{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T14:37:20Z","timestamp":1777387040383,"version":"3.51.4"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,12,20]],"date-time":"2021-12-20T00:00:00Z","timestamp":1639958400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100003196","name":"Italian Ministry of Health","doi-asserted-by":"crossref","award":["GR-2016-02361272"],"award-info":[{"award-number":["GR-2016-02361272"]}],"id":[{"id":"10.13039\/501100003196","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Alliance Against Cancer funds"},{"name":"Italian Ministry of Health with Ricerca Corrente and 5x1000 fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Tumor mutational burden (TMB) has been proposed as a predictive biomarker for immunotherapy response in cancer patients, as it is thought to enrich for tumors with high neoantigen load. TMB assessed by whole-exome sequencing is considered the gold standard but remains confined to research settings. In the clinical setting, targeted gene panels sampling various genomic sizes along with diverse strategies to estimate TMB were proposed and no real standard has emerged yet.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We provide the community with TMBleR, a tool to measure the clinical impact of various strategies of panel-based TMB measurement.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>R package and docker container (GPL-3 Open Source license): https:\/\/acc-bioinfo.github.io\/TMBleR\/. Graphical-user interface website: https:\/\/bioserver.ieo.it\/shiny\/app\/tmbler.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab836","type":"journal-article","created":{"date-parts":[[2021,12,14]],"date-time":"2021-12-14T12:13:29Z","timestamp":1639484009000},"page":"1724-1726","source":"Crossref","is-referenced-by-count":2,"title":["TMBleR: a bioinformatic tool to optimize TMB estimation and predictive power"],"prefix":"10.1093","volume":"38","author":[{"given":"Laura","family":"Fancello","sequence":"first","affiliation":[{"name":"Unit\u00e9 Biosant\u00e9, Institut de Recherche Interdisciplinaire de Grenoble (IRIG) , Grenoble, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7160-750X","authenticated-orcid":false,"given":"Alessandro","family":"Guida","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , Milan, Italy"},{"name":"Biomedical Translational Imaging Centre, IWK Health Center , Halifax, NS, Canada"},{"name":"Department of Diagnostic Radiology, Dalhousie University , Halifax, NS, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3253-7091","authenticated-orcid":false,"given":"Gianmaria","family":"Frige","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9533-4246","authenticated-orcid":false,"given":"Arnaud Gerard Michel","family":"Ceol","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriele","family":"Babini","sequence":"additional","affiliation":[{"name":"Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS , Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giovanni Luca","family":"Scaglione","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Oncology, IDI-IRCCS, Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mario","family":"Zanfardino","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics and Statistics, IRCCS SDN, Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0434-8533","authenticated-orcid":false,"given":"Tommaso","family":"Mazza","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza , San Giovanni Rotondo, FG, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lorenzo","family":"Ferrando","sequence":"additional","affiliation":[{"name":"Dipartimento di Medicina Interna, Universit\u00e0 Degli Studi di Genova , Genova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pier Giuseppe","family":"Pelicci","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , Milan, Italy"},{"name":"Department of Oncology and Hemato-Oncology, University of Milan , 20142 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4043-3279","authenticated-orcid":false,"given":"Luca","family":"Mazzarella","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , Milan, Italy"},{"name":"Division of Early Drug Development, IEO, European Institute of Oncology IRCCS , Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,12,20]]},"reference":[{"key":"2023020108572396100_btab836-B1","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1038\/s41586-020-1943-3","article-title":"The repertoire of mutational signatures in human cancer","volume":"578","author":"Alexandrov","year":"2020","journal-title":"Nature"},{"key":"2023020108572396100_btab836-B2","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/s43018-019-0008-8","article-title":"Multimodal genomic features predict outcome of immune checkpoint blockade in non-small-cell lung cancer","volume":"1","author":"Anagnostou","year":"2020","journal-title":"Nat. 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