A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer.
Due to advancement in sequencing technology, genomes of thousands of cancer tissues or cell-lines have been sequenced. Identification of cancer-specific epitopes or neoepitopes from cancer genomes is one of the major challenges in the field of immunotherapy or vaccine development. This paper describes a platform Cancertope, developed for designing genome-based immunotherapy or vaccine against a cancer cell. Broadly, the integrated resources on this platform are apportioned into three precise sections. First section explains a cancer-specific database of neoepitopes generated from genome of 905 cancer cell lines. This database harbors wide range of epitopes (e.g., B-cell, CD8+ T-cell, HLA class I, HLA class II) against 60 cancer-specific vaccine antigens. Second section describes a partially personalized module developed for predicting potential neoepitopes against a user-specific cancer genome. Finally, we describe a fully personalized module developed for identification of neoepitopes from genomes of cancerous and healthy cells of a cancer-patient. In order to assist the scientific community, wide range of tools are incorporated in this platform that includes screening of epitopes against human reference proteome (http://www.imtech.res.in/raghava/cancertope/).
Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.
Sudheer
S
Gupta
Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.
Kumardeep
K
Chaudhary
Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.
Sandeep Kumar
SK
Dhanda
Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.
Rahul
R
Kumar
Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.
Shailesh
S
Kumar
Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.
Manika
M
Sehgal
Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.
Gandharva
G
Nagpal
Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.
Gajendra P S
http://orcid.org/0000-0002-8902-2876
GP
Raghava
D019496:Cancer Vaccines / Q000235:genetics* / Q000627:therapeutic use; D003198:Computer Simulation; D000939:Epitopes / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D007167:Immunotherapy / Q000379:methods*; D020407:Internet; D009154:Mutation; D009369:Neoplasms / Q000235:genetics* / Q000517:prevention & control; D010455:Peptides / Q000235:genetics / Q000627:therapeutic use; D057285:Precision Medicine
D019496:Cancer Vaccines; D000939:Epitopes; D010455:Peptides