Full Text

Turn on search term navigation

© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

Background and Objectives: Panel-based next-generation sequencing (NGS) has been carried out in daily clinical settings for the diagnosis and treatment guidance of patients with non-small cell lung cancer (NSCLC). The success of genomic tests including NGS depends in large part on preparing better-quality DNA or RNA; however, there are no established operating methods for preparing genomic DNA and RNA samples. Materials and Methods: We compared the following two quantitative methods, the QubitTM and NanoDropTM, using 585 surgical specimens, 278 biopsy specimens, and 82 cell block specimens of lung cancer that were used for genetic tests, including NGS. We analyzed the success rate of the genomic tests, including NGS, which were performed with DNA and RNA with concentrations that were outliers for the Qubit Fluorometer. Results: The absolute value for DNA concentrations had a tendency to be higher when measured with NanoDropTM regardless of the type of specimen; however, this was not the case for RNA. The success rate of DNA-based genomic tests using specimens with a concentration below the lower limit of QubitTM detection was as high as approximately 96%. At less than 60%, the success rate of RNA-based genomic tests, including RT-PCR, was not as satisfactory. The success rates of the AmpliSeqTM DNA panel sequencing and RNA panel sequencing were 77.8% and 91.5%, respectively. If at least one PCR amplification product could be obtained, then all RNA-based sequencing was performed successfully. Conclusions: The concentration measurements with NanoDropTM are reliable. The success rate of NGS with samples at concentrations below the limit of detection of QubitTM was relatively higher than expected, and it is worth performing PCR-based panel sequencing, especially in cases where re-biopsy cannot be performed.

Details

Title
Comparison between Fluorimetry (Qubit) and Spectrophotometry (NanoDrop) in the Quantification of DNA and RNA Extracted from Frozen and FFPE Tissues from Lung Cancer Patients: A Real-World Use of Genomic Tests
Author
Masago, Katsuhiro 1   VIAFID ORCID Logo  ; Fujita, Shiro 2   VIAFID ORCID Logo  ; Oya, Yuko 3 ; Takahashi, Yusuke 3 ; Matsushita, Hirokazu 4 ; Sasaki, Eiichi 1   VIAFID ORCID Logo  ; Kuroda, Hiroaki 3   VIAFID ORCID Logo 

 Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya 4648681, Japan; [email protected] 
 Department of Respiratory Medicine, Kobe Central Hospital, Kobe 651115, Japan; [email protected] 
 Department of Thoracic Surgery, Aichi Cancer Center, Nagoya 4648681, Japan; [email protected] (Y.O.); [email protected] (Y.T.); [email protected] (H.K.) 
 Division of Translational Oncoimmunology, Aichi Cancer Research Institute, Nagoya 4648681, Japan; [email protected] 
First page
1375
Publication year
2021
Publication date
2021
Publisher
MDPI AG
ISSN
1010660X
e-ISSN
16489144
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2612792976
Copyright
© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.