From Somatic Variants Toward Precision Oncology: An Investigation of Reporting Practice for Next-Generation Sequencing-Based Circulating Tumor DNA Analysis

Abstract

Background: With the accelerated development of next-generation sequencing (NGS), identified variants, and targeted therapies, clinicians who confront the complicated and multifarious genetic information may not effectively incorporate NGS-based circulating tumor DNA (ctDNA) analysis into routine patient care. Consequently, standardized ctDNA testing reports are of vital importance. In an effort to guarantee high-quality reporting performance, we conducted an investigation of the current detection and reporting practices for NGS-based ctDNA analysis.

Materials and methods: A set of simulated ctDNA samples with known variants at known allelic frequencies and a corresponding case scenario were distributed to 66 genetic testing laboratories for ctDNA analysis. Written reports were collected to evaluate the detection accuracy, reporting integrity, and information sufficiency using 21 predefined criteria.

Results: Current reporting practices for NGS-based ctDNA analysis were found to be far from satisfactory, especially regarding testing interpretation and methodological details. Only 42.4% of laboratories reported the results in complete concordance with the expected results. Moreover, 74.2% of reports only listed aberrations with direct and well-known treatment consequences for the tumor type in question. Genetic aberrations for which experimental agents and/or drug access programs are available may thus be overlooked. Furthermore, methodological details for the interpretation of results were missing from the majority of reports (87.9%).

Conclusion: This proof-of-principle study suggests that the capacity for accurate identification of variants, rational interpretation of genotypes, comprehensive recommendation of potential medications, and detailed description of methodologies need to be further improved before ctDNA analysis can be formally implemented in the clinic.

Implications for practice: Accurate, comprehensive, and standardized clinical sequencing reports can help to translate complex genetic information into patient-centered clinical decisions, thereby shepherding precision oncology into daily practice. However, standards, guidelines, and quality requirements for clinical reports of next-generation sequencing (NGS)-based circulating tumor DNA (ctDNA) analysis are currently absent. By using a set of simulated clinical ctDNA samples and a corresponding case scenario, current practices were evaluated to identify deficiencies in clinical sequencing reports of ctDNA analysis. The recommendations provided here may serve as a roadmap for the improved implementation of NGS-based ctDNA analysis in the clinic.

Keywords: Circulating tumor DNA; Clinical reports; Next-generation sequencing; Quality control; Standardization.

Figure 1

Preparation of the simulated ctDNA samples. (A): The validation results of our simulated ctDNA samples by using capillary electrophoresis. (B): The validation results of our simulated ctDNA samples by using digital PCR. Abbreviation: dPCR, digital polymerase chain reaction; MAF, mutant allele frequency.

Figure 2

The distribution of laboratories in different characteristics. (A): The distribution of laboratories using different targeted enrichment strategies. (B): The distribution of laboratories using specific sequencing platforms. (C): The distribution of laboratories with different limit of detection. Abbreviation: PCR, polymerase chain reaction.

Figure 3

Overview of the whole reporting performance of 66 participants. (A): The scoring record of the written reports from 66 participating laboratories. (B): The detail reporting performance of 66 participating laboratories. Abbreviation: ID, identifier.

Figure 4

Overview of the performance for qualitative detection. The testing results of each laboratory are indicated by columns. A blue box indicates that the intended variants were correctly reported; a gray box indicates that the intended variants were not reported as the expected variant beyond the specific detectable range or lower than the validated limit of detection (LOD); a yellow box stand for a false‐negative result; a red box stand for a false‐positive result; an orange box stand for the result lower than LOD. The allele frequencies reported are shown inside the boxes.

Figure 5

An overview of the critical elements next‐generation sequencing (NGS)‐based circulating tumor (ctDNA) analysis. (A): The importance of clinical reports in NGS‐based ctDNA analysis. (B): The critical elements for a comprehensive ctDNA analysis report. Abbreviation: HGVS, Human Genome Variation Society.