alexa Tissue Requirements and DNA Quality Control for Clinical Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Samples: A Mini-Review of Practical Issues
ISSN: 1747-0862

Journal of Molecular and Genetic Medicine
Open Access

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Mini Review

Tissue Requirements and DNA Quality Control for Clinical Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Samples: A Mini-Review of Practical Issues

Chung MJ1,2, Lin W1, Dong L1 and Li X1*

1Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA

2Department of Pathology, Chonbuk National University Medical School, San 2-20 Keumam-Dong, Jeonju 561-180, Republic of Korea

*Corresponding Author:
Dr. Xinmin Li
Department of Pathology and Laboratory Medicine
David Geffen School of Medicine
University of California
Los Angeles, California, USA
Tel: 3108253664
Fax: 3108253570
E-mail: [email protected]

Received date: April 10, 2017; Accepted date: May 02, 2017; Published date: May 05, 2017

Citation: Chung MJ, Lin W, Dong L, Li X (2017) 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 11:262 doi:10.4172/1747-0862.1000262

Copyright: © 2017 Chung MJ, et al . This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

 

Abstract

Most molecular pathology laboratories perform mutational analyses to diagnose somatic cancer mutations and evaluate therapeutic options on formalin fixed paraffin embedded (FFPE) samples as daily practice using various methods. Recent studies show that targeted next-generation sequencing (NGS) is a promising diagnostic method with many benefits including simultaneous detection of multiple mutations in various genes in a single test. High quality DNA is essential for an efficient and successful NGS performance. However, low tumor tissue percentage and low DNA quality are the main limitations to use FFPE DNA for NGS assay. We reviewed and discussed the required tissue amount for the NGS assay, the effect of formalin fixation on DNA integrity, and the method for reduction of formalin-induced sequencing artifacts. We also review DNA extraction methods, DNA quality control methods and quality control workflow for nucleic acids and libraries. This review provides an overview for molecular pathology laboratories or researcher considering NGS to detect somatic cancer mutations using small FFPE samples.

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