Preanalytic variables in quality and quantity of nucleic acids extracted from FNA specimens of thyroid gland nodules collected in CytoLyt: Cellularity and storage time. Issue 9 (8th April 2020)

• Record Type: Journal Article
• Authors: Heymann, Jonas J.; Yoxtheimer, Lorene M.; Park, Hyeon Jin; Fernandez, Evan M.; Facey, Kirk E.; Alperstein, Susan A.; Tran, Hung V.; Baek, Inji; Scognamiglio, Theresa; Rennert, Hanna; Siddiqui, Momin T.; Song, Wei
• Other Names: Rossi Esther Diana guestEditor.; Roy‐Chowdhuri Sinchita guestEditor.
• Is Part Of: Cancer cytopathology. Volume 128:Issue 9(2020)
• Page Start: 656
• Page End: 672
• Publication Date: 2020-04-08
• Subjects: cellularity -- fine‐needle aspiration (FNA) -- liquid‐based cytology -- molecular testing -- next‐generation sequencing (NGS) -- nucleic acid quality -- nucleic acid yield -- papillary thyroid carcinoma -- storage time -- thyroid neoplasms; Cancer -- Cytopathology -- Periodicals; Pathology, Cellular -- Periodicals; Cytology -- Technique -- Periodicals; 611.01815
• DOI: 10.1002/cncy.22270
• Languages: English
• ISSNs: 1934-662X

Abstract

Abstract : Background: Morphologic and genetic analysis of thyroid nodules may be performed from a single vial. Preanalytic variables that affect nucleic acid extracted from a single vial are evaluated. Methods: Thyroid fine‐needle aspiration (FNA) specimens collected in CytoLyt were evaluated. A ThinPrep slide was prepared. Extracted nucleic acids were analyzed using Oncomine Comprehensive Panel, version 2, after Ion AmpliSeq library preparation. A pathologist and a cytotechnologist enumerated specimen cellularity. Results: Fifty‐six samples were collected from 55 nodules in 53 patients. Bethesda category correlated with cellularity ( P = .01), and storage time (median, 43 days; range, 7‐77 days) was longer for specimens in categories II and III than for those in categories IV and VI ( P = .01). The mean specimen DNA concentration was 4.5 ng/µL (range, 0‐23.8 ng/µL), and 25 (45%) had concentrations >3.3 ng/µL. The mean specimen RNA concentration was 4.8 ng/µL (range, 0‐42.4 ng/µL), and 31 (55%) had concentrations >1.4 ng/µL. Nucleic acid quantity increased with epithelial cellularity. Storage time weakly correlated with the quantity of extracted DNA, independent of cellularity, but not extracted RNA. Greater proportions of cell‐free DNA and lesser proportions of long, intact RNA fragments were extracted from a subset of samples with longer storage time. Among 15 single nucleotide variants, the median mutant allelic fraction was 15.1%. One false‐negative result was identified. Five specimens subsequently determined to harbor a genetic alteration failed quality metrics. Conclusions: Cellularity and storage time affect the quantity and quality of nucleic acid extracted from thyroid FNA specimens collected in CytoLyt. Further investigation will serve to quantify the magnitude of such effects and to elucidate other contributing factors. Abstract : Combined morphologic evaluation and molecular testing from material in a single vial is feasible and practical for fine‐needle aspiration biopsy specimens of the thyroid gland. The effect on quality and quantity of nucleic acid extracted from specimens collected in CytoLyt is evaluated for 2 key preanalytic variables: cellularity and storage time.