The characteristics of ctDNA reveal the high complexity in matching the corresponding tumor tissues

Abstract

BackgroundNext-generation sequencing (NGS) is an efficient and sensitive method to detect mutations from ctDNA. Many features and clinical conditions could significantly affect the concordance between ctDNA and corresponding tumor tissues. Our goal was to systematically investigate the critical factors contributing to different concordance between ctDNA and corresponding tumor tissues.MethodsWe recruited two groups of IIIB or IV lung cancer patients: The standard group to evaluate the accuracy of our method and the concordance between ctDNA and tumor tissues, and the study group with various clinical conditions. We applied our unique identification (UID) indexed capturing-based sequencing (UC-Seq) to ctDNA samples, and confirm the results by Droplet digital PCR (ddPCR).ResultsConsidering mutations detected from NGS of tumor tissues as golden standard, UC-Seq achieved overall 93.6% sensitivity for SNVs and Indels, and 0.8 Pearson correlation between tumor TMB and bTMB. Efficacious treatments, long sampling date (more than 2 weeks) between tumor tissues and ctDNA and low concentrations of cfDNA (less than 9 ng/ml) could significantly decrease the concordance between ctDNA and tumor tissues. About 84% mutations showed shorter mutant fragment length than that of wild-type fragments, and the AFs of mutations could be significantly enriched in small-size ctDNA.ConclusionsIn late-stage lung cancer patients, ctDNA generally has high concordance with tumor tissues. However it could be significantly affected by three clinical conditions which could dynamically change the content of ctDNA. Moreover, the detection limit could be further extended by enriching small-size ctDNA in the preparation of samples.Electronic supplementary materialThe online version of this article (10.1186/s12885-018-4199-7) contains supplementary material, which is available to authorized users.

Single tube liquid biopsy for advanced non‐small cell lung cancer

“…In 11 of the 16 patients (69%) mutations could be identified in plasma with variant allele frequencies ranging from 0.1% to 5.3%, which is consistent with the respective low z ‐scores. Yet, our concordance rate was slightly lower than those reported for metastatic NSCLC patients that range between 74 and 85% . However, given our small samples size and the low amount of DNA input (which might lead to sampling errors at low variant allele frequencies), our data might not be representative.…”

“…Yet, our concordance rate was slightly lower than those reported for metastatic NSCLC patients that range between 74 and 85%. 39 However, given our small samples size and the low amount of DNA input (which might lead to sampling errors at low variant allele frequencies), our data might not be representative. Nevertheless, these data show that the high-resolution assessment of mutations might yield in increased ctDNA detection rates, and therefore improve patients stratification based on tumor fraction.…”

Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions

“…Reports show that the sensitivity and accuracy of TMB assay results from liquid samples depend on, among other factors, variability in tumor DNA in the blood. ctDNA can have heterogeneous origins and can be altered by treatment, thereby leading to variation in the final TMB score . Several ongoing studies are evaluating reliability of TMB assessment from blood samples and harmonizing tissue and blood‐derived TMB, including use of the bTMB assay developed by Foundation Medicine .…”

Everolimus‐containing therapy vs conventional therapy in the treatment of refractory breast cancer patients with PI3K/AKT/mTOR mutations: A retrospective study

“…Tumor samples from primary surgery or blood samples could also be used as a substitute when a metastatic site biopsy or resection was not accessible or the biopsy sample was not qualified for NGS testing. Circulating tumor DNA (ctDNA) was processed and 150 cancer‐associated genes (include the 19 genes involved in PI3K/AKT/mTOR pathway) were sequenced in the NGS platform Illumina Nextseq 500 to >1000X coverage as previously reported …”