e20031 Background: Molecular Residual Disease (MRD) test detects tumor-specific mutations in circulating tumor DNA (ctDNA), which can indicate the risk of tumor recurrence. However, without tumor-specific mutations, detecting mutations in blood tissue alone is extremely challenging due to the low concentration of ctDNA in blood. To address this challenge, we proposed an innovative mutation filtering and calling strategy by simulating noise’s distribution and quality assessment to greatly boost the performance. Methods: We performed 406 pairs of MRD tests on both tumor and blood tissue of postoperative patients with mixed cancer types, including lung, gastrointestinal (GI), hepatobiliary, and pancreatic. Patients that possess one or more tumor-specific mutations in their blood tissue were classified as recurrence high-risk (n = 66), others were classified as recurrence low-risk (n = 340). All sequence data were analyzed using both traditional and proposed method. In the traditional method, VAF threshold, end-reads, multiple-align reads and population frequencies were used as filtering criteria. While in the proposed method, VAF threshold was excluded and two new parameters were introduced: The distribution of variant allele frequency (VAF) of sequencing noise, which simulated 42 healthy individuals’ background noise with conf > 0.995; The normalized proportion of supported unique and total variants, to assess the likelihood of mutations originated from ctDNA. Results: Among 406 patients of mixed tumor types, the traditional approach barely reached a sensitivity of 39.4% and a specificity of 89.1%, while our strategy achieved a sensitivity of 71.2% and a specificity of 80.9%. Particularly among the 92 patients with gastrointestinal tumor, by filtering specific noise caused by the MRD panel (e.g. multi-alignment error of MUC gene family), we further boost the sensitivity from 47.1% to 82.4% with a loss of specificity from 93.3% to 90.7%. Moreover, among 248 patients with lung tumors, the sensitivity and specificity between traditional approach and proposed method were 15.8%, 93.9%, and 52.6%, 90.0% respectively, which might be caused by the low recurrence rate in the patient cohort (19 out of 248). Conclusions: The novel strategy based on simulated noise distribution and read quality assessment surpasses the traditional threshold-based approaches in mutation detection, especially in deep sequencing like MRD tests. The findings of the study indicate that the recurrence monitoring strategy is applicable across various tumor types and exhibits superior performance in GI tumor, albeit with certain limitations. In conclusion, this study boosts the feasibility of MRD as a non-invasive alternative for tissue biopsy by providing a novel mutation filtering strategy, which further strengthen the potential of MRD testing in enhancing cancer patients’ long-term prognosis and treatment.
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