{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T19:06:10Z","timestamp":1743447970757,"version":"3.37.3"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2022,2,18]],"date-time":"2022-02-18T00:00:00Z","timestamp":1645142400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"crossref","award":["CPII18\/00026, PI17\/01304"],"award-info":[{"award-number":["CPII18\/00026, PI17\/01304"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Instituto de Salud Carlos III, the Ag\u00e8ncia de Gesti\u00f3 d\u2019Ajuts Universitaris i de Recerca, Generalitat de Catalunya","award":["2017 SGR 1035"],"award-info":[{"award-number":["2017 SGR 1035"]}]},{"DOI":"10.13039\/501100002704","name":"Fundaci\u00f3n Cient\u00edfica de la Asociaci\u00f3n Espa\u00f1ola Contra el C\u00e1ncer","doi-asserted-by":"crossref","award":["GCB13131592CAST"],"award-info":[{"award-number":["GCB13131592CAST"]}],"id":[{"id":"10.13039\/501100002704","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"crossref","award":["FI18\/00221"],"award-info":[{"award-number":["FI18\/00221"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"crossref"}]},{"name":"MICINN\/MINECO","award":["BES-2017-081286"],"award-info":[{"award-number":["BES-2017-081286"]}]},{"name":"Fundaci\u00f3 Universit\u00e0ria Agust\u00ed Pedro i Pons"},{"name":"COST Action","award":["CA17118"],"award-info":[{"award-number":["CA17118"]}]},{"DOI":"10.13039\/501100000921","name":"COST","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000921","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genomic alterations can modulate the tumor immunophenotype depending on their nature and tissue of origin. Although this immune\u2013genomic interaction may shape disease progression and response to immunotherapy, the factors governing such dynamics and the influence of each tissue-specific context remain poorly understood.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we have developed the PanCancer ImmunoGenomics (PCIG) tool, a web-based resource that provides researchers with the opportunity to mine immunome\u2013genome relationships across several cancer types using data from the Pan-Cancer Analysis of Whole-Genomes (PCAWG) study, which comprises &amp;gt;2,600 samples spanning across 20 different cancer primary sites. PCIG yields an integrative analysis of the crosstalk between somatic genomic alterations and different immune features, thus helping to understand immune response-related processes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PCIG is freely available at https:\/\/pcig.vhio.net and is supported by all major web browsers. PCIG was developed with Django, which is a Python-based free and open-source framework, and it uses SQL Server as a relational database management system. The code is freely available for download at GitHub https:\/\/github.com\/AnnaPG\/PCIG and in its online supplementary material.<\/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\/btac111","type":"journal-article","created":{"date-parts":[[2022,2,16]],"date-time":"2022-02-16T20:13:44Z","timestamp":1645042424000},"page":"2374-2376","source":"Crossref","is-referenced-by-count":3,"title":["PCIG: a web-based application to explore immune\u2013genomics interactions across cancer types"],"prefix":"10.1093","volume":"38","author":[{"given":"Anna","family":"Pedrola","sequence":"first","affiliation":[{"name":"Oncology Data Science (ODysSey) Group, Vall d\u2019Hebron Institute of Oncology , Barcelona 08035, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebasti\u00e0","family":"Franch-Exp\u00f3sito","sequence":"additional","affiliation":[{"name":"Marie-Jos\u00e9e and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center , New York, NY 10065, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sara","family":"Lahoz","sequence":"additional","affiliation":[{"name":"Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, IDIBAPS, Hospital Cl\u00ednic de Barcelona, CIBEREHD , Barcelona 08036, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roger","family":"Esteban-Fabr\u00f3","sequence":"additional","affiliation":[{"name":"Liver Cancer Translational Research Group, Liver Unit, IDIBAPS, Hospital Cl\u00ednic de Barcelona, CIBEREHD , Barcelona 08036, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rodrigo","family":"Dienstmann","sequence":"additional","affiliation":[{"name":"Oncology Data Science (ODysSey) Group, Vall d\u2019Hebron Institute of Oncology , Barcelona 08035, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laia","family":"Bassaganyas","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus , Cambridge CB2 0QQ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2929-4228","authenticated-orcid":false,"given":"Jordi","family":"Camps","sequence":"additional","affiliation":[{"name":"Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology Team, IDIBAPS, Hospital Cl\u00ednic de Barcelona, CIBEREHD , Barcelona 08036, Spain"},{"name":"Department of Cell Biology, Physiology and Immunology, Universitat Aut\u00f2noma de Barcelona , Bellaterra 08193, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,2,18]]},"reference":[{"key":"2023020109030564900_btac111-B1","doi-asserted-by":"crossref","first-page":"6350","DOI":"10.1158\/1078-0432.CCR-20-1497","article-title":"Copy-number alteration burden differentially impacts immune profiles and molecular features of hepatocellular carcinoma","volume":"26","author":"Bassaganyas","year":"2020","journal-title":"Clin. Cancer Res"},{"key":"2023020109030564900_btac111-B2","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.celrep.2016.12.019","article-title":"Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade","volume":"18","author":"Charoentong","year":"2017","journal-title":"Cell Rep"},{"key":"2023020109030564900_btac111-B3","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/s41588-019-0576-7","article-title":"Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing","volume":"52","author":"Cort\u00e9s-Ciriano","year":"2020","journal-title":"Nat. Genet"},{"key":"2023020109030564900_btac111-B4","doi-asserted-by":"crossref","first-page":"eaaf8399","DOI":"10.1126\/science.aaf8399","article-title":"Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy","volume":"355","author":"Davoli","year":"2017","journal-title":"Science"},{"key":"2023020109030564900_btac111-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7554\/eLife.50267","article-title":"CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications","volume":"9","author":"Franch-Exp\u00f3sito","year":"2020","journal-title":"Elife"},{"key":"2023020109030564900_btac111-B6","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1038\/s41586-020-1969-6","article-title":"Pan-cancer analysis of whole genomes","volume":"578","year":"2020","journal-title":"Nature"},{"key":"2023020109030564900_btac111-B7","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1016\/j.cell.2021.01.002","article-title":"Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition","volume":"184","author":"Litchfield","year":"2021","journal-title":"Cell"},{"key":"2023020109030564900_btac111-B8","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-021-95287-x","article-title":"Immunogenomic pan-cancer landscape reveals immune escape mechanisms and immunoediting histories","author":"Mizuno","year":"2021"},{"key":"2023020109030564900_btac111-B9","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/s41568-019-0144-6","article-title":"Tertiary lymphoid structures in the era of cancer immunotherapy","volume":"19","author":"Saut\u00e8s-Fridman","year":"2019","journal-title":"Nat. Rev. Cancer"},{"key":"2023020109030564900_btac111-B10","doi-asserted-by":"crossref","first-page":"3717","DOI":"10.1158\/1078-0432.CCR-17-3509","article-title":"A Pan-cancer landscape of interactions between solid tumors and infiltrating immune cell populations","volume":"24","author":"Tamborero","year":"2018","journal-title":"Clin. Cancer Res"},{"key":"2023020109030564900_btac111-B11","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1016\/j.immuni.2018.03.023","article-title":"The immune landscape of cancer","volume":"48","author":"Thorsson","year":"2018","journal-title":"Immunity"},{"key":"2023020109030564900_btac111-B12","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1158\/0008-5472.CAN-16-2490","article-title":"Systematic pan-cancer analysis reveals immune cell interactions in the tumor microenvironment","volume":"77","author":"Varn","year":"2017","journal-title":"Cancer Res"},{"key":"2023020109030564900_btac111-B13","doi-asserted-by":"crossref","first-page":"2612","DOI":"10.1038\/ncomms3612","article-title":"Inferring tumour purity and stromal and immune cell admixture from expression data","volume":"4","author":"Yoshihara","year":"2013","journal-title":"Nat. Commun"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac111\/42675466\/btac111.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/8\/2374\/49010040\/btac111.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/8\/2374\/49010040\/btac111.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T20:54:45Z","timestamp":1675284885000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/8\/2374\/6531962"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,2,18]]},"references-count":13,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2022,4,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac111","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2022,4,15]]},"published":{"date-parts":[[2022,2,18]]}}}