Comparative analysis of EGFR mutations in circulating tumor DNA and primary tumor tissues from lung cancer patients using BEAMing PCR
Abstract In this study, we measured human epidermal growth factor receptor (EGFR) mutations in both tissue and circulating tumor DNA (ctDNA) by using beads, emulsions, amplifications and magnetic polymerase chain reaction (BEAMing PCR). Noninvasive mutation detection by assessing circulating tumor D...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41598-025-85160-6 |
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| author | Duhita Mirikar Nandini Banerjee Kumar Prabhash Rajiv Kumar Kaushal Vanita Naronha C. S. Pramesh George Karimundackal Amit Joshi Swapnil Rane Ranjan Basak |
| author_facet | Duhita Mirikar Nandini Banerjee Kumar Prabhash Rajiv Kumar Kaushal Vanita Naronha C. S. Pramesh George Karimundackal Amit Joshi Swapnil Rane Ranjan Basak |
| author_sort | Duhita Mirikar |
| collection | DOAJ |
| description | Abstract In this study, we measured human epidermal growth factor receptor (EGFR) mutations in both tissue and circulating tumor DNA (ctDNA) by using beads, emulsions, amplifications and magnetic polymerase chain reaction (BEAMing PCR). Noninvasive mutation detection by assessing circulating tumor DNA (ctDNA) offers many advantages over tumor biopsy. One hundred non-small cell lung cancer (NSCLC) patients were enrolled, and both preoperative plasma samples and formalin-fixed and paraffin-embedded (FFPE) samples were collected for the study. The EGFR mutation status was determined by BEAMing PCR in ctDNA. Real-time quantitative PCR (qPCR) data were collected from our hospital database (EMR-qPCR, Electronic Medical Records) for comparative analysis. Additionally, qPCR was also performed on FFPE tissues using a Diatech EGFR qPCR kit. The concordance rates were 98.8%, 98.9% and 95.5% for exons 19, 20 and 21, respectively, when the BEAMing data were compared with the EMR-qPCR data. Additionally, when the BEAMing and Diatech qPCR data were compared, 90%, 100%, 96% and 98% of the genes were obtained for exons 19, 20, 21 (L858R) and 21 (L861Q), respectively. For both comparisons, Cohen’s kappa agreement was significant. The advantage of BEAMing is its ability to identify mutated DNA sequences in cancer cells in the background of normal cell DNA contamination. This could be useful for disease monitoring and progression. |
| format | Article |
| id | doaj-art-4bd046642afc43598023665dd885e4ee |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-4bd046642afc43598023665dd885e4ee2025-01-12T12:17:58ZengNature PortfolioScientific Reports2045-23222025-01-0115111010.1038/s41598-025-85160-6Comparative analysis of EGFR mutations in circulating tumor DNA and primary tumor tissues from lung cancer patients using BEAMing PCRDuhita Mirikar0Nandini Banerjee1Kumar Prabhash2Rajiv Kumar Kaushal3Vanita Naronha4C. S. Pramesh5George Karimundackal6Amit Joshi7Swapnil Rane8Ranjan Basak9Translational Research Laboratory, Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial CentreTranslational Research Laboratory, Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial CentreDepartment of Medical Oncology, Tata Memorial HospitalDepartment of Pathology, Tata Memorial HospitalDepartment of Medical Oncology, Tata Memorial HospitalDepartment of Surgical Oncology, Tata Memorial HospitalDepartment of Surgical Oncology, Tata Memorial HospitalDepartment of Medical Oncology, Tata Memorial HospitalDepartment of Pathology, Tata Memorial HospitalTranslational Research Laboratory, Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial CentreAbstract In this study, we measured human epidermal growth factor receptor (EGFR) mutations in both tissue and circulating tumor DNA (ctDNA) by using beads, emulsions, amplifications and magnetic polymerase chain reaction (BEAMing PCR). Noninvasive mutation detection by assessing circulating tumor DNA (ctDNA) offers many advantages over tumor biopsy. One hundred non-small cell lung cancer (NSCLC) patients were enrolled, and both preoperative plasma samples and formalin-fixed and paraffin-embedded (FFPE) samples were collected for the study. The EGFR mutation status was determined by BEAMing PCR in ctDNA. Real-time quantitative PCR (qPCR) data were collected from our hospital database (EMR-qPCR, Electronic Medical Records) for comparative analysis. Additionally, qPCR was also performed on FFPE tissues using a Diatech EGFR qPCR kit. The concordance rates were 98.8%, 98.9% and 95.5% for exons 19, 20 and 21, respectively, when the BEAMing data were compared with the EMR-qPCR data. Additionally, when the BEAMing and Diatech qPCR data were compared, 90%, 100%, 96% and 98% of the genes were obtained for exons 19, 20, 21 (L858R) and 21 (L861Q), respectively. For both comparisons, Cohen’s kappa agreement was significant. The advantage of BEAMing is its ability to identify mutated DNA sequences in cancer cells in the background of normal cell DNA contamination. This could be useful for disease monitoring and progression.https://doi.org/10.1038/s41598-025-85160-6EGFRNSCLCctDNABEAMingqPCR |
| spellingShingle | Duhita Mirikar Nandini Banerjee Kumar Prabhash Rajiv Kumar Kaushal Vanita Naronha C. S. Pramesh George Karimundackal Amit Joshi Swapnil Rane Ranjan Basak Comparative analysis of EGFR mutations in circulating tumor DNA and primary tumor tissues from lung cancer patients using BEAMing PCR Scientific Reports EGFR NSCLC ctDNA BEAMing qPCR |
| title | Comparative analysis of EGFR mutations in circulating tumor DNA and primary tumor tissues from lung cancer patients using BEAMing PCR |
| title_full | Comparative analysis of EGFR mutations in circulating tumor DNA and primary tumor tissues from lung cancer patients using BEAMing PCR |
| title_fullStr | Comparative analysis of EGFR mutations in circulating tumor DNA and primary tumor tissues from lung cancer patients using BEAMing PCR |
| title_full_unstemmed | Comparative analysis of EGFR mutations in circulating tumor DNA and primary tumor tissues from lung cancer patients using BEAMing PCR |
| title_short | Comparative analysis of EGFR mutations in circulating tumor DNA and primary tumor tissues from lung cancer patients using BEAMing PCR |
| title_sort | comparative analysis of egfr mutations in circulating tumor dna and primary tumor tissues from lung cancer patients using beaming pcr |
| topic | EGFR NSCLC ctDNA BEAMing qPCR |
| url | https://doi.org/10.1038/s41598-025-85160-6 |
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