Direct next‐generation sequencing analysis using endometrial liquid‐based cytology specimens for rapid cancer genomic profiling

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.

Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care

“…A recent study reported on the turnaround time of commercially-available plasma tests, reporting a median turnaround time of 9 days [15]. Another report describes rapid NGSbased testing on cytology samples, available within 5 days [16]. To our knowledge, this is the first reported series of cases with comprehensive biomarkers reported in as little as 3 days.…”

Sequential evaluation of MUC promoter methylation using next‐generation sequencing‐based custom‐made panels in liquid‐based cytology specimens of pancreatic cancer

“…14 However, as previously reported, the use of LBC specimens for NGS analysis has a few disadvantages. 28 First, NGS analysis from LBC specimens is performed using residual samples. Although we confirmed the presence of tumor cells in most of the residual LBC specimens and then applied them for DNA extraction, there is a possibility of false-negative materials being applied to NGS.…”

“…Fluorometer with a dsDNA BR assay kit (Life Technologies, Grand Island, NY, USA), and DNA quality was confirmed using a QIAseq DNA Quantimize kit (Qiagen). 13,14,16,28…”

Impact of LBC fixative type and fixation time on molecular analysis of pancreatic cancer cells: A comparative study of cell morphology, antigenicity and nucleic acids

“…Recent studies have reported the usefulness of LBC samples for NGS analysis. [ 23 24 ] For pancreatic cancer, NGS analysis using LBC specimens was reported to contribute to a possible improvement in the evaluation of pancreatic tumor malignancies and the application of molecular-targeted therapeutic agents. [ 25 ] Preservation of samples is a key step to successful NGS analyses.…”