{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T12:22:35Z","timestamp":1762431755037,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2019,10,7]],"date-time":"2019-10-07T00:00:00Z","timestamp":1570406400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002426","name":"Telethon Foundation","doi-asserted-by":"publisher","award":["TGT11D1","TGT16B01","TGT16B03"],"award-info":[{"award-number":["TGT11D1","TGT16B01","TGT16B03"]}],"id":[{"id":"10.13039\/501100002426","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ISCRA","award":["HP10CEUWXF"],"award-info":[{"award-number":["HP10CEUWXF"]}]},{"name":"Giovani Ricercatori","award":["GR-2016-02363681"],"award-info":[{"award-number":["GR-2016-02363681"]}]},{"name":"University and Research flagship initiative Interomics"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Retroviruses and their vector derivatives integrate semi-randomly in the genome of host cells and are inherited by their progeny as stable genetic marks. The retrieval and mapping of the sequences flanking the virus-host DNA junctions allows the identification of insertion sites in gene therapy or virally infected patients, essential for monitoring the evolution of genetically modified cells in vivo. However, since \u223c30% of insertions land in low complexity or repetitive regions of the host cell genome, they cannot be correctly assigned and are currently discarded, limiting the accuracy and predictive power of clonal tracking studies. Here, we present \u03b3-TRIS, a new graph-based genome-free alignment tool for identifying insertion sites even if embedded in low complexity regions. By using \u03b3-TRIS to reanalyze clinical studies, we observed improvements in clonal quantification and tracking.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code at https:\/\/bitbucket.org\/bereste\/g-tris.<\/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\/btz747","type":"journal-article","created":{"date-parts":[[2019,10,1]],"date-time":"2019-10-01T19:27:59Z","timestamp":1569958079000},"page":"1622-1624","source":"Crossref","is-referenced-by-count":8,"title":["\u03b3-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3515-3384","authenticated-orcid":false,"given":"Andrea","family":"Calabria","sequence":"first","affiliation":[{"name":"San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) , IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefano","family":"Beretta","sequence":"additional","affiliation":[{"name":"Universit\u00e0 degli Studi di Milano Bicocca, Dipartimento di Informatica Sistemistica e Comunicazione (DiSCO) , Viale Sarca, 336, 20126, Milano, Italy"},{"name":"National Research Council, Institute for Biomedical Technologies , Via Fratelli Cervi, 93, 20090, Segrate, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivan","family":"Merelli","sequence":"additional","affiliation":[{"name":"National Research Council, Institute for Biomedical Technologies , Via Fratelli Cervi, 93, 20090, Segrate, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giulio","family":"Spinozzi","sequence":"additional","affiliation":[{"name":"San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) , IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy"},{"name":"Universit\u00e0 degli Studi di Milano Bicocca, Dipartimento di Informatica Sistemistica e Comunicazione (DiSCO) , Viale Sarca, 336, 20126, Milano, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefano","family":"Brasca","sequence":"additional","affiliation":[{"name":"San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) , IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuri","family":"Pirola","sequence":"additional","affiliation":[{"name":"Universit\u00e0 degli Studi di Milano Bicocca, Dipartimento di Informatica Sistemistica e Comunicazione (DiSCO) , Viale Sarca, 336, 20126, Milano, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabrizio","family":"Benedicenti","sequence":"additional","affiliation":[{"name":"San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) , IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erika","family":"Tenderini","sequence":"additional","affiliation":[{"name":"San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) , IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paola","family":"Bonizzoni","sequence":"additional","affiliation":[{"name":"Universit\u00e0 degli Studi di Milano Bicocca, Dipartimento di Informatica Sistemistica e Comunicazione (DiSCO) , Viale Sarca, 336, 20126, Milano, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luciano","family":"Milanesi","sequence":"additional","affiliation":[{"name":"National Research Council, Institute for Biomedical Technologies , Via Fratelli Cervi, 93, 20090, Segrate, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eugenio","family":"Montini","sequence":"additional","affiliation":[{"name":"San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) , IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,10,7]]},"reference":[{"key":"2023060910375072300_btz747-B1","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.omtn.2016.12.001","article-title":"GENE-IS: time-efficient and accurate analysis of viral integration events in large-scale gene therapy data","volume":"6","author":"Afzal","year":"2017","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"2023060910375072300_btz747-B2","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.omtm.2016.11.003","article-title":"INSPIIRED: quantification and visualization tools for analyzing integration site distributions","volume":"4","author":"Berry","year":"2017","journal-title":"Mol. Ther. Methods Clin. Dev"},{"key":"2023060910375072300_btz747-B3","doi-asserted-by":"crossref","first-page":"1233158","DOI":"10.1126\/science.1233158","article-title":"Lentiviral hematopoietic stem cell gene therapy benefits metachromatic leukodystrophy","volume":"341","author":"Biffi","year":"2013","journal-title":"Science"},{"key":"2023060910375072300_btz747-B4","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/s13073-014-0067-5","article-title":"VISPA: a computational pipeline for the identification and analysis of genomic vector integration sites","volume":"6","author":"Calabria","year":"2014","journal-title":"Genome Med"},{"key":"2023060910375072300_btz747-B5","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1016\/j.cell.2015.01.020","article-title":"HIV-1 integration landscape during latent and active infection","volume":"160","author":"Cohn","year":"2015","journal-title":"Cell"},{"key":"2023060910375072300_btz747-B6","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"2023060910375072300_btz747-B7","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1126\/science.1254194","article-title":"HIV latency. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells","volume":"345","author":"Maldarelli","year":"2014","journal-title":"Science"},{"key":"2023060910375072300_btz747-B8","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1038\/nature15818","article-title":"Gene therapy returns to centre stage","volume":"526","author":"Naldini","year":"2015","journal-title":"Nature"},{"key":"2023060910375072300_btz747-B9","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.omtm.2016.11.002","article-title":"INSPIIRED: a pipeline for quantitative analysis of sites of new DNA integration in cellular genomes","volume":"4","author":"Sherman","year":"2017","journal-title":"Mol. Ther. Methods Clin. Dev"},{"key":"2023060910375072300_btz747-B10","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1186\/s12859-017-1937-9","article-title":"VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites","volume":"18","author":"Spinozzi","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2023060910375072300_btz747-B11","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1126\/science.1256304","article-title":"HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection","volume":"345","author":"Wagner","year":"2014","journal-title":"Science"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz747\/30665044\/btz747.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/5\/1622\/50552826\/bioinformatics_36_5_1622.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/5\/1622\/50552826\/bioinformatics_36_5_1622.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,9]],"date-time":"2023-06-09T10:38:25Z","timestamp":1686307105000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/5\/1622\/5582675"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,10,7]]},"references-count":11,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2020,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz747","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2020,3]]},"published":{"date-parts":[[2019,10,7]]}}}