Toshiaki Akahane1,2, Ikumi Kitazono3, Yusuke Kobayashi4, Yukari Nishida-Kirita3, Tomomi Yamaguchi5, Shintaro Yanazume6, Kazuhiro Tabata1, Hiroaki Kobayashi4,6, Akihide Tanimoto1,2,3. 1. Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan. 2. Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Japan. 3. Unit of Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan. 4. Advanced Cancer Medicine for Gynecologic Cancer, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan. 5. Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan. 6. Department of Obstetrics and Gynecology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.
Abstract
BACKGROUND: Genomic examination of cytology specimens is often performed on cell blocks or conventional smears rather than on liquid-based cytology (LBC) specimens. Since LBC specimens preserve high-quality DNA, cancer genome profiling using next-generation sequencing (NGS) is also attainable from residual LBC specimens. One of the advantages of using LBC specimens for NGS is that it allows direct extraction of DNA from residual specimens, avoiding a sacrifice of smear slides and minimizing genomic profiling processing time. METHODS: Endometrial LBC specimens were subjected to NGS analysis to validate the practicality of rapid cancer genomic profiling in a pathology laboratory. The extracted DNA was subjected to NGS using a customized cancer gene panel comprising 56 genes and 17 microsatellite regions. The workflow strategy was defined, and the processing time estimated for specimen sampling, cell counting, NGS run, and genome profiling. RESULTS: NGS analysis of most LBC specimens revealed somatic mutations, tumor mutation burden, and microsatellite instability, which were almost identical to those obtained from formalin-fixed paraffin-embedded tissues. The processing time for direct NGS analysis and cancer genomic profiling of the residual LBC specimens was approximately 5 days. CONCLUSION: The residual LBC specimens collected using endometrial cytology were verified to carry a high tumor fraction for NGS analysis and could serve as an alternate source for rapid molecular classification and diagnosis of endometrial cancers, as a routine process in a pathology laboratory.
BACKGROUND: Genomic examination of cytology specimens is often performed on cell blocks or conventional smears rather than on liquid-based cytology (LBC) specimens. Since LBC specimens preserve high-quality DNA, cancer genome profiling using next-generation sequencing (NGS) is also attainable from residual LBC specimens. One of the advantages of using LBC specimens for NGS is that it allows direct extraction of DNA from residual specimens, avoiding a sacrifice of smear slides and minimizing genomic profiling processing time. METHODS: Endometrial LBC specimens were subjected to NGS analysis to validate the practicality of rapid cancer genomic profiling in a pathology laboratory. The extracted DNA was subjected to NGS using a customized cancer gene panel comprising 56 genes and 17 microsatellite regions. The workflow strategy was defined, and the processing time estimated for specimen sampling, cell counting, NGS run, and genome profiling. RESULTS: NGS analysis of most LBC specimens revealed somatic mutations, tumor mutation burden, and microsatellite instability, which were almost identical to those obtained from formalin-fixed paraffin-embedded tissues. The processing time for direct NGS analysis and cancer genomic profiling of the residual LBC specimens was approximately 5 days. CONCLUSION: The residual LBC specimens collected using endometrial cytology were verified to carry a high tumor fraction for NGS analysis and could serve as an alternate source for rapid molecular classification and diagnosis of endometrial cancers, as a routine process in a pathology laboratory.
Authors: Brandon S Sheffield; Andrea Beharry; Joanne Diep; Kirstin Perdrizet; Marco A J Iafolla; William Raskin; Shaan Dudani; Mary Anne Brett; Blerta Starova; Brian Olsen; Parneet K Cheema Journal: Curr Oncol Date: 2022-02-23 Impact factor: 3.677