{"doi":"10.1101/2022.10.07.510944","title":"BamQuery: a proteogenomic tool for the genome-wide exploration of the immunopeptidome","abstract":"ABSTRACT MHC-I-associated peptides (MAPs) derive from selective yet highly diverse genomic regions, including allegedly non-protein-coding sequences, such as endogenous retroelements (EREs). Quantifying canonical (exonic) and non-canonical MAPs-encoding RNA expression in malignant and benign cells is critical for identifying tumor antigens (TAs) but represents a challenge for immunologists. We present BamQuery, a computational tool attributing an exhaustive RNA expression to MAPs of any origin (exon, intron, UTR, intergenic) from bulk and single-cell RNA-sequencing data. We show that non-canonical MAPs (including TAs) can derive from multiple different genomic regions (up to 35,343 for EREs), abundantly expressed in normal tissues. We also show that supposedly tumor-specific mutated MAPs, viral MAPs, and MAPs derived from proteasomal splicing can arise from different unmutated non-canonical genomic regions. The genome-wide approach of BamQuery allows comprehensive mapping of all MAPs in healthy and cancer tissues. BamQuery can also help predict MAP immunogenicity and identify safe and actionable TAs.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":304541,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9502,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":623174,"name":"Marie‐Pierre Hardy","orcid":"0000-0003-1316-6483","position":1,"is_corresponding":false},{"id":316386,"name":"Jean‐David Larouche","orcid":"0000-0003-3056-0714","position":2,"is_corresponding":false},{"id":897389,"name":"Anca Apavaloaei","orcid":"0000-0001-6896-1199","position":3,"is_corresponding":false},{"id":997432,"name":"Eralda Kina","orcid":"0000-0001-6191-7523","position":4,"is_corresponding":false},{"id":316391,"name":"Krystel Vincent","orcid":"0000-0001-6180-5345","position":5,"is_corresponding":false},{"id":316393,"name":"Patrick Gendron","orcid":"0000-0001-9829-2600","position":6,"is_corresponding":false},{"id":316394,"name":"Jean‐Philippe Laverdure","orcid":"0000-0002-9245-6413","position":7,"is_corresponding":false},{"id":316392,"name":"Chantal Durette","orcid":"0000-0002-6692-1262","position":8,"is_corresponding":false},{"id":304775,"name":"Pierre Thibault","orcid":"0000-0001-5993-0331","position":9,"is_corresponding":false},{"id":316396,"name":"Sébastien Lemieux","orcid":"0000-0001-5477-1386","position":10,"is_corresponding":false},{"id":316397,"name":"Claude Perreault","orcid":"0000-0001-9453-7383","position":11,"is_corresponding":false},{"id":316389,"name":"Grégory Ehx","orcid":"0000-0002-7018-1770","position":12,"is_corresponding":false},{"id":623173,"name":"Maria Virginia Ruiz Cuevas","orcid":"0000-0002-9974-264X","position":0,"is_corresponding":true}],"reference_count":62,"raw_metadata":null,"created_at":"2026-07-19T00:32:32.651796Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}