Next-generation sequencing of circulating tumor DNA to predict recurrence in triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy

Abstract

Next-generation sequencing to detect circulating tumor DNA is a minimally invasive method for tumor genotyping and monitoring therapeutic response. The majority of studies have focused on detecting circulating tumor DNA from patients with metastatic disease. Herein, we tested whether circulating tumor DNA could be used as a biomarker to predict relapse in triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy. In this study, we analyzed samples from 38 early-stage triple-negative breast cancer patients with matched tumor, blood, and plasma. Extracted DNA underwent library preparation and amplification using the Oncomine Research Panel consisting of 134 cancer genes, followed by high-coverage sequencing and bioinformatics. We detected high-quality somatic mutations from primary tumors in 33 of 38 patients. TP53 mutations were the most prevalent (82%) followed by PIK3CA (16%). Of the 33 patients who had a mutation identified in their primary tumor, we were able to detect circulating tumor DNA mutations in the plasma of four patients (three TP53 mutations, one AKT1 mutation, one CDKN2A mutation). All four patients had recurrence of their disease (100% specificity), but sensitivity was limited to detecting only 4 of 13 patients who clinically relapsed (31% sensitivity). Notably, all four patients had a rapid recurrence (0.3, 4.0, 5.3, and 8.9 months). Patients with detectable circulating tumor DNA had an inferior disease free survival (p < 0.0001; median disease-free survival: 4.6 mos. vs. not reached; hazard ratio = 12.6, 95% confidence interval: 3.06–52.2). Our study shows that next-generation circulating tumor DNA sequencing of triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy can predict recurrence with high specificity, but moderate sensitivity. For those patients where circulating tumor DNA is detected, recurrence is rapid.

Breast cancer development and progression: Risk factors, cancer stem cells, signaling pathways, genomics, and molecular pathogenesis

“…Furthermore, the drastic improvements over detection sensitivity and throughput of whole genome sequencing technologies will enable us to reliably detect genomic changes in circulating tumor cells. 369 , 370 , 371 , 372 , 373 Till then the full potential of personalized precision medicine will be realized in the clinical management of breast cancers.…”

Liquid biopsy in breast cancer: A comprehensive review

“…cfDNA concentration in the blood may range from 13 ng/mL in healthy individuals to approximately 180 ng/mL in later stages of cancer . Increased amounts of cfDNA may serve as a diagnostic tool for cancer, while genomic analysis of ctDNA could also provide valuable information as a prognostic and predictive tool . These methods can be used complementary to each other in the liquid biopsy analysis of breast cancer …”

“…65 Increased amounts of cfDNA may serve as a diagnostic tool for cancer, while genomic analysis of ctDNA could also provide valuable information as a prognostic and predictive tool. [66][67][68][69] These methods can be used complementary to each other in the liquid biopsy analysis of breast cancer. 70 cfDNA/ctDNA are released in both apoptosis and necrosis of the cells at the interface of tumor and circulation, or active release.…”

Identifying Biomarkers to Pair with Targeting Treatments within Triple Negative Breast Cancer for Improved Patient Stratification

“…Presence of ctDNA within both the single time point and serial sampling could predict relapse across tumour types including within TNBC patients (p = 0.009 and 0.003) [65]. Sample size was small with just 11 and 13 TNBC patients with available samples for single time-point and serial sampling respectively, the results however are supported by other small studies restricted to TNBC patients with similar findings [66,67] suggesting the potential for ctDNA as a biomarker for relapse. What is currently less clear is whether ctDNA detection can be used to direct treatment.…”