Fixation Effects on Variant Calling in a Clinical Resequencing Panel.
Journal
The Journal of molecular diagnostics : JMD
ISSN: 1943-7811
Titre abrégé: J Mol Diagn
Pays: United States
ID NLM: 100893612
Informations de publication
Date de publication:
07 2019
07 2019
Historique:
received:
10
05
2018
revised:
15
03
2019
accepted:
20
03
2019
pubmed:
6
5
2019
medline:
20
6
2020
entrez:
6
5
2019
Statut:
ppublish
Résumé
Formalin 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. We identified an alternative fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathologic review.
Identifiants
pubmed: 31055024
pii: S1525-1578(18)30196-X
doi: 10.1016/j.jmoldx.2019.03.005
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
705-717Informations de copyright
Copyright © 2019 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.