNA fragments can be used to detect minimal residual disease (MRD) [ 176 ]. The combined analysis of both sequence variant and size fragmentation was reported to improve the stratification of patients into risk groups (low and high risk) for MRD in later-stage lung cancers (Stage II-IIIA) for guiding treatment decisions [ 177 ]. Fragmentomics data have also been used to detect early-stage lung cancer and to classify early-stage cancer patients [ 178 , 179 , 180 ].…”

The use of minimal residual disease in thoracic oncology: Gaps between promises and the on‐the‐ground reality of daily practice

“…Sensitivity can be improved by increasing the number of mutations and signal abundance. tions and methylation, 25,26 (ii) the fragmentation approach, which detects the size of the cf-DNA, 27 (iii) an approach that combines variant calling with analysis of cf-DNA fragment lengths, 28 and (iv)…”

Minimal Residual Disease Monitoring in Radically Treated Non-Small Cell Lung Cancer: Challenges and Future Directions

“…Vessie et al combined fragment length score and variant calling (using the AVENIO surveillance kit) to detect post operative MRD and predict recurrence. 38 A fragmentation score was developed by building a reference database of reads that contained tumor informed mutations and their respective lengths. Patients who had a greater fragmentation score, compared to controls with non-malignant disease, were considered positive for MRD.…”

“…When combined in a validation study of 36 stage II–IIIA NSCLC patients, the fragmentation score and variant calling was more accurate at predicting recurrence in a sample of early NSCLC patients compared to variant calling alone, and fragmentation score alone. 38 Further fragmentomic models are under development. 39 , 40 …”