SpotNeoMet

This repository contains the source code and related figures from SpotNeoMet pipeline described in the manuscript:

Recurrent immunogenic neoantigens and their cognate T-cell receptors in treatment-resistant metastatic prostate cancer. Gumpert N, Sagie S, Arnedo-Pac C, Babu T, Weller C, Gonzalez-Perez A, Wang Y, Michel Todó L, Levy R, Chen X, Greenberg P, Dayan-Rubinov M, Yakubovich E, Wasserman-Bartov T, Zerbib M, Gong J, Rebernick RJ, Oliveira Tercero A, Agundez Muriel L, Benedek G, Kedmi M, Oren R, Ben-Dor S, Levin Y, Troyanskaya OG, Munzur AD, Wyatt AW, Cieslik MP, Quigley DA, Van Allen EM, Anandasabapathy N, Mateo J, Yang X, Martínez-Jiménez F, Lopez-Bigas N, Samuels Y. Cancer Discov. 2025 Oct 8. doi: 10.1158/2159-8290.CD-24-1213. Epub ahead of print. PMID: 41056506.

Contents

1. Pipeline

   1. Hotspot identification (HotspotFinder)

   2. Processing of hotspots (VEP annotation)

   3. Generation of peptides overlapping hotspots

   4. Run neoantigen identification (MHCnuggets, MHCFlurry, NetMHCpan)

   5. Merge predictions from neoantigen identification

   6. Pre-process sample-specific metadata (e.g., mutations, HLAs, BoostDM driver predictions)

   7. Merge neoantigen identification outputs and metadata

   8. Neoantigen prioritisation

2. Figures

3. Data