Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma
Abstract Background With the development of sequencing technologies, there may be some disputes on sequencing analysis. The aim of this study was to investigate different allele frequency thresholds of mutations in targeted genes on prognostic analyses using a panel of cancer associated gene exons (...
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doaj-d3c508d0988b40168b1e71bce6babb1f2020-11-24T21:55:18ZengBMCBMC Cancer1471-24072018-07-0118111010.1186/s12885-018-4481-8Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinomaJie Ma0Yong Fu1Yao-yao Tu2Ying Liu3Yi-ran Tan4Wu-tong Ju5Curtis R. Pickering6Jeffrey N. Myers7Zhi-yuan Zhang8Lai-ping Zhong9Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People’s Hospital, Shanghai Jiao Tong University School of MedicineDepartment of Oral & Maxillofacial-Head & Neck Oncology, Ninth People’s Hospital, Shanghai Jiao Tong University School of MedicineDepartment of Oral & Maxillofacial-Head & Neck Oncology, Ninth People’s Hospital, Shanghai Jiao Tong University School of MedicineDepartment of Oral & Maxillofacial-Head & Neck Oncology, Ninth People’s Hospital, Shanghai Jiao Tong University School of MedicineDepartment of Oral & Maxillofacial-Head & Neck Oncology, Ninth People’s Hospital, Shanghai Jiao Tong University School of MedicineDepartment of Oral & Maxillofacial-Head & Neck Oncology, Ninth People’s Hospital, Shanghai Jiao Tong University School of MedicineDepartment of Head & Neck Surgery, University of Texas MD Anderson Cancer CenterDepartment of Head & Neck Surgery, University of Texas MD Anderson Cancer CenterDepartment of Oral & Maxillofacial-Head & Neck Oncology, Ninth People’s Hospital, Shanghai Jiao Tong University School of MedicineDepartment of Oral & Maxillofacial-Head & Neck Oncology, Ninth People’s Hospital, Shanghai Jiao Tong University School of MedicineAbstract Background With the development of sequencing technologies, there may be some disputes on sequencing analysis. The aim of this study was to investigate different allele frequency thresholds of mutations in targeted genes on prognostic analyses using a panel of cancer associated gene exons (CAGE) in oral squamous cell carcinoma (OSCC). Methods Forty-six patients were included in this study. Twelve genes were sequenced and analyzed using next-generation sequencing from formalin-fixed paraffin-embedded tissues. Allele frequency thresholds of 10, 5, and 3% were used for prognostic analyses. Results With a mean sequence depth of 3199-fold, 99% of CAGE were represented by at least 10 reads. Ninety-four non-synonymous (missense [70.2%], nonsense [11.7%], splice site [10.6%], and insertion/deletion [7.5%]) mutations were detected in 40 OSCC patients with an allele frequency threshold of 10%. TP53 (78.3%), NOTCH1 (30.4%), CASP8 (13.0%), CDKN2A (10.9%), and CDH1 (6.5%) were the most frequently mutated genes. Using allele frequency thresholds of 10, 5, and 3%, there were no significant differences in clinical outcomes between patients with non-synonymous mutations and wild type genotypes. Conclusions TP53, NOTCH1, CASP8, CDKN2A, and CDH1 are the most frequently mutated genes in OSCC patients. The allele frequency threshold used in this study does not affect the results of clinical outcome analysis.http://link.springer.com/article/10.1186/s12885-018-4481-8Oral squamous cell carcinomaNext-generation sequencingMutation allele frequency |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jie Ma Yong Fu Yao-yao Tu Ying Liu Yi-ran Tan Wu-tong Ju Curtis R. Pickering Jeffrey N. Myers Zhi-yuan Zhang Lai-ping Zhong |
spellingShingle |
Jie Ma Yong Fu Yao-yao Tu Ying Liu Yi-ran Tan Wu-tong Ju Curtis R. Pickering Jeffrey N. Myers Zhi-yuan Zhang Lai-ping Zhong Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma BMC Cancer Oral squamous cell carcinoma Next-generation sequencing Mutation allele frequency |
author_facet |
Jie Ma Yong Fu Yao-yao Tu Ying Liu Yi-ran Tan Wu-tong Ju Curtis R. Pickering Jeffrey N. Myers Zhi-yuan Zhang Lai-ping Zhong |
author_sort |
Jie Ma |
title |
Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma |
title_short |
Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma |
title_full |
Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma |
title_fullStr |
Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma |
title_full_unstemmed |
Mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma |
title_sort |
mutation allele frequency threshold does not affect prognostic analysis using next-generation sequencing in oral squamous cell carcinoma |
publisher |
BMC |
series |
BMC Cancer |
issn |
1471-2407 |
publishDate |
2018-07-01 |
description |
Abstract Background With the development of sequencing technologies, there may be some disputes on sequencing analysis. The aim of this study was to investigate different allele frequency thresholds of mutations in targeted genes on prognostic analyses using a panel of cancer associated gene exons (CAGE) in oral squamous cell carcinoma (OSCC). Methods Forty-six patients were included in this study. Twelve genes were sequenced and analyzed using next-generation sequencing from formalin-fixed paraffin-embedded tissues. Allele frequency thresholds of 10, 5, and 3% were used for prognostic analyses. Results With a mean sequence depth of 3199-fold, 99% of CAGE were represented by at least 10 reads. Ninety-four non-synonymous (missense [70.2%], nonsense [11.7%], splice site [10.6%], and insertion/deletion [7.5%]) mutations were detected in 40 OSCC patients with an allele frequency threshold of 10%. TP53 (78.3%), NOTCH1 (30.4%), CASP8 (13.0%), CDKN2A (10.9%), and CDH1 (6.5%) were the most frequently mutated genes. Using allele frequency thresholds of 10, 5, and 3%, there were no significant differences in clinical outcomes between patients with non-synonymous mutations and wild type genotypes. Conclusions TP53, NOTCH1, CASP8, CDKN2A, and CDH1 are the most frequently mutated genes in OSCC patients. The allele frequency threshold used in this study does not affect the results of clinical outcome analysis. |
topic |
Oral squamous cell carcinoma Next-generation sequencing Mutation allele frequency |
url |
http://link.springer.com/article/10.1186/s12885-018-4481-8 |
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