Diagnostic accuracy of droplet digital PCR for detection of EGFR T790M mutation in circulating tumor DNA

Zhang, Rui; Chen, Bojiang; Xiang, Tong; Wang, Ye; Wang, Chengdi; Jin, Jing; Tian, Panwen; Liu, Weimin

doi:10.2147/cmar.s161382

Cited by 29 publications

(15 citation statements)

References 47 publications

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“…The most popular methods such as ddPCR and NGS-based techniques have their own advantages and disadvantages, separately. ddPCR is associated with high analytical sensitivity down to single molecules and has lower turnaround time than NGS-based approaches when testing single mutations only, 39,40 but the main disadvantages included sequential testing of mutations and detection of previously unknown mutations is impossible. 18 In contrast, NGS-targeted sequencing method utilises enrichment of recurrently altered loci by PCR amplification or hybrid capture, allowing de novo identification of molecular alterations, but this inevitably introduces random errors in the amplification process.…”

Section: Discussionmentioning

confidence: 99%

Preoperative detection of KRAS G12D mutation in ctDNA is a powerful predictor for early recurrence of resectable PDAC patients

et al. 2020

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BACKGROUND: About 25-37% of resectable pancreatic ductal adenocarcinoma (PDAC) had a great chance of early recurrence after radical resection, which is mainly due to preoperative micrometastasis. We herein demonstrated the profiles of ctDNA in resectable PDAC and use of ctDNA to identify patients with potential micrometastasis. METHODS: A total of 113 and 44 resectable PDACs were enrolled in discovery and validation cohorts, separately. A panel containing 50 genes was used to screen ctDNA by an NGS-based assessment with high specificity. RESULTS: In the discovery cohort, the overall detection rate was 38.05% (43/113). Among positive ctDNA, KRAS mutation had the highest detection rate (23.01%, 26/113), while the others were <5%. Survival analysis showed that plasma KRAS mutations, especially KRAS G12D mutation, had significant association with OS and RFS of resectable PDAC. Plasma KRAS G12D mutation showed a strong correlation with early distant metastasis. In the validation cohort, survival analysis showed similar association between plasma KRAS G12D mutation and poor outcomes. CONCLUSIONS: This study demonstrated that plasma KRAS mutations, especially KRAS G12D mutation, served as a useful predictive biomarker for prognosis of resectable PDAC. More importantly, due to high correlation with micrometastasis, preoperative detection of plasma KRAS G12D mutation helps in optimising surgical selection of resectable PDAC.

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Section: Discussionmentioning

confidence: 99%

Preoperative detection of KRAS G12D mutation in ctDNA is a powerful predictor for early recurrence of resectable PDAC patients

et al. 2020

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“…Similarly, a recent meta-analysis of 11 non-small cell lung carcinoma (NSCLC) studies showed that ddPCR displays a good performance for the detection of EGFR T790M mutation in ctDNA samples from a total of 872 advanced NSCLC patients. In particular, the overall concordance between plasma and tissue estimation was 81.2%, while the pooled analysis revealed that ddPCR test performs with 86.9% (95% CI, 80.6%–91.7%) of specificity and 70.1% (95% CI, 62.7%–76.7%) of sensitivity in detecting the T790M EGFR mutation in ctDNA samples from NSCLC patients [84]. Other similar studies were performed involving oral cancer patients [85], breast cancer patients [86], chronic myelogenous leukemia patients [87], and others.…”

Section: Ngs Ddpcr and Liquid Biopsy For Ctdna Analysismentioning

confidence: 99%

Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements

Tuaeva

Falzone

Porozov

et al. 2019

Cells

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In recent years, the introduction of new molecular techniques in experimental and clinical settings has allowed researchers and clinicians to propose circulating-tumor DNA (ctDNA) analysis and liquid biopsy as novel promising strategies for the early diagnosis of cancer and for the definition of patients’ prognosis. It was widely demonstrated that through the non-invasive analysis of ctDNA, it is possible to identify and characterize the mutational status of tumors while avoiding invasive diagnostic strategies. Although a number of studies on ctDNA in patients’ samples significantly contributed to the improvement of oncology practice, some investigations generated conflicting data about the diagnostic and prognostic significance of ctDNA. Hence, to highlight the relevant achievements obtained so far in this field, a clearer description of the current methodologies used, as well as the obtained results, are strongly needed. On these bases, this review discusses the most relevant studies on ctDNA analysis in cancer, as well as the future directions and applications of liquid biopsy. In particular, special attention was paid to the early diagnosis of primary cancer, to the diagnosis of tumors with an unknown primary location, and finally to the prognosis of cancer patients. Furthermore, the current limitations of ctDNA-based approaches and possible strategies to overcome these limitations are presented.

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“…Although patients with cancer usually have higher average plasma/serum levels of ctDNA, they are often present in fragmented form at very low concentrations 8 . Digital PCR (dPCR) is the third generation and the most advanced PCR technique that permits highly sensitive genotyping and absolute quantification of mutant copies in ctDNA 9,10 . While dPCR is highly accurate, it is cost-intensive, time consuming, and requires sophisticated instruments and trained personnel.…”

mentioning

confidence: 99%

Non-invasive detection of EGFR mutations by cell-free loop-mediated isothermal amplification (CF-LAMP)

Arjuna

Venkataram

Dechamma

et al. 2020

Sci Rep

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Targeting epidermal growth factor receptor (EGFR) through tyrosine kinase inhibitors (TKI) is a successful therapeutic strategy in non-small cell lung cancer. However, the response to TKI therapy depends on specific activating and acquired mutations in the tyrosine kinase domain of the EGFR gene. Therefore, confirming the EGFR status of patients is crucial, not only for determining the eligibility, but also for monitoring the emergence of mutations in patients under TKI therapy. In this study, our aim was to develop a cost effective, yet sensitive, technique that allows the detection of therapeutically-relevant EGFR hotspot mutations at isothermal conditions in a non-invasive manner. Previously, we developed an allele-specific loop-mediated isothermal amplification (AS-LAMP) assay for screening germline and somatic de novo T790M EGFR mutation in lung cancer patients. In this study, we used cell free DNA as a template in AS-LAMP assay (CF-LAMP) for non-invasive detection of two hotspot EGFR mutations (T790M, and L858R) and compared its efficiency with ultrasensitive droplet digital PCR (ddPCR) assay. The results of CF-LAMP assay were consistent with those obtained in ddPCR assay, indicating the robustness of the method. CF-LAMP may serve as a valuable and cost-effective alternative for liquid biopsy techniques used in molecular diagnosis of non-small cell lung cancer.

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Diagnostic accuracy of droplet digital PCR for detection of EGFR T790M mutation in circulating tumor DNA

Cited by 29 publications

References 47 publications

Preoperative detection of KRAS G12D mutation in ctDNA is a powerful predictor for early recurrence of resectable PDAC patients

Preoperative detection of KRAS G12D mutation in ctDNA is a powerful predictor for early recurrence of resectable PDAC patients

Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements

Non-invasive detection of EGFR mutations by cell-free loop-mediated isothermal amplification (CF-LAMP)

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