Formalin a key problem for molecular diagnostics

Formalin preserves tissues by cross-linking proteins with its surroundings, however, this negatively impacts downstream molecular assays

Experts broadly agree formalin is a key problem for molecular diagnostics (dx). Background references: 

1.  Lewis F, Maughan NJ, Smith V, Hillan K, Quirke P. Unlocking the archive–gene expression in paraffin‐embedded tissue. J Pathol, 2001, 195:66–71

2.  Hunt JL. Molecular pathology in anatomic pathology practice: a review of basic principles. Arch Pathol Lab Med, 2008, 132:248–60

3.  Ascierto PA, Bifulco C, Palmieri G, Peters S, Sidiropoulos N. Preanalytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis. J Mol Diagnostics, 2019, 21:756–67

4.  Williams C, Pontén F, Moberg C, Söderkvist P, Uhlén M, Pontén J, Sitbon G, Lundeberg J. A high frequency of sequence alterations is due to formalin fixation of archival specimens. Am J Pathol, 1999, 155:1467–71

5.  Ye X, Zhu Z-Z, Zhong L, Lu Y, Sun Y, Yin X, Yang Z, Zhu G, Ji Q. High T790M detection rate in TKI-naive NSCLC with EGFR sensitive mutation: truth or artifact? J Thorac Oncol, 2013, 8:1118–20

6  Cox ML, Ph D, Arbor A. Working with Fixatives , Fixation , and Tissue Processing to Improve Morphology and RNA Quality Morphology and RNA Quality. Quality, 2006

7.  Arreaza G, Qiu P, Pang L, Albright A, Hong LZ, Marton MJ, Levitan D. Pre-analytical considerations for successful next-generation sequencing (NGS): challenges and opportunities for formalin-fixed and paraffin-embedded tumor tissue (FFPE) samples. Int J Mol Sci, 2016, 17:1579

8.  Kim S-W, Roh J, Park C-S. Immunohistochemistry for Pathologists: Protocols, Pitfalls, and Tips. J Pathol Transl Med, 2016, 50:411–8

9.  Miller MA, Ramos-Vara JA, Kleiboeker SB, Larson RL. Effects of delayed or prolonged fixation on immunohistochemical detection of bovine viral diarrhea virus type I in skin of two persistently infected calves. J Vet Diagnostic Investig, 2005, 17:461–3

10.  Pikkarainen M, Martikainen P, Alafuzoff I. The effect of prolonged fixation time on immunohistochemical staining of common neurodegenerative disease markers. J Neuropathol Exp Neurol, 2010, 69:40–52

11.  Webster JD, Miller MA, DuSold D, Ramos-Vara J. Effects of prolonged formalin fixation on the immunohistochemical detection of infectious agents in formalin-fixed, paraffin-embedded tissues. Vet Pathol, 2010, 47:529–35