{"id":"https://openalex.org/W4410184057","doi":"https://doi.org/10.1186/s13073-026-01821-9","title":"Identification of (ultra-)rare candidate functional promoter mutations in cancer using sequence-based deep learning models","display_name":"Identification of (ultra-)rare candidate functional promoter mutations in cancer using sequence-based deep learning models","publication_year":2026,"publication_date":"2026-11-11","ids":{"openalex":"https://openalex.org/W4410184057","doi":"https://doi.org/10.1186/s13073-026-01821-9"},"language":"en","primary_location":{"id":"doi:10.1186/s13073-026-01821-9","doi":"https://doi.org/10.1186/s13073-026-01821-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13073-026-01821-9","pdf_url":null,"source":{"id":"https://openalex.org/S149201819","display_name":"Genome Medicine","issn_l":"1756-994X","issn":["1756-994X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Medicine","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s13073-026-01821-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092832794","display_name":"Tijs van Lieshout","orcid":"https://orcid.org/0000-0003-0441-0309","observed_orcids":["https://orcid.org/0000-0003-0441-0309"]},"institutions":[{"id":"https://openalex.org/I1334415907","display_name":"University Medical Center Groningen","ror":"https://ror.org/03cv38k47","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I1334415907"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Tijs van Lieshout","raw_affiliation_strings":["Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, HPC CB50, UMCG, P.O. Box 30001, Groningen, 9700 RB, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0003-0441-0309","affiliations":[{"raw_affiliation_string":"Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, HPC CB50, UMCG, P.O. Box 30001, Groningen, 9700 RB, The Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088951094","display_name":"Carlos G. Urz\u00faa-Traslavi\u00f1a","orcid":"https://orcid.org/0000-0003-1146-1630","observed_orcids":["https://orcid.org/0000-0003-1146-1630"]},"institutions":[{"id":"https://openalex.org/I1334415907","display_name":"University Medical Center Groningen","ror":"https://ror.org/03cv38k47","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I1334415907"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Carlos G. Urz\u00faa-Traslavi\u00f1a","raw_affiliation_strings":["Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, HPC CB50, UMCG, P.O. Box 30001, Groningen, 9700 RB, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, HPC CB50, UMCG, P.O. Box 30001, Groningen, 9700 RB, The Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104431824","display_name":"Luc\u00eda Barbadilla-Mart\u00ednez","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I3018483916","display_name":"University Medical Center Utrecht","ror":"https://ror.org/0575yy874","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I3018483916"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Luc\u00eda Barbadilla-Mart\u00ednez","raw_affiliation_strings":["Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I3018483916"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104431831","display_name":"Minh Chau Luong Boi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Minh Chau Luong Boi","raw_affiliation_strings":["Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047168944","display_name":"Harm-Jan Westra","orcid":"https://orcid.org/0000-0001-7038-567X","observed_orcids":["https://orcid.org/0000-0001-7038-567X"]},"institutions":[{"id":"https://openalex.org/I1334415907","display_name":"University Medical Center Groningen","ror":"https://ror.org/03cv38k47","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I1334415907"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Harm-Jan Westra","raw_affiliation_strings":["Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, HPC CB50, UMCG, P.O. Box 30001, Groningen, 9700 RB, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, HPC CB50, UMCG, P.O. Box 30001, Groningen, 9700 RB, The Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5146909239","display_name":"Francisco Cam\u00f5es Magalh\u00e3es","orcid":"https://orcid.org/0009-0004-5473-9561","observed_orcids":["https://orcid.org/0009-0004-5473-9561"]},"institutions":[{"id":"https://openalex.org/I1334415907","display_name":"University Medical Center Groningen","ror":"https://ror.org/03cv38k47","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I1334415907"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Francisco Cam\u00f5es Magalh\u00e3es","raw_affiliation_strings":["Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, HPC CB50, UMCG, P.O. Box 30001, Groningen, 9700 RB, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, HPC CB50, UMCG, P.O. Box 30001, Groningen, 9700 RB, The Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016566179","display_name":"Noud H.M. Klaassen","orcid":"https://orcid.org/0009-0006-4904-0654","observed_orcids":["https://orcid.org/0009-0006-4904-0654"]},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Noud H. M. Klaassen","raw_affiliation_strings":["Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000074907","display_name":"Vin\u00edcius H. Franceschini-Santos","orcid":"https://orcid.org/0000-0001-9276-0370","observed_orcids":["https://orcid.org/0000-0001-9276-0370"]},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Vin\u00edcius H. Franceschini-Santos","raw_affiliation_strings":["Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122786856","display_name":"Miguel Parra-Martinez","orcid":"https://orcid.org/0009-0007-8052-8225","observed_orcids":["https://orcid.org/0009-0007-8052-8225"]},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Miguel Parra-Mart\u00ednez","raw_affiliation_strings":["Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068125480","display_name":"G. Ridder","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I3018483916","display_name":"University Medical Center Utrecht","ror":"https://ror.org/0575yy874","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I3018483916"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]},{"id":"https://openalex.org/I4210127118","display_name":"Princess M\u00e1xima Center","ror":"https://ror.org/02aj7yc53","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210127118"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Jeroen de Ridder","raw_affiliation_strings":["Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands","Oncode Institute, Utrecht, The Netherlands","Prinses M\u00e1xima Centrum, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I3018483916"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]},{"raw_affiliation_string":"Prinses M\u00e1xima Centrum, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210127118"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5161471545","display_name":"Bas van Steensel","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Bas van Steensel","raw_affiliation_strings":["Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5161474123","display_name":"Emile Voest","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Emile Voest","raw_affiliation_strings":["Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082560822","display_name":"Lude Franke","orcid":"https://orcid.org/0000-0002-5159-8802","observed_orcids":["https://orcid.org/0000-0002-5159-8802"]},"institutions":[{"id":"https://openalex.org/I1334415907","display_name":"University Medical Center Groningen","ror":"https://ror.org/03cv38k47","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I1334415907"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]},{"id":"https://openalex.org/I4210111138","display_name":"Oncode Institute","ror":"https://ror.org/01n92vv28","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210111138"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Lude H. Franke","raw_affiliation_strings":["Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, HPC CB50, UMCG, P.O. Box 30001, Groningen, 9700 RB, The Netherlands","Oncode Institute, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, HPC CB50, UMCG, P.O. Box 30001, Groningen, 9700 RB, The Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]},{"raw_affiliation_string":"Oncode Institute, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I4210111138"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5068125480","https://openalex.org/A5082560822","https://openalex.org/A5092832794","https://openalex.org/A5161471545","https://openalex.org/A5161474123"],"corresponding_institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384","https://openalex.org/I2898336195","https://openalex.org/I3018483916","https://openalex.org/I4210111138","https://openalex.org/I4210127118"],"apc_list":{"value":5290,"currency":"USD","value_usd":5290},"apc_paid":{"value":5290,"currency":"USD","value_usd":5290},"fwci":1.9314,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.78240168,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9136000275611877,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9136000275611877,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.07119999825954437,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12820","display_name":"Chromatin Remodeling and Cancer","score":0.006399999838322401,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ultra-rare-variants","display_name":"ultra-rare variants","score":0.7789999842643738},{"id":"https://openalex.org/keywords/somatic-mutations","display_name":"somatic mutations","score":0.6579999923706055},{"id":"https://openalex.org/keywords/promoter-mutations","display_name":"promoter mutations","score":0.8330000042915344},{"id":"https://openalex.org/keywords/sequence-based-deep-learning","display_name":"sequence-based deep learning","score":0.7950000166893005},{"id":"https://openalex.org/keywords/massively-parallel-reporter-assay","display_name":"massively parallel reporter assay","score":0.8330000042915344},{"id":"https://openalex.org/keywords/candidate-cancer-genes","display_name":"candidate cancer genes","score":0.6340000033378601},{"id":"https://openalex.org/keywords/gene-expression-regulation","display_name":"gene expression regulation","score":0.6919999718666077},{"id":"https://openalex.org/keywords/tert","display_name":"telomerase reverse transcriptase","score":0.8669999837875366},{"id":"https://openalex.org/keywords/tp53","display_name":"TP53","score":0.9079999923706055},{"id":"https://openalex.org/keywords/pms2","display_name":"PMS2","score":0.9890000224113464},{"id":"https://openalex.org/keywords/aimp2","display_name":"AIMP2","score":0.7379999756813049},{"id":"https://openalex.org/keywords/rpl13a","display_name":"RPL13A","score":0.9710000157356262},{"id":"https://openalex.org/keywords/regulatory-elements","display_name":"regulatory elements","score":0.5239999890327454}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7043160796165466},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6854898929595947},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6073391437530518},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.475872665643692},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.42444878816604614},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4016234278678894},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3954417109489441},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3892252445220947},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3364470899105072},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13073-026-01821-9","doi":"https://doi.org/10.1186/s13073-026-01821-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13073-026-01821-9","pdf_url":null,"source":{"id":"https://openalex.org/S149201819","display_name":"Genome Medicine","issn_l":"1756-994X","issn":["1756-994X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Medicine","raw_type":"journal-article"},{"id":"doi:10.1101/2025.05.06.25327057","doi":"https://doi.org/10.1101/2025.05.06.25327057","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.05.06.25327057","pdf_url":"https://www.medrxiv.org/content/medrxiv/early/2025/05/06/2025.05.06.25327057.full.pdf","source":{"id":"https://openalex.org/S3005729997","display_name":"medRxiv","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"medRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pure.rug.nl:openaire/0cf16173-e71f-40f5-be91-ffe9ad19bc70","doi":null,"is_oa":true,"landing_page_url":"https://research.rug.nl/en/publications/0cf16173-e71f-40f5-be91-ffe9ad19bc70","pdf_url":null,"source":{"id":"https://openalex.org/S4306400420","display_name":"University of Groningen research database (University of Groningen / Centre for Information Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I169381384","host_organization_name":"University of Groningen","host_organization_lineage":["https://openalex.org/I169381384"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"van Lieshout, T, Urz\u00faa-Traslavi\u00f1a, C G, Barbadilla-Mart\u00ednez, L, Luong Boi, M C, Westra, H-J, Klaassen, N H M, Franceschini-Santos, V H, Parra-Mart\u00ednez, M, de Ridder, J, van Steensel, B, Voest, E & Franke, L H 2025 'Identification of (ultra-)rare functional promoter mutations in cancer using sequence-based deep learning models' MedRxiv. https://doi.org/10.1101/2025.05.06.25327057","raw_type":"workingPaper"}],"best_oa_location":{"id":"doi:10.1186/s13073-026-01821-9","doi":"https://doi.org/10.1186/s13073-026-01821-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13073-026-01821-9","pdf_url":null,"source":{"id":"https://openalex.org/S149201819","display_name":"Genome Medicine","issn_l":"1756-994X","issn":["1756-994X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Medicine","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.9391000270843506,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G7609741974","display_name":null,"funder_award_id":"09150182010019","funder_id":"https://openalex.org/F4320321007","funder_display_name":"ZonMw"}],"funders":[{"id":"https://openalex.org/F4320321007","display_name":"ZonMw","ror":"https://ror.org/01yaj9a77"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410184057.pdf","grobid_xml":"https://content.openalex.org/works/W4410184057.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1587447328","https://openalex.org/W1985646870","https://openalex.org/W2055567028","https://openalex.org/W2083295043","https://openalex.org/W2096458947","https://openalex.org/W2124649657","https://openalex.org/W2335717063","https://openalex.org/W2606495925","https://openalex.org/W2609153336","https://openalex.org/W2768013244","https://openalex.org/W2889473065","https://openalex.org/W2894573839","https://openalex.org/W2921650138","https://openalex.org/W2944340292","https://openalex.org/W2952020316","https://openalex.org/W2953622121","https://openalex.org/W3004859565","https://openalex.org/W3025310710","https://openalex.org/W3043270904","https://openalex.org/W3047825284","https://openalex.org/W3133859624","https://openalex.org/W3138025188","https://openalex.org/W3203588026","https://openalex.org/W4224006698","https://openalex.org/W4224993560","https://openalex.org/W4321611595","https://openalex.org/W4361001523","https://openalex.org/W4390616142","https://openalex.org/W4390878940","https://openalex.org/W4394539210","https://openalex.org/W4395447546","https://openalex.org/W4399781527","https://openalex.org/W4400656884","https://openalex.org/W4403115234","https://openalex.org/W4403670271","https://openalex.org/W4404535307","https://openalex.org/W4406178430","https://openalex.org/W7127576249"],"related_works":["https://openalex.org/W4402856009","https://openalex.org/W6922251695","https://openalex.org/W2567596952","https://openalex.org/W7160325309","https://openalex.org/W2741089644","https://openalex.org/W2117396697","https://openalex.org/W4399331428","https://openalex.org/W7148727148","https://openalex.org/W2784773015","https://openalex.org/W7168045606"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"The":[2],"identification":[3],"of":[4,54,69,119,278],"non-coding":[5,285,291],"somatic":[6,56,292],"cancer-driver":[7,226],"mutations":[8,32,103,177,286,293],"remains":[9],"challenging":[10],"due":[11],"to":[12,28,49,109,251,295],"difficulties":[13],"in":[14,61,116,182],"interpreting":[15],"rare":[16],"and":[17,165,196,258,287],"ultra-rare":[18],"variants.":[19],"We":[20,64,199],"hypothesized":[21],"that":[22,44,100,104,207,289],"sequence-based":[23,47,279],"models":[24,48,280],"can":[25],"be":[26],"used":[27],"systematically":[29],"prioritize":[30],"such":[31,162],"for":[33,82,173,216,225,281],"their":[34],"functional":[35,52,218,284],"relevance.":[36],"Methods":[37],"Here,":[38],"we":[39,84,125],"developed":[40],"a":[41,128,202],"computational":[42],"framework":[43],"leverages":[45],"two":[46],"assess":[50],"the":[51,67,276],"impact":[53],"(ultra-)rare":[55],"single":[57],"nucleotide":[58],"variants":[59],"(SNVs)":[60],"promoter":[62,102],"regions.":[63],"first":[65],"tested":[66],"validity":[68],"our":[70,105],"approach":[71],"by":[72,144,265],"analysing":[73],"SNVs":[74],"derived":[75],"from":[76,80,245],"3,825":[77],"whole-tumour":[78],"genomes":[79],"patients":[81],"whom":[83],"also":[85,169],"had":[86],"matching":[87],"RNA-seq":[88],"data":[89],"available.":[90],"Results":[91],"This":[92],"very":[93],"strict":[94],"validation":[95],"strategy":[96],"yielded":[97],"57":[98],"genes":[99,124,156,161,221,227,240],"contain":[101],"model":[106],"consistently":[107],"predicts":[108],"preferentially":[110],"activate":[111],"or":[112],"repress":[113],"gene":[114,134],"expression":[115,135],"three":[117],"cohorts":[118],"different":[120],"patients.":[121],"For":[122],"nine":[123],"could":[126],"confirm":[127],"nominally":[129],"significant":[130],"change":[131],"using":[132],"actual":[133],"level":[136],"measurements":[137],"as":[138,163],"well":[139,158],"(6.32\u00d7":[140],"higher":[141],"than":[142,263],"expected":[143,264],"chance,":[145],"p":[146,229,242,268],"-value":[147,230,269],"=":[148,231,270],"1.16":[149],"\u00d7":[150,233,247,253],"10":[151,234,248,254],"\u2212":[152,235,249,255],"5":[153],").":[154],"These":[155,220,273],"include":[157],"known":[159],"cancer":[160,296],"TERT":[164],"PMS2":[166],",":[167,186,188,190,192,194],"but":[168],"several":[170],"new":[171],"candidates":[172],"which":[174],"no":[175],"coding":[176],"have":[178],"previously":[179],"been":[180],"implicated":[181],"cancer,":[183],"including":[184],"AIMP2":[185],"SASS6":[187],"ALKBH4":[189],"FICD":[191],"TTK":[193],"YAE1":[195],"ETF1":[197],".":[198],"subsequently":[200],"conducted":[201],"meta-analysis":[203],"across":[204],"24,529":[205],"samples":[206],"revealed":[208],"619":[209],"genes,":[210],"whose":[211],"promoters":[212],"are":[213,222,259],"significantly":[214,223],"enriched":[215,224],"candidate":[217,283],"SNVs.":[219],"(":[228,241,267],"5.94":[232],"3":[236,250],"),":[237],"cell":[238],"cycle":[239],"-values":[243],"ranging":[244],"1.24":[246],"2.82":[252],"2":[256],")":[257],"more":[260],"evolutionary":[261],"conserved":[262],"chance":[266],"0.022).":[271],"Conclusions":[272],"findings":[274],"demonstrate":[275],"utility":[277],"identifying":[282],"suggest":[288],"many":[290],"contribute":[294],"development.":[297]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2025-05-08T00:00:00"}
