Nicolas Guibert1, Hisashi Tsukada2, David H Hwang3, Emily Chambers4, Edmund S Cibas3, Tejus Bale3, Julianna Supplee5, Bryan Ulrich5, Lynette M Sholl3, Cloud P Paweletz5, Geoffrey R Oxnard6. 1. Translational Research Laboratory, Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, United States; Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, United States. 2. Division of Thoracic Surgery, Brigham and Women's Hospital, United States. 3. Department of Pathology, Brigham and Women's Hospital, Boston, MA United States. 4. Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, United States. 5. Translational Research Laboratory, Belfer Center for Applied Cancer Science, Dana Farber Cancer Institute, United States. 6. Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, United States. Electronic address: geoffrey_oxnard@dfci.harvard.edu.
Abstract
BACKGROUND: Tumor genotyping is transforming lung cancer care but requires adequate tumor tissue. Advances in minimally invasive biopsy techniques have increased access to difficult-to-access lesions, but often result in smaller samples. With the advent of highly sensitive DNA genotyping methods used for plasma analysis, we hypothesized that these same methods might allow genotyping of free DNA derived from fine needle aspiration supernatant (FNA-S). METHODS: We studied patients with known or suspected lung cancer undergoing fine needle aspirate (FNA). After spinning the sample for cellblock, the FNA-S (usually discarded) was saved for genotyping. Supernatant cell-free DNA (SN-cfDNA) was extracted and tested by both droplet digital PCR (EGFR, BRAF, KRAS mutations) and highly sensitive amplicon-based next-generation sequencing (NGS). RESULTS: 17 samples were studied, including 11 FNAs from patients with suspected lung cancer and 6 FNAs from patients with lung cancer and acquired drug resistance. Of 6 newly diagnosed adenocarcinomas, 4 had a driver mutations (1 EGFR, 2 KRAS, 1 HER2) found on tissue; all of these could be detected in SN-cfDNA. The EGFR driver mutation was detected in all 5 adenocarcinomas with acquired EGFR resistance and the EGFR T790 M in three cases, in agreement with cellblock. CONCLUSIONS: FNA-S is a rich source of fresh tumor DNA, potentially increasing the diagnostic yield from small FNAs. Through use of emerging techniques for highly sensitive genotyping, this widely available biospecimen has potential for facilitating rapid cancer genotyping at diagnosis and after drug resistance.
BACKGROUND:Tumor genotyping is transforming lung cancer care but requires adequate tumor tissue. Advances in minimally invasive biopsy techniques have increased access to difficult-to-access lesions, but often result in smaller samples. With the advent of highly sensitive DNA genotyping methods used for plasma analysis, we hypothesized that these same methods might allow genotyping of free DNA derived from fine needle aspiration supernatant (FNA-S). METHODS: We studied patients with known or suspected lung cancer undergoing fine needle aspirate (FNA). After spinning the sample for cellblock, the FNA-S (usually discarded) was saved for genotyping. Supernatant cell-free DNA (SN-cfDNA) was extracted and tested by both droplet digital PCR (EGFR, BRAF, KRAS mutations) and highly sensitive amplicon-based next-generation sequencing (NGS). RESULTS: 17 samples were studied, including 11 FNAs from patients with suspected lung cancer and 6 FNAs from patients with lung cancer and acquired drug resistance. Of 6 newly diagnosed adenocarcinomas, 4 had a driver mutations (1 EGFR, 2 KRAS, 1 HER2) found on tissue; all of these could be detected in SN-cfDNA. The EGFR driver mutation was detected in all 5 adenocarcinomas with acquired EGFR resistance and the EGFR T790 M in three cases, in agreement with cellblock. CONCLUSIONS: FNA-S is a rich source of fresh tumor DNA, potentially increasing the diagnostic yield from small FNAs. Through use of emerging techniques for highly sensitive genotyping, this widely available biospecimen has potential for facilitating rapid cancer genotyping at diagnosis and after drug resistance.
Authors: Joseph R Habib; Yayun Zhu; Lingdi Yin; Ammar A Javed; Ding Ding; Jonathan Tenior; Michael Wright; Syed Z Ali; Richard A Burkhart; William Burns; Christopher L Wolfgang; Eunji Shin; Jun Yu; Jin He Journal: J Gastrointest Surg Date: 2021-07-09 Impact factor: 3.452
Authors: Izhar S Batth; Qing Meng; Qi Wang; Keila E Torres; Jared Burks; Jing Wang; Richard Gorlick; Shulin Li Journal: BMC Cancer Date: 2020-07-31 Impact factor: 4.430