Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Mutational signature analysis

ZC Zhang-Hua Chen
SY Shu-Mei Yan
XC Xi-Xi Chen
QZ Qi Zhang
SL Shang-Xin Liu
YL Yang Liu
YL Yi-Ling Luo
CZ Chao Zhang
MX Miao Xu
YZ Yi-Fan Zhao
LH Li-Yun Huang
BL Bin-Liu Liu
TX Tian-Liang Xia
DX Da-Zhi Xu
YL Yao Liang
YC Yong-Ming Chen
WW Wei Wang
SY Shu-Qiang Yuan
HZ Hui-Zhong Zhang
JY Jing-Ping Yun
WZ Wei-Wei Zhai
MZ Mu-Sheng Zeng
FB Fan Bai
QZ Qian Zhong
request Request a Protocol
ask Ask a question
Favorite

Single nucleotide variations (SNVs) could be categorized into 6 directions, namely, C > T, C > A, C > G, T > C, T > G, and T > A. Considering the 5′ and 3′ flanking nucleotides of a specific mutated base, a total of 96 substitution types exist. We first plotted the “lego” plots to compare the frequency of mutations within specific contexts in precursor lesions and EBVaGCs of 20 patients. As the set of mutational contexts of tumor samples was an imprint of the mutational process that shaped the cancer genome, we then performed a mutational signature analysis of all silent and non-silent mutations in our study. To extract the underlying mutational signatures in single precursor lesion samples and EBVaGCs, we applied the R package deconstructSigs [16] to each sample using the 30 signatures documented by the COSMIC as reference. After extraction, we calculated and compared the mean weights of different signatures in 45 precursor lesions and 65 EBVaGCs.

Copyright and License information: The Author(s) ©2021
Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A