Fixation Effects on Variant Calling in a Clinical Resequencing Panel

Publication date: Available online 2 May 2019Source: The Journal of Molecular DiagnosticsAuthor(s): Jeremy D.K. Parker, Shyong Q. Yap, Elizabeth Starks, Jillian Slind, Lucas Swanson, T. Roderick Docking, Megan Fuller, Chen Zhou, Blair Walker, Douglas Filipenko, Wei Xiong, Ahmer A. Karimuddin, P. Terry Phang, Manoj Raval, Carl J. Brown, Aly KarsanFormalin fixation is the standard method for the preservation of tissue for diagnostic purposes, including pathologic review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic test results. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade, laboratory-developed targeted resequencing assay. Several parameters relating to sequencing quality and variant calling were examined and quantified in tumor and normal colon epithelial tissues. An alternative fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathologic review was identified.
Source: The Journal of Molecular Diagnostics - Category: Pathology Source Type: research