Related Experiment Video
Updated: Mar 28, 2026
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
Published on: June 8, 2020
Using "residual" FNA rinse and body fluid specimens for next-generation sequencing: An institutional experience
Shuanzeng Wei1, David Lieberman1, Jennifer J D Morrissette1
1Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.
Background:
Tissue specimens are typically considered optimal for molecular testing; however, in the current era of personalized medicine, cytopathology specimens are increasingly recognized as potential sources for molecular testing. This is often accomplished by using cell block specimens and/or fine-needle aspiration (FNA) smear preparations. In this study, the authors investigated the feasibility, performance, and quality of "residual" FNA rinse and body effusion fluids used for next-generation sequencing (NGS).
Methods:
Sequence data were generated from 17 malignancies in 16 patients from 13 FNA (10 lymph nodes, 1 lung, and 2 bone lesions) and 4 effusion (3 pleural and 1 pericardial) specimens. Malignancies included carcinomas (lung, breast, ovarian, and unknown primary), melanoma, and myeloma. Paired NGS testing was performed in 7 patients who had surgical biopsy or cell block specimens available. Routinely processed residual FNA rinse material and body fluids were used for DNA extraction and NGS (targeted gene panel).
Results:
NGS was successfully performed on all 17 specimens. A significant amount of DNA was obtained from the residual FNA rinse (176.3 ng/μL) compared with the paired cell block slides (10.6 ng/μL). Two of the 10 lung adenocarcinomas (20%) demonstrated epidermal growth factor receptor (EGFR) mutations, including 1 leucine-to-arginine substitution at codon 858 (L858R) in exon 21 and 1 codon 2235_2249 deletion (resulting in an in-frame deletion of 5 amino acids from position 746 to 750 [glutamic acid, leucine, arginine, glutamic acid, and alanine]; E746_A750del) in exon 19. Three KRAS [Kirsten rat sarcoma viral oncogene homolog] mutations, 1 BRAF (v-Raf murine sarcoma viral oncogene homolog B1) mutation, and 1 NRAS (neuroblastoma RAS viral oncogene homolog) mutation were identified in the remaining lung adenocarcinomas. Patients who underwent paired testing demonstrated 100% concordant mutations.
Conclusions:
Targeted NGS can be performed on residual FNA rinse and body fluid specimens. This approach is particularly important when a paucicellular cell block or biopsy specimen is encountered. Cancer Cytopathol 2016;124:324-29. © 2015 American Cancer Society.
