PMID- 32090262
OWN - NLM
STAT- MEDLINE
DCOM- 20201119
LR  - 20201119
IS  - 1758-0463 (Electronic)
IS  - 1758-0463 (Linking)
VI  - 2020
DP  - 2020 Jan 1
TI  - dbPepNeo: a manually curated database for human tumor neoantigen peptides.
LID - 10.1093/database/baaa004 [doi]
LID - baaa004
AB  - Neoantigens can function as actual antigens to facilitate tumor rejection, which 
      play a crucial role in cancer immunology and immunotherapy. Emerging evidence 
      revealed that neoantigens can be used to develop personalized, cancer-specific 
      vaccines. To date, large numbers of immunogenomic peptides have been 
      computationally predicted to be potential neoantigens. However, experimental 
      validation remains the gold standard for potential clinical application. 
      Experimentally validated neoantigens are rare and mostly appear scattered among 
      scientific papers and various databases. Here, we constructed dbPepNeo, a 
      specific database for human leukocyte antigen class I (HLA-I) binding neoantigen 
      peptides based on mass spectrometry (MS) validation or immunoassay in human 
      tumors. According to the verification methods of these neoantigens, the 
      collection of peptides was classified as 295 high confidence, 247 medium 
      confidence and 407 794 low confidence neoantigens, respectively. This can serve 
      as a valuable resource to aid further screening for effective neoantigens, 
      optimize a neoantigen prediction pipeline and study T-cell receptor (TCR) 
      recognition. Three applications of dbPepNeo are shown. In summary, this work 
      resulted in a platform to promote the screening and confirmation of potential 
      neoantigens in cancer immunotherapy. Database URL: 
      www.biostatistics.online/dbPepNeo/.
CI  - (c) The Author(s) 2020. Published by Oxford University Press.
FAU - Tan, Xiaoxiu
AU  - Tan X
AD  - School of Medical Instrument and Food Engineering, University of Shanghai for 
      Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, 
      China.
AD  - Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and 
      Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China.
FAU - Li, Daixi
AU  - Li D
AD  - School of Medical Instrument and Food Engineering, University of Shanghai for 
      Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, 
      China.
FAU - Huang, Pengjie
AU  - Huang P
AD  - School of Medical Instrument and Food Engineering, University of Shanghai for 
      Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, 
      China.
AD  - Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and 
      Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China.
FAU - Jian, Xingxing
AU  - Jian X
AD  - Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and 
      Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China.
AD  - Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education; Key 
      Laboratory of Carcinogenesis, National Health and Family Planning Commission, 
      Xiangya Hospital, Central South University, Central South University, No. 932, 
      South Lushan Road, Yuelu District, Changsha 410083, China.
FAU - Wan, Huihui
AU  - Wan H
AD  - School of Medical Instrument and Food Engineering, University of Shanghai for 
      Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, 
      China.
AD  - Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and 
      Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China.
FAU - Wang, Guangzhi
AU  - Wang G
AD  - Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and 
      Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China.
AD  - College of Food Science and Technology, Shanghai Ocean University, No. 999, 
      Hucheng Ring Road, Pudong New District, Shanghai 201306, China.
FAU - Li, Yuyu
AU  - Li Y
AD  - Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and 
      Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China.
AD  - College of Food Science and Technology, Shanghai Ocean University, No. 999, 
      Hucheng Ring Road, Pudong New District, Shanghai 201306, China.
FAU - Ouyang, Jian
AU  - Ouyang J
AD  - Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and 
      Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China.
FAU - Lin, Yong
AU  - Lin Y
AD  - School of Medical Instrument and Food Engineering, University of Shanghai for 
      Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, 
      China.
FAU - Xie, Lu
AU  - Xie L
AD  - Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and 
      Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China.
LA  - eng
PT  - Dataset
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Database (Oxford)
JT  - Database : the journal of biological databases and curation
JID - 101517697
RN  - 0 (Antigens, Neoplasm)
RN  - 0 (Cancer Vaccines)
RN  - 0 (Peptides)
SB  - IM
MH  - *Antigens, Neoplasm
MH  - Cancer Vaccines
MH  - Humans
MH  - Immunotherapy
MH  - Neoplasms/chemistry/immunology/metabolism
MH  - *Peptides
PMC - PMC7043295
EDAT- 2020/02/25 06:00
MHDA- 2020/11/20 06:00
PMCR- 2020/02/22
CRDT- 2020/02/25 06:00
PHST- 2019/10/01 00:00 [received]
PHST- 2019/12/24 00:00 [revised]
PHST- 2020/01/09 00:00 [accepted]
PHST- 2020/02/25 06:00 [entrez]
PHST- 2020/02/25 06:00 [pubmed]
PHST- 2020/11/20 06:00 [medline]
PHST- 2020/02/22 00:00 [pmc-release]
AID - 5747759 [pii]
AID - baaa004 [pii]
AID - 10.1093/database/baaa004 [doi]
PST - ppublish
SO  - Database (Oxford). 2020 Jan 1;2020:baaa004. doi: 10.1093/database/baaa004.