Abstract 2297: Sensitive mutation detection by simultaneous targeted sequencing of the Watson and Crick strands
Authors: Kebede Firaol T. , Bian Weiwei , Cho William C. , Zheng Zongli 
Published: June 2023

Background Detecting mutations in circulating cell-free DNA (ccfDNA) allows for non-invasive monitoring of tumors, however, is hampered by low fractions of tumor DNA and low efficiencies of current technologies.

Methods We describe a new and simple method for simultaneous multiplex targeted next-generation sequencing (NGS) of the Watson and Crick strands. We also develop a custom bin-based algorithm and unique molecule identifier (UMI)-aware data algorithm to segregate and suppress background noises. The performance of the method was evaluated with a reference standard DNA that contains 44 mutations, and experimented with dilutions for low mutant allele frequencies (MAFs) and with various amounts of DNA inputs. We validated our methods using blood samples collected from lung cancer patients with various stages and at follow-ups. A commercial droplet digital PCR (ddPCR) for a seven-plex KRAS mutation detection assay was used as an orthogonal method to validate the sensitivity and specificity of our NGS methods.

Results Using merely 1 ng of DNA (300 genome equivalent) containing 44 known mutations at 1% minor allele frequencies (MAFs) across 19 genes, our method detected 43 known and 0 false mutations, demonstrating a superior enrichment efficiency (&gt; 99%) approaching the theoretical limit that misses target molecules owning to random sampling alone and high specificity. In the analysis of cfDNA obtained from plasma (1 mL per patient) of 77 lung cancer cases, mutations were identified in 47 (61%) of the cancer patients. Using the equal-volume (1 mL) aliquot plasma available from 70 patients (7 cases had insufficient samples), the ddPCR assay showed 6 samples were positive and 64 samples were negative. Among the 6 ddPCR-positive samples, all were tested positive by our NGS method, demonstrating similar sensitivity as the ddPCR assay while having the advantage of the capacity to test a panel of genes. Among the 64 ddPCR-negative samples, our method showed 63 were KRAS-negative and 1 was positive, indicating a specificity of 98.4%. With a detailed examination of the “false-positive” sample when using the ddPCR as the gold standard, the image of ddPCR result in fact showed two dots in the ‘grey zone’, indicating a possibility of a false-negative ddPCR result for the sample, rather than a false-positive in our NGS method. Using 1 mL of plasma, our method can detect mutation at 0.05% MAF and predict lung cancer relapse prior to current clinical methods.

Conclusion Our new NGS method enables sensitive detection of mutations when only a trace amount of material is available and may be useful for cancer minimal residual disease monitoring.

Citation Format: Firaol T. Kebede, Weiwei Bian, William C. Cho, Zongli Zheng. Sensitive mutation detection by simultaneous targeted sequencing of the Watson and Crick strands [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2297.