Table Info

Table 2.

AUC receiver operating characteristic (ROC) of best performing methods on in-house dataset

Category	Method	AUC ROC
i	MHCflurry processing	0.609
iv	PRIME score	0.604
i	Variant allele frequency	0.6
iv	INeo-Epp neoantigen	0.584
i	HLAthena MSiCE	0.58
i	ProteaSMM c	0.58
i	HLAthena MSiC	0.576
i	MHCflurry PS	0.571
i	NetCTLpan TAP	0.568
i	ProteaSMM i	0.561
N/A	MixMHCpred	0.556
iv	TA predictor	0.552

Tools are grouped by categories established in this article (i: biological features; iv: tumor immunogenicity)

Supplementary materials

The supplementary Figure, Tables, and Supplementary methods in Supplementary materials for this article are available at: https://www.explorationpub.com/uploads/Article/file/100391_sup_1.xlsx and https://www.explorationpub.com/uploads/Article/file/100391_sup_2.pdf.

Declarations

Acknowledgments

We dedicate this work to our patients. This work has been performed using the Danish National Life Science Supercomputing Center, Computerome. We thank Emilio Fenoy for insightful discussions about this research.

Author contributions

IC, MN, and MMB: Conceptualization, Writing—original draft. IC: Formal analysis. IC, ES, EP, and HMGA: Investigation. IC and HMGA: Software. IC: Visualization. JM, MN, and MMB: Funding acquisition, Resources. MMB: Supervision. IC, ES, EP, HMGA, JM, MN, and MMB: Writing—review & editing. All authors read and approved the submitted version.

Conflicts of interest

The authors declare that they have no conflicts of interest.

Ethical approval

The CASVAC-0401 study was carried out after approval of the Ethics Committee of the Instituto Alexander Fleming. The study was also approved by the Argentine Regulatory Agency (ANMAT, Disposition 1299/09).

Consent to participate

Informed written consent to participate in the CASVAC study and for the use of their samples in the research projects associated with the vaccination protocol was obtained from all participants.

Consent to publication

Not applicable.

Availability of data and materials

The dataset generated for this study is included in the supplementary files.

Funding

This work was supported by grants from CONICET, Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Instituto Nacional del Cáncer—Ministerio de Salud de la Nación Argentina (INC-MSal), Fundación Sales, Fundación Cáncer, and Fundación Pedro F. Mosoteguy, Argentina. The CASVAC-0401 Phase II clinical study (Clinical Trials.gov, NCT 01729663) was sponsored by Laboratorio Pablo Cassará S.R.L. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright

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