Using "residual" FNA rinse and body fluid specimens for next-generation sequencing: An institutional experience

Cancer Cytopathology

Volumn 124, Issue 5, 2016, Pages 324-329

  Wei, Shuanzeng ^a   Lieberman, David ^a   Morrissette, Jennifer J D ^a   Baloch, Zubair W ^a   Roth, David B ^a   McGrath, Cindy ^a  

^a HOSPITAL OF THE UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

cytopathology; fine needle aspiration (FNA); next generation sequencing (NGS); personalized medicine

Indexed keywords

ALANINE; ARGININE; B RAF KINASE; EPIDERMAL GROWTH FACTOR RECEPTOR; GENOMIC DNA; GLUTAMIC ACID; LEUCINE; TUMOR MARKER;

AMINO ACID SUBSTITUTION; ARTICLE; BODY FLUID; BONE BIOPSY; BREAST CARCINOMA; CANCER OF UNKNOWN PRIMARY SITE; CLINICAL ARTICLE; CODON; DNA EXTRACTION; EPIDERMAL GROWTH FACTOR RECEPTOR GENE; EXON; FEMALE; FINE NEEDLE ASPIRATION BIOPSY; GENE MUTATION; HUMAN; HUMAN TISSUE; LUNG ADENOCARCINOMA; LUNG BIOPSY; LYMPH NODE BIOPSY; MELANOMA; MYELOMA; NEXT GENERATION SEQUENCING; ONCOGENE K RAS; ONCOGENE N RAS; OVARY CARCINOMA; PERICARDIAL EFFUSION; PLEURA EFFUSION; PRIORITY JOURNAL; V RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1; CHEMISTRY; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; MUTATION; NEOPLASMS; PROCEDURES;

BIOMARKERS, TUMOR; BIOPSY, FINE-NEEDLE; BODY FLUIDS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; NEOPLASMS;

EID: 84968638550     PISSN: 1934662X     EISSN: 19346638     Source Type: Journal    
DOI: 10.1002/cncy.21666     Document Type: Article

References (22)

1. Aziz N, Zhao Q, Bry L, et al., College of American Pathologists' laboratory standards for next-generation sequencing clinical tests. Arch Pathol Lab Med. 2015; 139: 481-493.
2. Sanger F, Nicklen S, Coulson AR,. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977; 74: 5463-5467.
3. Rehm HL, Bale SJ, Bayrak-Toydemir P, et al., ACMG clinical laboratory standards for next-generation sequencing. Genet Med. 2013; 15: 733-747.
4. Sehgal AR, Gimotty PA, Zhao J, et al., DNMT3A mutational status affects the results of dose-escalated induction therapy in acute myelogenous leukemia. Clin Cancer Res. 2015: 21: 1614-1620.
5. Gleeson FC, Kipp BR, Voss JS, et al., Endoscopic ultrasound fine-needle aspiration cytology mutation profiling using targeted next-generation sequencing personalized care for rectal cancer. Am J Clin Pathol. 2015; 143: 879-888.
6. Valero V 3rd, Saunders TJ, He J, et al., Reliable detection of somatic mutations in fine needle aspirates of pancreatic cancer with next-generation sequencing: implications for surgical management [published online ahead of print May 27, 2015]. Ann Surg. doi: 10.1097/SLA.1156.
7. Hinrichs JW, van Blokland WM, Moons MJ, et al., Comparison of next-generation sequencing and mutation-specific platforms in clinical practice. Am J Clin Pathol. 2015; 143: 573-578.
8. Gleeson FC, Kipp BR, Levy MJ, et al., Lung cancer adrenal gland metastasis: optimal fine-needle aspirate and touch preparation smear cellularity characteristics for successful theranostic next-generation sequencing. Cancer Cytopathol. 2014; 122: 822-832.
9. Lindeman NI, Cagle PT, Beasley MB, et al., Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology. J Mol Diagn. 2013; 15: 415-453.
10. Williams C, Ponten F, Moberg C, et al., A high frequency of sequence alterations is due to formalin fixation of archival specimens. Am J Pathol. 1999; 155: 1467-1471.
11. Spencer DH, Sehn JK, Abel HJ, Watson MA, Pfeifer JD, Duncavage EJ,. Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens. J Mol Diagn. 2013; 15: 623-633.
12. Srinivasan M, Sedmak D, Jewell S,. Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am J Pathol. 2002; 161: 1961-1971.
13. Gailey MP, Stence AA, Jensen CS, Ma D,. Multiplatform comparison of molecular oncology tests performed on cytology specimens and formalin-fixed, paraffin-embedded tissue. Cancer Cytopathol. 2015; 123: 30-39.
14. Kanagal-Shamanna R, Portier BP, Singh RR, et al., Next-generation sequencing-based multi-gene mutation profiling of solid tumors using fine needle aspiration samples: promises and challenges for routine clinical diagnostics. Mod Pathol. 2014; 27: 314-327.
15. Karnes HE, Duncavage EJ, Bernadt CT,. Targeted next-generation sequencing using fine-needle aspirates from adenocarcinomas of the lung. Cancer Cytopathol. 2014; 122: 104-113.
16. Nikiforov YE, Carty SE, Chiosea SI, et al., Highly accurate diagnosis of cancer in thyroid nodules with follicular neoplasm/suspicious for a follicular neoplasm cytology by ThyroSeq v2 next-generation sequencing assay. Cancer. 2014; 120: 3627-3634.
17. Nikiforova MN, Wald AI, Roy S, Durso MB, Nikiforov YE,. Targeted next-generation sequencing panel (ThyroSeq) for detection of mutations in thyroid cancer. J Clin Endocrinol Metab. 2013; 98: E1852-E1860.
18. Hadd AG, Houghton J, Choudhary A, et al., Targeted, high-depth, next-generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens. J Mol Diagn. 2013; 15: 234-247.
19. Billah S, Stewart J, Staerkel G, Chen S, Gong Y, Guo M,. EGFR and KRAS mutations in lung carcinoma. Cancer Cytopathol. 2011; 119: 111-117.
20. Viray H, Li K, Long TA, et al., A prospective, multi-institutional diagnostic trial to determine pathologist accuracy in estimation of percentage of malignant cells. Arch Pathol Lab Med. 2013; 137: 1545-1549.
21. Warth A, Penzel R, Brandt R, et al., Optimized algorithm for Sanger sequencing-based EGFR mutation analyses in NSCLC biopsies. Virchows Arch. 2012; 460: 407-414.
22. de Biase D, Visani M, Malapelle U, et al., Next-generation sequencing of lung cancer EGFR exons 18-21 allows effective molecular diagnosis of small routine samples (cytology and biopsy) [serial online]. PLoS One. 2013; 8: e83607.