Plasma next generation sequencing and droplet digital PCR‐based detection of epidermal growth factor receptor (EGFR) mutations in patients with advanced lung cancer treated with subsequent‐line osimertinib
Background Gene mutation analysis from plasma circulating tumor DNA (ctDNA) can provide timely information regarding the mechanism of resistance that could translate to personalised treatment. We compared concordance rate of next generation sequencing (NGS) and droplet digital polymerase chain react...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2019-10-01
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| Series: | Thoracic Cancer |
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| Online Access: | https://doi.org/10.1111/1759-7714.13154 |
| _version_ | 1818246074023804928 |
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| author | Pei N. Ding Therese Becker Victoria Bray Wei Chua Yafeng Ma Bo Xu David Lynch Paul de Souza Tara Roberts |
| author_facet | Pei N. Ding Therese Becker Victoria Bray Wei Chua Yafeng Ma Bo Xu David Lynch Paul de Souza Tara Roberts |
| author_sort | Pei N. Ding |
| collection | DOAJ |
| description | Background Gene mutation analysis from plasma circulating tumor DNA (ctDNA) can provide timely information regarding the mechanism of resistance that could translate to personalised treatment. We compared concordance rate of next generation sequencing (NGS) and droplet digital polymerase chain reaction (ddPCR) in the detection of the EGFR activating and T790M mutation from plasma ctDNA with diagnostic tissue biopsy‐based assays. The second objective was to test whether putative osimertinib resistance associated mutations were detectable from plasma using NGS. Methods From January 2016 to December 2017, we prospectively collected plasma samples from patients prior to commencement of second‐ or third‐line osimertinib therapy and upon disease progression, in a single tertiary hospital in South Western Sydney, Australia. Amplicon‐based NGS and ddPCR assays were used to detect activating epidermal growth factor receptor (EGFR) and T790M mutations in 18 plasma samples from nine patients; all patients were required to have tissue biopsies with known EGFR status. Results High concordance of allelic fractions were seen in matched plasma NGS and ddPCR for activating EGFR mutations and T790M mutations (R2 = 0.92, P < 0.0001). Using tissue biopsies as reference standard, sensitivity was 100% for NGS and 94% for ddPCR. Several possible osimertinib resistance associated mutations, including PIK3CA, BRAF and TP53 mutations, were detected by NGS in samples upon progression on osimertinib therapy. Conclusion ddPCR assays for EGFR mutations appear to be as sensitive and highly concordant as amplicon‐based NGS. NGS has the ability to detect novel resistance mutations. |
| first_indexed | 2024-12-12T14:43:01Z |
| format | Article |
| id | doaj.art-41ee61caf787449a842cbc2450a62f97 |
| institution | Directory Open Access Journal |
| issn | 1759-7706 1759-7714 |
| language | English |
| last_indexed | 2024-12-12T14:43:01Z |
| publishDate | 2019-10-01 |
| publisher | Wiley |
| record_format | Article |
| series | Thoracic Cancer |
| spelling | doaj.art-41ee61caf787449a842cbc2450a62f972022-12-22T00:21:10ZengWileyThoracic Cancer1759-77061759-77142019-10-0110101879188410.1111/1759-7714.13154Plasma next generation sequencing and droplet digital PCR‐based detection of epidermal growth factor receptor (EGFR) mutations in patients with advanced lung cancer treated with subsequent‐line osimertinibPei N. Ding0Therese Becker1Victoria Bray2Wei Chua3Yafeng Ma4Bo Xu5David Lynch6Paul de Souza7Tara Roberts8Centre for Circulating Tumor Cell Diagnostics & Research Ingham Institute for Applied Medical Research Liverpool New South Wales, AustraliaCentre for Circulating Tumor Cell Diagnostics & Research Ingham Institute for Applied Medical Research Liverpool New South Wales, AustraliaCentre for Circulating Tumor Cell Diagnostics & Research Ingham Institute for Applied Medical Research Liverpool New South Wales, AustraliaCentre for Circulating Tumor Cell Diagnostics & Research Ingham Institute for Applied Medical Research Liverpool New South Wales, AustraliaCentre for Circulating Tumor Cell Diagnostics & Research Ingham Institute for Applied Medical Research Liverpool New South Wales, AustraliaThermofisher Scientific Scoresby Victoria, AustraliaCentre for Circulating Tumor Cell Diagnostics & Research Ingham Institute for Applied Medical Research Liverpool New South Wales, AustraliaCentre for Circulating Tumor Cell Diagnostics & Research Ingham Institute for Applied Medical Research Liverpool New South Wales, AustraliaCentre for Circulating Tumor Cell Diagnostics & Research Ingham Institute for Applied Medical Research Liverpool New South Wales, AustraliaBackground Gene mutation analysis from plasma circulating tumor DNA (ctDNA) can provide timely information regarding the mechanism of resistance that could translate to personalised treatment. We compared concordance rate of next generation sequencing (NGS) and droplet digital polymerase chain reaction (ddPCR) in the detection of the EGFR activating and T790M mutation from plasma ctDNA with diagnostic tissue biopsy‐based assays. The second objective was to test whether putative osimertinib resistance associated mutations were detectable from plasma using NGS. Methods From January 2016 to December 2017, we prospectively collected plasma samples from patients prior to commencement of second‐ or third‐line osimertinib therapy and upon disease progression, in a single tertiary hospital in South Western Sydney, Australia. Amplicon‐based NGS and ddPCR assays were used to detect activating epidermal growth factor receptor (EGFR) and T790M mutations in 18 plasma samples from nine patients; all patients were required to have tissue biopsies with known EGFR status. Results High concordance of allelic fractions were seen in matched plasma NGS and ddPCR for activating EGFR mutations and T790M mutations (R2 = 0.92, P < 0.0001). Using tissue biopsies as reference standard, sensitivity was 100% for NGS and 94% for ddPCR. Several possible osimertinib resistance associated mutations, including PIK3CA, BRAF and TP53 mutations, were detected by NGS in samples upon progression on osimertinib therapy. Conclusion ddPCR assays for EGFR mutations appear to be as sensitive and highly concordant as amplicon‐based NGS. NGS has the ability to detect novel resistance mutations.https://doi.org/10.1111/1759-7714.13154Circulating tumor DNAdroplet digital PCRnext generation sequencingplasma genotypingresistance mechanisms |
| spellingShingle | Pei N. Ding Therese Becker Victoria Bray Wei Chua Yafeng Ma Bo Xu David Lynch Paul de Souza Tara Roberts Plasma next generation sequencing and droplet digital PCR‐based detection of epidermal growth factor receptor (EGFR) mutations in patients with advanced lung cancer treated with subsequent‐line osimertinib Thoracic Cancer Circulating tumor DNA droplet digital PCR next generation sequencing plasma genotyping resistance mechanisms |
| title | Plasma next generation sequencing and droplet digital PCR‐based detection of epidermal growth factor receptor (EGFR) mutations in patients with advanced lung cancer treated with subsequent‐line osimertinib |
| title_full | Plasma next generation sequencing and droplet digital PCR‐based detection of epidermal growth factor receptor (EGFR) mutations in patients with advanced lung cancer treated with subsequent‐line osimertinib |
| title_fullStr | Plasma next generation sequencing and droplet digital PCR‐based detection of epidermal growth factor receptor (EGFR) mutations in patients with advanced lung cancer treated with subsequent‐line osimertinib |
| title_full_unstemmed | Plasma next generation sequencing and droplet digital PCR‐based detection of epidermal growth factor receptor (EGFR) mutations in patients with advanced lung cancer treated with subsequent‐line osimertinib |
| title_short | Plasma next generation sequencing and droplet digital PCR‐based detection of epidermal growth factor receptor (EGFR) mutations in patients with advanced lung cancer treated with subsequent‐line osimertinib |
| title_sort | plasma next generation sequencing and droplet digital pcr based detection of epidermal growth factor receptor egfr mutations in patients with advanced lung cancer treated with subsequent line osimertinib |
| topic | Circulating tumor DNA droplet digital PCR next generation sequencing plasma genotyping resistance mechanisms |
| url | https://doi.org/10.1111/1759-7714.13154 |
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