{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T02:33:03Z","timestamp":1761964383906},"reference-count":47,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2012,4,10]],"date-time":"2012-04-10T00:00:00Z","timestamp":1334016000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Br J Haematol"],"published-print":{"date-parts":[[2012,6]]},"abstract":"<jats:title>Summary<\/jats:title><jats:p>As an approach to determining the aetiology of chronic lymphocytic leukaemia (<jats:styled-content style=\"fixed-case\">CLL<\/jats:styled-content>), we searched for a virus expressed in human <jats:styled-content style=\"fixed-case\">CLL B<\/jats:styled-content>\u2010cells by combining high\u2010throughput sequencing and digital subtraction. Pooled <jats:styled-content style=\"fixed-case\">B<\/jats:styled-content>\u2010cell m<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content> transcriptomes from five <jats:styled-content style=\"fixed-case\">CLL<\/jats:styled-content> patients and five healthy donors were sequenced with 454 <jats:styled-content style=\"fixed-case\">L<\/jats:styled-content>ife <jats:styled-content style=\"fixed-case\">S<\/jats:styled-content>ciences technology. Human reads were excluded by <jats:styled-content style=\"fixed-case\">BLAST<\/jats:styled-content> (<jats:styled-content style=\"fixed-case\">B<\/jats:styled-content>asic <jats:styled-content style=\"fixed-case\">L<\/jats:styled-content>ocal <jats:styled-content style=\"fixed-case\">A<\/jats:styled-content>lignment <jats:styled-content style=\"fixed-case\">S<\/jats:styled-content>earch <jats:styled-content style=\"fixed-case\">T<\/jats:styled-content>ool) and <jats:styled-content style=\"fixed-case\">BLAT<\/jats:styled-content> (<jats:styled-content style=\"fixed-case\">BLAST<\/jats:styled-content>\u2010like alignment tool) searches. Remaining reads were screened with <jats:styled-content style=\"fixed-case\">BLAST<\/jats:styled-content> against viral databases. Purified <jats:styled-content style=\"fixed-case\">B<\/jats:styled-content>\u2010cells from two <jats:styled-content style=\"fixed-case\">CLL<\/jats:styled-content> patients, with and without stimulation by phorbol\u2010esters, were sequenced using Illumina technology to achieve depth of sequencing. Burrows\u2010<jats:styled-content style=\"fixed-case\">W<\/jats:styled-content>heeler <jats:styled-content style=\"fixed-case\">A<\/jats:styled-content>ligner mapping and <jats:styled-content style=\"fixed-case\">BLAST<\/jats:styled-content> searches were used for the Illumina data. Pyrosequencing resulted in about 400\u00a0000 reads per sample. No viral candidate could be found. Illumina single\u2010end sequencing for 115 cycles yielded an average of 26\u00a0\u00b1\u00a02\u00b75\u00a0million filtered reads per sample, of which 2\u00b72\u00a0\u00b1\u00a00\u00b76\u00a0million remained unmapped to human references. <jats:styled-content style=\"fixed-case\">BLAST<\/jats:styled-content> searches of these reads against viral and human databases assigned nine reads to an <jats:styled-content style=\"fixed-case\">E<\/jats:styled-content>pstein\u2010<jats:styled-content style=\"fixed-case\">B<\/jats:styled-content>arr virus origin, in one sample following phorbol\u2010ester stimulation. Other reads showing a putative viral origin were dismissed after further analysis. Despite an in\u2010depth analysis of the <jats:styled-content style=\"fixed-case\">CLL<\/jats:styled-content> transcriptome reaching more than 100\u00a0million sequences, we have not found evidence for a putative viral candidate in <jats:styled-content style=\"fixed-case\">CLL<\/jats:styled-content>.<\/jats:p>","DOI":"10.1111\/j.1365-2141.2012.09116.x","type":"journal-article","created":{"date-parts":[[2012,4,10]],"date-time":"2012-04-10T14:46:30Z","timestamp":1334069190000},"page":"709-717","update-policy":"http:\/\/dx.doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Search for an aetiological virus candidate in chronic lymphocytic leukaemia by extensive transcriptome analysis"],"prefix":"10.1111","volume":"157","author":[{"given":"Natalia","family":"Rego","sequence":"first","affiliation":[{"name":"Institut Pasteur de Montevideo Montevideo"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sergio","family":"Bianchi","sequence":"additional","affiliation":[{"name":"Institut Pasteur de Montevideo Montevideo"},{"name":"Departamento de Fisiopatolog\u00eda Hospital de Cl\u00ednicas Montevideo"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pilar","family":"Moreno","sequence":"additional","affiliation":[{"name":"Institut Pasteur de Montevideo Montevideo"},{"name":"Laboratorio de Virolog\u00eda Molecular Facultad de Ciencias Montevideo Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helena","family":"Persson","sequence":"additional","affiliation":[{"name":"Department of Oncology, Clinical Sciences Lund University Lund Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anders","family":"Kvist","sequence":"additional","affiliation":[{"name":"Department of Oncology, Clinical Sciences Lund University Lund Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alvaro","family":"Pena","sequence":"additional","affiliation":[{"name":"Institut Pasteur de Montevideo Montevideo"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pablo","family":"Oppezzo","sequence":"additional","affiliation":[{"name":"Institut Pasteur de Montevideo Montevideo"},{"name":"Departamento de Inmunobiolog\u00eda Facultad de Medicina, Universidad de la Rep\u00fablica Montevideo Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hugo","family":"Naya","sequence":"additional","affiliation":[{"name":"Institut Pasteur de Montevideo Montevideo"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos","family":"Rovira","sequence":"additional","affiliation":[{"name":"Department of Oncology, Clinical Sciences Lund University Lund Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guillermo","family":"Dighiero","sequence":"additional","affiliation":[{"name":"Institut Pasteur de Montevideo Montevideo"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Otto","family":"Pritsch","sequence":"additional","affiliation":[{"name":"Institut Pasteur de Montevideo Montevideo"},{"name":"Departamento de Inmunobiolog\u00eda Facultad de Medicina, Universidad de la Rep\u00fablica Montevideo Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2012,4,10]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"e_1_2_8_3_1","first-page":"1","article-title":"Protein kinase C as the receptor for the phorbol ester tumor promoters: sixth Rhoads memorial award lecture","volume":"48","author":"Blumberg P.M.","year":"1988","journal-title":"Cancer Research"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12033-008-9131-y"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.510"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(08)60456-0"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/1750-9378-5-22"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20110921"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1152586"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq1064"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1186\/1742-4690-4-18"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2007-06-093906"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.leu.2402748"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229202. Article published online before March 2002"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229102"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.2741\/klein"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.bjc.6605306"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2009.03.024"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0024758"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0019838"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2004-08-3344"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa073785"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2010-02-269829"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn721"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature10113"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.1032"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1155\/2012\/782353"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2011-08-373159"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2007-05-091561"},{"key":"e_1_2_8_31_1","doi-asserted-by":"publisher","DOI":"10.1002\/ijc.24510"},{"key":"e_1_2_8_32_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1213841"},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2010-09-308205"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(86)90323-5"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2141.2010.08368.x"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.1002\/cncr.24839"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.leukres.2011.01.032"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.CCR-0670-3"},{"key":"e_1_2_8_39_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2010-03-273177"},{"key":"e_1_2_8_40_1","doi-asserted-by":"publisher","DOI":"10.1080\/10428190500398856"},{"key":"e_1_2_8_41_1","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00033-07"},{"key":"e_1_2_8_42_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1109016"},{"key":"e_1_2_8_43_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng818"},{"key":"e_1_2_8_44_1","first-page":"139","article-title":"Geographical variation in the incidence of the leukemias and the lymphomas","volume":"53","author":"Weiss N.S.","year":"1979","journal-title":"National Cancer Institute Monograph"},{"key":"e_1_2_8_45_1","doi-asserted-by":"publisher","DOI":"10.1186\/1741-7007-8-124"},{"key":"e_1_2_8_46_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0911353107"},{"key":"e_1_2_8_47_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0888-7543(02)00043-5"},{"key":"e_1_2_8_48_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gnh031"}],"container-title":["British Journal of Haematology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1111%2Fj.1365-2141.2012.09116.x","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/j.1365-2141.2012.09116.x","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T11:57:28Z","timestamp":1700567848000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/j.1365-2141.2012.09116.x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,4,10]]},"references-count":47,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2012,6]]}},"alternative-id":["10.1111\/j.1365-2141.2012.09116.x"],"URL":"https:\/\/doi.org\/10.1111\/j.1365-2141.2012.09116.x","archive":["Portico"],"relation":{},"ISSN":["0007-1048","1365-2141"],"issn-type":[{"value":"0007-1048","type":"print"},{"value":"1365-2141","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,4,10]]},"assertion":[{"value":"2011-12-22","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2012-03-06","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2012-04-10","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}