Protocol to evaluate clinical tumor tissue sample for genetic studies

DOI: https://doi.org/10.29296/24999490-2021-02-01

A.M. Borbat(1), I.V. Yatsenko(2) 1-Burnasyan Federal Medical Biophysical Center of the Federal Medical Biological Agency, Zhivopisnaya street, 46, Moscow, 123098, Russian Federation; 2-Oncology Diagnostics Atlas LLC, Malaya Nilitskaya street, 31, Moscow, 212069, Russian Federation E-mail: [email protected]

The article represents a literature review on the molecular genetic methods with routine histological material for clinical purposes within oncology service. The protocol to evaluate the quality of tumor tissue samples for molecular genetic studies is proposed. The protocol includes a sample identification section, a descriptive section containing tumor tissue evaluation, necrosis within a sample, background tissue and tissue artifacts, summary, and graphical schema of the slide to measure tissue area. The protocol is accessible for download as a pdf file. The protocol should improve the standardization of the procedure and communication between laboratory departments and increase the quality of medical service.
Keywords: 
histology, molecular genetics, quality evaluation, tumor nuclei count, tumor tissue area
Список литературы: 
  1. Cho M., Ahn S., Hong M., Bang H., Van Vrancken M., Kim S., Lee J., Park S.H., Park J.O., Park Y.O., Lim H.Y., Kang W., Sun J.M., Lee S.H., Ahn M.J., Park K., Kim D.H., Lee S., Park W., and Kim K.M. Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center’s experiences. Oncotarget. 2017; 8 (26): 42478–86. DOI: 10.18632/oncotarget.17199.
  2. Kokkat T.J., Patel M.S., McGarvey D., LiVolsi V.A., and Baloch Z.W. Archived Formalin-Fixed Paraffin-Embedded (FFPE) Blocks: A Valuable Underexploited Resource for Extraction of DNA, RNA, and Protein. Biopreserv Biobank. 2013; 11 (2): 101–6. DOI: 10.1089/bio.2012.0052.
  3. Chung M.J., Lin W., Dong L., and Li X. Tissue Requirements and DNA Quality Control for Clinical Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Samples: A Mini-Review of Practical Issues. J. Mol. Genet Med. 2017; 11: 2. DOI: 10.4172/1747-0862.1000262.
  4. FoundationOne CDx Specimen Instructions. URL: https://www.foundationmedicine.com/genomic-testing/foundation-one-cdx (data obraschenija: 22.06.2020)
  5. Specimen Preparation Instructions Caris Molecular Intelligence URL https://www.carismolecularintelligence.com/wp-content/uploads/2017/12/TN0252-v8_Specimen_Prep_Instructions_hi-rez.pdf (data obraschenija: 22.06.2020)
  6. Lindeman N.I., Cagle P.T., Aisner D.L., Arcila M.E., Beth Beasley M., Bernicker E.H., Colasacco C., Dacic S., Hirsch F.R., Kerr K., Kwiatkowski D.J., Ladanyi M., Nowak J.A., Sholl L., Temple-Smolkin R., Solomon B., Souter L.H., Thunnissen E., Tsao M.S., Ventura C.B., Wynes N.W., and Yatabe Y. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors. Arch Pathol Lab Med. 2018; 142: 321–46. DOI: 10.5858/arpa.2017-0388-CP.
  7. Otvety na voprosy ob osobennostjah raboty s FFPE obraztsami tkanej. Beckman Coulter Life Sciences. URL: https://www.mybeckman.ru/resources/technologies/next-generation-sequencing/challenges-with-ffpe-tissue-samples (data obraschenija: 22.06.2020).
  8. Solutions for Cancer Genomics. URL: https://www.agilent.com/en/solutions/genomics/ngs-for-pathology (data obraschenija: 22.06.2020)
  9. Ivanov M., Laktionov K., Breder V., Chernenko P., Novikova E., Telysheva E., Musienko S., Baranova A., Mileyko V. Towards standardization of next-generation sequencing of FFPE samples for clinical oncology: intrinsic obstacles and possible solutions. J. Transl Med. 2017; 15 (1): 22. DOI: 10.1186/s12967-017-1125-8.
  10. Smits A.J., Kummer J.A., Bruin P.C., Bol M., van den Tweel J.G., Seldenrijk K.A., Willems S.M., Offerhaus G.J.A., de Weger R.A., van Diest P.J., Vink A. The estimation of tumor cell percentage for molecular testing by pathologists is not accurate. Modern Pathology. 2014; 27: 168–74. DOI: 10.1038/modpathol.2013.134.
  11. Loree L.M., Kopetz S., Raghav K.P.S. Current companion diagnostics in advanced colorectal cancer; getting a bigger and better piece of the pie. J. Gastrointest Oncol. 2017; 8 (1): 199–212. DOI: 10.21037/jgo.2017.01.01.
  12. Dufraing K., van Krieken J.H., De Hertogh G., Hoefler G., Oniscu A., Kuhlmann T.P., Weichert W., Marchiò C., Ristimäki A., Ryška A., Scoazec J.Y., and Dequeker E. Neoplastic cell percentage estimation in tissue samples for molecular oncology: recommendations from a modified Delphi study. Histopathology. 2019; 75 (3): 312–9. DOI: 10.1111/his.13891.
  13. Park S., Holmes-Tisch A.J., Yoon Cho E., Mog Shim Y., Kim J., Song Kim H., Lee J., Hee Park Y., Seok Ahn J., Park K., Jänne P.A., Ahn M-Ju. Discordance of Molecular Biomarkers Associated with Epidermal Growth Factor Receptor Pathway between Primary Tumors and Lymph Node Metastasis in Non-small Cell Lung Cancer. J. Thorac Oncol. 2009; 4: 809–15. DOI: 10.1097/JTO.0b013e3181a94af4.
  14. Thunnissen E., Kerr K.M., Herth F.J.F., Lantuejoul S., Papotti M., Rintoul R.C., Rossi G., Skov B.G., Weynand B., Bubendorf L., Katrien G., Johansson L., López-Rios F., Ninane V., Olszewski W., Popper H., Jaume S., Schnabel P., Thiberville L., Laenger F. The challenge of NSCLC diagnosis and predictive analysis on small samples. Practical approach of a working group. Lung Cancer. 2012; 76 (1): 1–18. DOI: 10.1016/j.lungcan.2011.10.017.
  15. Lhermitte B., Egele C., Weingertner N., Ambrosetti D., Dadone B., Kubiniek V., Burel-Vandenbos F., Coyne J., Michiels J.F., Chenard M.P., Rouleau E., Sabourin J.C., Bellocq J.P. Adequately Defining Tumor Cell Proportion in Tissue Samples for Molecular Testing Improves Interobserver Reproducibility of Its Assessment. Virchows Arch. 2017; 470 (1): 21–7. DOI: 10.1007/s00428-016-2042-6.
  16. Dufraing K., Hertogh G., Tack V., Keppens C., Dequeker E.M.C., Hanvan Krieken J. External Quality Assessment Identifies Training Needs to Determine the Neoplastic Cell Content for Biomarker Testing. The Journal of Molecular Diagnostics. 2018; 20 (4): 455–64. DOI: 10.1016/j.jmoldx.2018.03.003.
  17. Brown R.W., Della Speranza V., O Alvarez J., Eisen R.N., Frishberg D.P., Rosai J., Santiago J., Tunnicliffe J., Colasacco C., Lacchetti C., Thomas N.E. Uniform Labeling of Blocks and Slides in Surgical Pathology. Arch Pathol Lab Med. 2015; 139: 1515–24. DOI: 10.5858/arpa.2014-0340-SA.