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Updated: May 28, 2026
Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
Published on: August 24, 2017
Quantitative detection of EGFR mutations in circulating tumor DNA derived from lung adenocarcinomas
Kazuya Taniguchi1, Junji Uchida, Kazumi Nishino
1Research Institute, Departments of Thoracic Oncology and Thoracic Surgery, Osaka Medical Center for Cancer and Cardiovascular Diseases, Higashinari-ku, Osaka, Japan.
Purpose:
Examination of somatic epidermal growth factor receptor (EGFR) mutations is now a diagnostic routine for treatment of cancer using EGFR tyrosine kinase inhibitors (EGFR-TKI). Circulating tumor DNA is a promising target for noninvasive diagnostics. We evaluated its utility by quantitatively detecting activating and resistant mutations, which were measured with BEAMing (beads, emulsion, amplification, and magnetics).
Experimental Design:
Twenty-three patients with lung cancer with progressive disease after EGFR-TKI treatment and 21 patients who had never been treated with EGFR-TKIs were studied. Their primary tumors were confirmed to have activating mutations. In the plasma DNA of each patient, the activating mutation found in the corresponding primary tumor and the T790M resistance mutation were quantified by BEAMing.
Results:
In 32 of 44 patients, activating mutations were detected in the plasma DNA [72.7%; 95% confidence interval (CI), 58.0%-83.6%]. The T790M mutation was detected in 10 of 23 patients in the first group (43.5%; 95% CI, 25.6%-53.4%). The ratio of T790M to activating mutations ranged from 13.3% to 94.0%. The peak of the distribution of the mutation allele fraction in the plasma DNA was in the 0.1% to 1% range.
Conclusions:
The major advantage of BEAMing is its ability to calculate the fraction of T790M-positive alleles from the alleles with activating mutations. This feature enables the detection of increases and decreases in the number of T790M mutations in cancer cells, regardless of normal cell DNA contamination, which may be useful for monitoring disease progression. Circulating tumor DNA could potentially be used as an alternative method for EGFR mutation detection.
Insights
Detecting epidermal growth factor receptor (EGFR) mutations in circulating tumor DNA using BEAMing is a promising noninvasive method for cancer diagnostics. This technique can quantify both activating and T790M resistance mutations, aiding in monitoring disease progression.
Area of Science:
- Oncology
- Molecular Diagnostics
- Genetics
Background:
- Somatic epidermal growth factor receptor (EGFR) mutation analysis is standard for cancer treatment with EGFR tyrosine kinase inhibitors (EGFR-TKIs).
- Circulating tumor DNA (ctDNA) offers a noninvasive approach for molecular diagnostics.
Purpose of the Study:
- To evaluate the utility of ctDNA for quantitatively detecting activating and T790M resistance mutations in lung cancer patients.
- To assess the BEAMing method for quantifying these mutations in plasma DNA.
Main Methods:
- BEAMing (beads, emulsion, amplification, and magnetics) was used to quantify activating and T790M mutations in plasma DNA.
- Patients included 23 with lung cancer post-EGFR-TKI treatment and 21 treatment-naïve patients with confirmed primary tumor activating mutations.
Main Results:
- Activating EGFR mutations were detected in plasma DNA of 72.7% of patients (32/44).
- The T790M resistance mutation was found in 43.5% of previously treated patients (10/23).
- The ratio of T790M to activating mutations varied, with peak allele fractions in plasma DNA between 0.1% and 1%.
Conclusions:
- BEAMing allows calculation of T790M-positive alleles relative to activating mutations, useful for monitoring mutation dynamics.
- This method is valuable for tracking changes in T790M mutations irrespective of normal DNA contamination.
- ctDNA analysis via BEAMing presents a potential alternative for EGFR mutation detection in cancer patients.
