Adoptive neoantigen-reactive T cell therapy: improvement strategies and current clinical researches

Biomarker Research

Table 1 Common platforms and algorithms for neoantigen prediction

Tools Name	Function	Tool type	Ref
Burrows-Wheeler Alignment tool (BWA)	Alignment tool for mutation identification	software	[34]
ANNOVAR	Mutation identification and functional annotation	software	[35]
MuTect,SomaticSniper	Mutation calling and screening	software	[36, 37]
VarScan	Mutations and copy number alterations calling	software	[38]
FusionCatcher	Fusion gene mutation identification	software	http://code.google.com/p/fusioncatcher/
NetMHCpan/NetMHCpanII, MHCflurry	MHC-I/II binding affinity prediction	software	[41, 48,49,50]
MixMHCpred score, HLAthena	MHC-I binding ligands prediction	algorithm	[42, 51]
MHCnuggets	MHC-I or MHC-II binding ligands prediction	software	[43]
ProGeo-Neo	Mutation calling, MHC-I and MHC-II binding affinity and binding ligands prediction	software	[44]
Differential agretopic index(DAI)	Difference identification between mutant and wild sequences	algorithm	[39]
NetCTLpan	T cell epitope and MHC-I binding ligands prediction	software	[52]
TCRMatch	T cell epitope prediction	software	[46]
PyClone	Clonal population prediction	algorithm	[53]
MuPeXI	Neoantigen Immunogenicity identification	software	[54]
Immune Epitope Database (IEDB)	Epitope data	database	[45]
Tumor Neoantigen Selection Alliance(TESLA)	Epitope and sequencing data	database	[47]

ISSN: 2050-7771