PMID- 30223042
OWN - NLM
STAT- MEDLINE
DCOM- 20181211
LR  - 20181211
IS  - 2210-3244 (Electronic)
IS  - 1672-0229 (Print)
IS  - 1672-0229 (Linking)
VI  - 16
IP  - 4
DP  - 2018 Aug
TI  - TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data 
      Analysis.
PG  - 276-282
LID - S1672-0229(18)30306-1 [pii]
LID - 10.1016/j.gpb.2018.06.003 [doi]
AB  - Tumor-specific neoantigens have attracted much attention since they can be used 
      as biomarkers to predict therapeutic effects of immune checkpoint blockade 
      therapy and as potential targets for cancer immunotherapy. In this study, we 
      developed a comprehensive tumor-specific neoantigen database (TSNAdb v1.0), based 
      on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte 
      antigen (HLA) allele information for 16 tumor types with 7748 tumor samples from 
      The Cancer Genome Atlas (TCGA) and The Cancer Immunome Atlas (TCIA). We predicted 
      binding affinities between mutant/wild-type peptides and HLA class I molecules by 
      NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 
      potential neoantigens generated by somatic mutations of all tumor samples. 
      Moreover, we employed recurrent mutations in combination with highly frequent HLA 
      alleles to predict potential shared neoantigens across tumor patients, which 
      would facilitate the discovery of putative targets for neoantigen-based cancer 
      immunotherapy. TSNAdb is freely available at http://biopharm.zju.edu.cn/tsnadb.
CI  - Copyright (c) 2018 The Authors. Production and hosting by Elsevier B.V. All rights 
      reserved.
FAU - Wu, Jingcheng
AU  - Wu J
AD  - Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial 
      Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, 
      Zhejiang University, Hangzhou 310058, China.
FAU - Zhao, Wenyi
AU  - Zhao W
AD  - Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, 
      Zhejiang University, Hangzhou 310058, China.
FAU - Zhou, Binbin
AU  - Zhou B
AD  - College of Computer Science and Technology, Zhejiang University, Hangzhou 310013, 
      China.
FAU - Su, Zhixi
AU  - Su Z
AD  - MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan 
      University, Shanghai 200438, China.
FAU - Gu, Xun
AU  - Gu X
AD  - Department of Genetics, Development and Cell Biology, Iowa State University, 
      Ames, IA 50011, USA.
FAU - Zhou, Zhan
AU  - Zhou Z
AD  - Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial 
      Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, 
      Zhejiang University, Hangzhou 310058, China. Electronic address: 
      zhanzhou@zju.edu.cn.
FAU - Chen, Shuqing
AU  - Chen S
AD  - Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial 
      Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, 
      Zhejiang University, Hangzhou 310058, China. Electronic address: 
      chenshuqing@zju.edu.cn.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20180915
PL  - England
TA  - Genomics Proteomics Bioinformatics
JT  - Genomics, proteomics & bioinformatics
JID - 101197608
RN  - 0 (Antigens, Neoplasm)
RN  - 0 (Tumor Suppressor Protein p53)
SB  - IM
MH  - Antigens, Neoplasm/*metabolism
MH  - *Data Analysis
MH  - *Databases, Genetic
MH  - Humans
MH  - Immunotherapy
MH  - Mutation/genetics
MH  - Neoplasms/*genetics/*immunology
MH  - Tumor Suppressor Protein p53/genetics
MH  - Urinary Bladder Neoplasms/genetics
PMC - PMC6203688
OTO - NOTNLM
OT  - Cancer immunotherapy
OT  - Database
OT  - Human leukocyte antigen
OT  - Neoantigen
OT  - Somatic mutation
EDAT- 2018/09/18 06:00
MHDA- 2018/12/12 06:00
PMCR- 2018/09/15
CRDT- 2018/09/18 06:00
PHST- 2018/03/19 00:00 [received]
PHST- 2018/05/18 00:00 [revised]
PHST- 2018/06/25 00:00 [accepted]
PHST- 2018/09/18 06:00 [pubmed]
PHST- 2018/12/12 06:00 [medline]
PHST- 2018/09/18 06:00 [entrez]
PHST- 2018/09/15 00:00 [pmc-release]
AID - S1672-0229(18)30306-1 [pii]
AID - 10.1016/j.gpb.2018.06.003 [doi]
PST - ppublish
SO  - Genomics Proteomics Bioinformatics. 2018 Aug;16(4):276-282. doi: 
      10.1016/j.gpb.2018.06.003. Epub 2018 Sep 15.