{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T19:46:56Z","timestamp":1789588016547,"version":"build-2803163510"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,5,6]],"date-time":"2022-05-06T00:00:00Z","timestamp":1651795200000},"content-version":"vor","delay-in-days":125,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000098","name":"National Institutes of Health Clinical Center","doi-asserted-by":"publisher","award":["1F30CA225136"],"award-info":[{"award-number":["1F30CA225136"]}],"id":[{"id":"10.13039\/100000098","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000098","name":"National Institutes of Health Clinical Center","doi-asserted-by":"publisher","award":["5R01CA201225"],"award-info":[{"award-number":["5R01CA201225"]}],"id":[{"id":"10.13039\/100000098","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000098","name":"National Institutes of Health Clinical Center","doi-asserted-by":"publisher","award":["R37CA247676"],"award-info":[{"award-number":["R37CA247676"]}],"id":[{"id":"10.13039\/100000098","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000098","name":"National Institutes of Health Clinical Center","doi-asserted-by":"publisher","award":["T32CA196589"],"award-info":[{"award-number":["T32CA196589"]}],"id":[{"id":"10.13039\/100000098","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of North Carolina University Cancer Research Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Splice variant neoantigens are a potential source of tumor-specific antigen (TSA) that are shared between patients in a variety of cancers, including acute myeloid leukemia. Current tools for genomic prediction of splice variant neoantigens demonstrate promise. However, many tools have not been well validated with simulated and\/or wet lab approaches, with no studies published that have presented a targeted immunopeptidome mass spectrometry approach designed specifically for identification of predicted splice variant neoantigens.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we describe NeoSplice, a novel computational method for splice variant neoantigen prediction based on (i) prediction of tumor-specific k-mers from RNA-seq data, (ii) alignment of differentially expressed k-mers to the splice graph and (iii) inference of the variant transcript with MHC binding prediction. NeoSplice demonstrates high sensitivity and precision (&amp;gt;80% on average across all splice variant classes) through in silico simulated RNA-seq data. Through mass spectrometry analysis of the immunopeptidome of the K562.A2 cell line compared against a synthetic peptide reference of predicted splice variant neoantigens, we validated 4 of 37 predicted antigens corresponding to 3 of 17 unique splice junctions. Lastly, we provide a comparison of NeoSplice against other splice variant prediction tools described in the literature. NeoSplice provides a well-validated platform for prediction of TSA vaccine targets for future cancer antigen vaccine studies to evaluate the clinical efficacy of splice variant neoantigens.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/Benjamin-Vincent-Lab\/NeoSplice<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics Advances online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioadv\/vbac032","type":"journal-article","created":{"date-parts":[[2022,5,4]],"date-time":"2022-05-04T19:09:38Z","timestamp":1651691378000},"source":"Crossref","is-referenced-by-count":43,"title":["NeoSplice: a bioinformatics method for prediction of splice variant neoantigens"],"prefix":"10.1093","volume":"2","author":[{"given":"Shengjie","family":"Chai","sequence":"first","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27514, USA"},{"name":"Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine , Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6517-0439","authenticated-orcid":false,"given":"Christof C","family":"Smith","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27514, USA"},{"name":"Department of Microbiology and Immunology, UNC School of Medicine , Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tavleen K","family":"Kochar","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of North Carolina , Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sally A","family":"Hunsucker","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27514, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wolfgang","family":"Beck","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27514, USA"},{"name":"Department of Microbiology and Immunology, UNC School of Medicine , Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly S","family":"Olsen","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27514, USA"},{"name":"Department of Microbiology and Immunology, UNC School of Medicine , Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"Vensko","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27514, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary L","family":"Glish","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of North Carolina , Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul M","family":"Armistead","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27514, USA"},{"name":"Division of Hematology, Department of Medicine, UNC School of Medicine , Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0853-6099","authenticated-orcid":false,"given":"Jan F","family":"Prins","sequence":"additional","affiliation":[{"name":"Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine , Chapel Hill, NC, 27599, USA"},{"name":"Department of Computer Science, University of North Carolina , Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1762-2282","authenticated-orcid":false,"given":"Benjamin G","family":"Vincent","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27514, USA"},{"name":"Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine , Chapel Hill, NC, 27599, USA"},{"name":"Department of Microbiology and Immunology, UNC School of Medicine , Chapel Hill, NC, 27599, USA"},{"name":"Division of Hematology, Department of Medicine, UNC School of Medicine , Chapel Hill, NC, 27599, USA"},{"name":"Computational Medicine Program, UNC School of Medicine , Chapel Hill, NC, 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,5,6]]},"reference":[{"key":"2022111617494774400_vbac032-B1","doi-asserted-by":"crossref","first-page":"e87361","DOI":"10.1371\/journal.pone.0087361","article-title":"A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events","volume":"9","author":"Brooks","year":"2014","journal-title":"PLoS One"},{"key":"2022111617494774400_vbac032-B2","doi-asserted-by":"crossref","first-page":"2059","DOI":"10.1056\/NEJMoa1301689","article-title":"Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia","volume":"368","author":"Cancer Genome Atlas Research Network","year":"2013","journal-title":"New Engl. J. Med"},{"key":"2022111617494774400_vbac032-B3","doi-asserted-by":"crossref","first-page":"e1001091","DOI":"10.1371\/journal.pbio.1001091","article-title":"Modernizing reference genome assemblies","volume":"9","author":"Church","year":"2011","journal-title":"PLoS Biol"},{"key":"2022111617494774400_vbac032-B4","article-title":"Aberrant splicing and drug resistance in AML","volume":"9, 85","author":"de Necochea-Campion","year":"2016","journal-title":"J. Hematol. Oncol"},{"key":"2022111617494774400_vbac032-B5","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2022111617494774400_vbac032-B6","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1016\/j.immuni.2021.03.001","article-title":"Atypical acute myeloid leukemia-specific transcripts generate shared and immunogenic MHC class-I-associated epitopes","volume":"54","author":"Ehx","year":"2021","journal-title":"Immunity"},{"key":"2022111617494774400_vbac032-B7","doi-asserted-by":"crossref","first-page":"2778","DOI":"10.1093\/bioinformatics\/btv272","article-title":"Polyester: simulating RNA-seq datasets with differential transcript expression","volume":"31","author":"Frazee","year":"2015","journal-title":"Bioinformatics"},{"key":"2022111617494774400_vbac032-B8","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nature24277","article-title":"Genetic effects on gene expression across human tissues","volume":"550","author":"GTEx Consortium","year":"2017","journal-title":"Nature"},{"key":"2022111617494774400_vbac032-B9","doi-asserted-by":"crossref","first-page":"2093","DOI":"10.1056\/NEJMoa1801946","article-title":"Nivolumab plus ipilimumab in lung cancer with a high tumor mutational burden","volume":"378","author":"Hellmann","year":"2018","journal-title":"New Engl. J. Med"},{"key":"2022111617494774400_vbac032-B10","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1056\/NEJMoa1003466","article-title":"Improved survival with ipilimumab in patients with metastatic melanoma","volume":"363","author":"Hodi","year":"2010","journal-title":"New Engl. J. Med"},{"key":"2022111617494774400_vbac032-B11","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13073-016-0264-5","article-title":"pVAC-Seq: a genome-guided in silico approach to identifying tumor neoantigens","volume":"8","author":"Hundal","year":"2016","journal-title":"Genome Med"},{"key":"2022111617494774400_vbac032-B12","article-title":"Cancer neoantigens: a promising source of immunogens for cancer immunotherapy","volume":"6, 2","author":"Ito","year":"2015","journal-title":"J. Clin. Cell Immunol"},{"key":"2022111617494774400_vbac032-B13","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1016\/j.celrep.2018.03.052","article-title":"Systematic analysis of splice-site-creating mutations in cancer","volume":"23","author":"Jayasinghe","year":"2018","journal-title":"Cell Rep"},{"key":"2022111617494774400_vbac032-B14","doi-asserted-by":"crossref","first-page":"3360","DOI":"10.4049\/jimmunol.1700893","article-title":"NetMHCpan-4.0: improved peptide\u2013MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data","volume":"199","author":"Jurtz","year":"2017","journal-title":"J. Immunol"},{"key":"2022111617494774400_vbac032-B15","doi-asserted-by":"crossref","first-page":"1840","DOI":"10.1093\/bioinformatics\/btw076","article-title":"SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data","volume":"32","author":"Kahles","year":"2016","journal-title":"Bioinformatics"},{"key":"2022111617494774400_vbac032-B16","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.ccell.2018.07.001","article-title":"Comprehensive analysis of alternative splicing across tumors from 8,705 patients","volume":"34","author":"Kahles","year":"2018","journal-title":"Cancer Cell"},{"key":"2022111617494774400_vbac032-B17","doi-asserted-by":"crossref","first-page":"e85902","DOI":"10.1172\/jci.insight.85902","article-title":"Claudin-low bladder tumors are immune infiltrated and actively immune suppressed","volume":"1","author":"Kardos","year":"2016","journal-title":"JCI Insight"},{"key":"2022111617494774400_vbac032-B18","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nrg2776","article-title":"Alternative splicing and evolution: diversification, exon definition and function","volume":"11","author":"Keren","year":"2010","journal-title":"Nat. Rev. Genet"},{"key":"2022111617494774400_vbac032-B19","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1038\/s41586-018-0792-9","article-title":"Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial","volume":"565","author":"Keskin","year":"2019","journal-title":"Nature"},{"key":"2022111617494774400_vbac032-B20","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1093\/annonc\/mdy022","article-title":"Neopepsee: accurate genome-level prediction of neoantigens by harnessing sequence and amino acid immunogenicity information","volume":"29","author":"Kim","year":"2018","journal-title":"Ann. Oncol"},{"key":"2022111617494774400_vbac032-B21","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1056\/NEJMoa1910836","article-title":"Five-year survival with combined nivolumab and ipilimumab in advanced melanoma","volume":"381","author":"Larkin","year":"2019","journal-title":"New Engl. J. Med"},{"key":"2022111617494774400_vbac032-B22","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1038\/nm.4097","article-title":"Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins","volume":"22","author":"Lee","year":"2016","journal-title":"Nat. Med"},{"key":"2022111617494774400_vbac032-B23","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1182\/blood.V45.3.321.321","article-title":"Human chronic myelogenous leukemia cell-line with positive philadelphia chromosome","volume":"45","author":"Lozzio","year":"1975","journal-title":"Blood"},{"key":"2022111617494774400_vbac032-B24","doi-asserted-by":"crossref","first-page":"R19","DOI":"10.1186\/gb-2014-15-1-r19","article-title":"MutPred splice: machine learning-based prediction of exonic variants that disrupt splicing","volume":"15","author":"Mort","year":"2014","journal-title":"Genome Biol"},{"key":"2022111617494774400_vbac032-B25","doi-asserted-by":"crossref","first-page":"2966","DOI":"10.1093\/bioinformatics\/btz033","article-title":"Improved indel detection in DNA and RNA via realignment with ABRA2","volume":"35","author":"Mose","year":"2019","journal-title":"Bioinformatics"},{"key":"2022111617494774400_vbac032-B26","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/nature22991","article-title":"An immunogenic personal neoantigen vaccine for patients with melanoma","volume":"547","author":"Ott","year":"2017","journal-title":"Nature"},{"key":"2022111617494774400_vbac032-B27","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1158\/2326-6066.CIR-17-0051","article-title":"SLC45A2: a melanoma antigen with high tumor selectivity and reduced potential for autoimmune toxicity","volume":"5","author":"Park","year":"2017","journal-title":"Cancer Immunol. Res"},{"key":"2022111617494774400_vbac032-B28","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1182\/blood-2014-04-567933","article-title":"Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia","volume":"124","author":"Rajasagi","year":"2014","journal-title":"Blood"},{"key":"2022111617494774400_vbac032-B29","doi-asserted-by":"crossref","first-page":"R4","DOI":"10.1186\/gb-2012-13-1-r4","article-title":"SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data","volume":"13","author":"Rogers","year":"2012","journal-title":"Genome Biol"},{"key":"2022111617494774400_vbac032-B30","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/nature23003","article-title":"Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer","volume":"547","author":"Sahin","year":"2017","journal-title":"Nature"},{"key":"2022111617494774400_vbac032-B31","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1126\/science.1203486","article-title":"Cancer immunoediting: integrating immunity\u2019s roles in cancer suppression and promotion","volume":"331","author":"Schreiber","year":"2011","journal-title":"Science"},{"key":"2022111617494774400_vbac032-B32","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1126\/science.aaa4971","article-title":"Neoantigens in cancer immunotherapy","volume":"348","author":"Schumacher","year":"2015","journal-title":"Science"},{"key":"2022111617494774400_vbac032-B33","doi-asserted-by":"crossref","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","article-title":"rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data","volume":"111","author":"Shen","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2022111617494774400_vbac032-B34","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1038\/nbt.4239","article-title":"Intron retention is a source of neoepitopes in cancer","volume":"36","author":"Smart","year":"2018","journal-title":"Nat. Biotechnol"},{"key":"2022111617494774400_vbac032-B35","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1038\/s41568-019-0162-4","article-title":"Alternative tumour-specific antigens","volume":"19","author":"Smith","year":"2019","journal-title":"Nat. Rev. Cancer"},{"key":"2022111617494774400_vbac032-B36","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1158\/2326-6066.CIR-19-0155","article-title":"Machine-learning prediction of tumor antigen immunogenicity in the selection of therapeutic epitopes","volume":"7","author":"Smith","year":"2019","journal-title":"Cancer Immunol. Res"},{"key":"2022111617494774400_vbac032-B37","doi-asserted-by":"crossref","first-page":"3310","DOI":"10.1093\/bioinformatics\/btu548","article-title":"OptiType: precision HLA typing from next-generation sequencing data","volume":"30","author":"Szolek","year":"2014","journal-title":"Bioinformatics"},{"key":"2022111617494774400_vbac032-B38","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/j.immuni.2019.08.004","article-title":"The immune landscape of cancer","volume":"51","author":"Thorsson","year":"2019","journal-title":"Immunity"},{"key":"2022111617494774400_vbac032-B39","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1016\/S1470-2045(17)30516-8","article-title":"Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis","volume":"18","author":"Turajlic","year":"2017","journal-title":"Lancet Oncol"},{"key":"2022111617494774400_vbac032-B40","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/nrc.2016.154","article-title":"Targeting neoantigens to augment antitumour immunity","volume":"17","author":"Yarchoan","year":"2017","journal-title":"Nat. Rev. Cancer"},{"key":"2022111617494774400_vbac032-B41","doi-asserted-by":"crossref","first-page":"14633","DOI":"10.18632\/aging.103516","article-title":"ASNEO: identification of personalized alternative splicing based neoantigens with RNA-seq","volume":"12","author":"Zhang","year":"2020","journal-title":"Aging"}],"container-title":["Bioinformatics Advances"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/advance-article-pdf\/doi\/10.1093\/bioadv\/vbac032\/43589458\/vbac032.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/2\/1\/vbac032\/47086023\/vbac032.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/2\/1\/vbac032\/47086023\/vbac032.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,16]],"date-time":"2022-11-16T17:50:16Z","timestamp":1668621016000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article\/doi\/10.1093\/bioadv\/vbac032\/6581739"}},"subtitle":[],"editor":[{"given":"Thomas","family":"Lengauer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,1,1]]},"references-count":41,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,1,10]]}},"URL":"https:\/\/doi.org\/10.1093\/bioadv\/vbac032","relation":{},"ISSN":["2635-0041"],"issn-type":[{"value":"2635-0041","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2022,1,1]]},"article-number":"vbac032"}}