{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T01:17:29Z","timestamp":1792027049252,"version":"4.4.0"},"reference-count":40,"publisher":"American Society of Hematology","issue":"8","content-domain":{"domain":["ashpublications.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2019,8,22]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Alterations in global DNA methylation patterns are a major hallmark of cancer and represent attractive biomarkers for personalized risk stratification. Chronic lymphocytic leukemia (CLL) risk stratification studies typically focus on time to first treatment (TTFT), time to progression (TTP) after treatment, and overall survival (OS). Whereas TTFT risk stratification remains similar over time, TTP and OS have changed dramatically with the introduction of targeted therapies, such as the Bruton tyrosine kinase inhibitor ibrutinib. We have shown that genome-wide DNA methylation patterns in CLL are strongly associated with phenotypic differentiation and patient outcomes. Here, we developed a novel assay, termed methylation-iPLEX (Me-iPLEX), for high-throughput quantification of targeted panels of single cytosine guanine dinucleotides from multiple independent loci. Me-iPLEX was used to classify CLL samples into 1 of 3 known epigenetic subtypes (epitypes). We examined the impact of epitype in 1286 CLL patients from 4 independent cohorts representing a comprehensive view of CLL disease course and therapies. We found that epitype significantly predicted TTFT and OS among newly diagnosed CLL patients. Additionally, epitype predicted TTP and OS with 2 common CLL therapies: chemoimmunotherapy and ibrutinib. Epitype retained significance after stratifying by biologically related biomarkers, immunoglobulin heavy chain mutational status, and ZAP70 expression, as well as other common prognostic markers. Furthermore, among several biological traits enriched between epitypes, we found highly biased immunogenetic features, including IGLV3-21 usage in the poorly characterized intermediate-programmed CLL epitype. In summary, Me-iPLEX is an elegant method to assess epigenetic signatures, including robust classification of CLL epitypes that independently stratify patient risk at diagnosis and time of treatment.<\/jats:p>","DOI":"10.1182\/blood.2019000490","type":"journal-article","created":{"date-parts":[[2019,7,11]],"date-time":"2019-07-11T04:25:23Z","timestamp":1562819123000},"page":"688-698","update-policy":"https:\/\/doi.org\/10.1182\/blood.2019cm0000","source":"Crossref","is-referenced-by-count":45,"title":["Developmental subtypes assessed by DNA methylation-iPLEX forecast the natural history of chronic lymphocytic leukemia"],"prefix":"10.1182","volume":"134","author":[{"given":"Brian","family":"Giacopelli","sequence":"first","affiliation":[{"name":"Division of Hematology, Department of Internal Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiuhong","family":"Zhao","sequence":"additional","affiliation":[{"name":"Division of Hematology, Department of Internal Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amy S.","family":"Ruppert","sequence":"additional","affiliation":[{"name":"Division of Hematology, Department of Internal Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akwasi","family":"Agyeman","sequence":"additional","affiliation":[{"name":"Division of Hematology, Department of Internal Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Weigel","sequence":"additional","affiliation":[{"name":"Division of Hematology, Department of Internal Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue-Zhong","family":"Wu","sequence":"additional","affiliation":[{"name":"Division of Hematology, Department of Internal Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madelyn M.","family":"Gerber","sequence":"additional","affiliation":[{"name":"Department of Pathology, The Ohio State University, Columbus, OH;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7313-1875","authenticated-orcid":false,"given":"Kari G.","family":"Rabe","sequence":"additional","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa C.","family":"Larson","sequence":"additional","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9211-0746","authenticated-orcid":false,"given":"Junyan","family":"Lu","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, Heidelberg, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James S.","family":"Blachly","sequence":"additional","affiliation":[{"name":"Division of Hematology, Department of Internal Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5748-7874","authenticated-orcid":false,"given":"Kerry A.","family":"Rogers","sequence":"additional","affiliation":[{"name":"Division of Hematology, Department of Internal Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William G.","family":"Wierda","sequence":"additional","affiliation":[{"name":"Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer R.","family":"Brown","sequence":"additional","affiliation":[{"name":"Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, MA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kanti R.","family":"Rai","sequence":"additional","affiliation":[{"name":"Division of Hematology-Oncology, North Shore\u2013Long Island Jewish Medical System, New Hyde Park, NY;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Keating","sequence":"additional","affiliation":[{"name":"Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura Z.","family":"Rassenti","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego, La Jolla, CA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas J.","family":"Kipps","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego, La Jolla, CA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thorsten","family":"Zenz","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology and Hematology, University Hospital and University of Z\u00fcrich, Z\u00fcrich, Switzerland;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tait D.","family":"Shanafelt","sequence":"additional","affiliation":[{"name":"Department of Medicine-Hematology, Stanford School of Medicine, Stanford, CA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5951-5055","authenticated-orcid":false,"given":"Neil E.","family":"Kay","sequence":"additional","affiliation":[{"name":"Division of Hematology, Mayo Clinic, Rochester, MN; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynne V.","family":"Abruzzo","sequence":"additional","affiliation":[{"name":"Department of Pathology, The Ohio State University, Columbus, OH;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7630-2123","authenticated-orcid":false,"given":"Kevin R.","family":"Coombes","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer A.","family":"Woyach","sequence":"additional","affiliation":[{"name":"Division of Hematology, Department of Internal Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John C.","family":"Byrd","sequence":"additional","affiliation":[{"name":"Division of Hematology, Department of Internal Medicine, and"},{"name":"Division of Pharmaceutics, College of Pharmacy, The Ohio State University, Columbus, OH"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher C.","family":"Oakes","sequence":"additional","affiliation":[{"name":"Division of Hematology, Department of Internal Medicine, and"},{"name":"Department of Biomedical Informatics and"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"234","reference":[{"issue":"16","key":"2020021109164302400_B1","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1056\/NEJM199510193331606","article-title":"Chronic lymphocytic leukemia","volume":"333","author":"Rozman","year":"1995","journal-title":"N Engl J Med"},{"issue":"6","key":"2020021109164302400_B2","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/S1470-2045(16)30029-8","article-title":"An international prognostic index for patients with chronic lymphocytic leukaemia (CLL-IPI): a meta-analysis of individual patient data","volume":"17","author":"International CLL-IPI working group","year":"2016","journal-title":"Lancet Oncol"},{"key":"2020021109164302400_B3","first-page":"103","article-title":"Immunoglobulin V-H gene analysis suggests that chronic lymphocytic leukaemia (CLL) may derive from either naive or memory B cells. Tumours of naive B cells have a much worse prognosis","volume":"105","author":"Hamblin","year":"1999","journal-title":"Br J Haematol"},{"issue":"6","key":"2020021109164302400_B4","doi-asserted-by":"crossref","first-page":"1848","DOI":"10.1182\/blood.V94.6.1848","article-title":"Unmutated Ig V(H) genes are associated with a more aggressive form of chronic lymphocytic leukemia","volume":"94","author":"Hamblin","year":"1999","journal-title":"Blood"},{"issue":"9","key":"2020021109164302400_B5","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1056\/NEJMoa040857","article-title":"ZAP-70 compared with immunoglobulin heavy-chain gene mutation status as a predictor of disease progression in chronic lymphocytic leukemia","volume":"351","author":"Rassenti","year":"2004","journal-title":"N Engl J Med"},{"issue":"1","key":"2020021109164302400_B6","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1182\/blood-2014-02-555722","article-title":"Validation of ZAP-70 methylation and its relative significance in predicting outcome in chronic lymphocytic leukemia","volume":"124","author":"Claus","year":"2014","journal-title":"Blood"},{"issue":"9747","key":"2020021109164302400_B7","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1016\/S0140-6736(10)61381-5","article-title":"Addition of rituximab to fludarabine and cyclophosphamide in patients with chronic lymphocytic leukaemia: a randomised, open-label, phase 3 trial","volume":"376","author":"Hallek","year":"2010","journal-title":"Lancet"},{"issue":"9980","key":"2020021109164302400_B8","doi-asserted-by":"crossref","first-page":"1814","DOI":"10.1016\/S0140-6736(15)60293-8","article-title":"Towards improved frontline treatment of CLL in the elderly","volume":"385","author":"Goede","year":"2015","journal-title":"Lancet"},{"issue":"6","key":"2020021109164302400_B9","doi-asserted-by":"crossref","first-page":"1580","DOI":"10.1182\/blood.V85.6.1580.bloodjournal8561580","article-title":"p53 gene deletion predicts for poor survival and non-response to therapy with purine analogs in chronic B-cell leukemias","volume":"85","author":"D\u00f6hner","year":"1995","journal-title":"Blood"},{"issue":"26","key":"2020021109164302400_B10","doi-asserted-by":"crossref","first-page":"1910","DOI":"10.1056\/NEJM200012283432602","article-title":"Genomic aberrations and survival in chronic lymphocytic leukemia","volume":"343","author":"D\u00f6hner","year":"2000","journal-title":"N Engl J Med"},{"issue":"4","key":"2020021109164302400_B11","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1182\/blood-2008-02-140582","article-title":"Long-term results of the fludarabine, cyclophosphamide, and rituximab regimen as initial therapy of chronic lymphocytic leukemia","volume":"112","author":"Tam","year":"2008","journal-title":"Blood"},{"issue":"3","key":"2020021109164302400_B12","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1200\/JCO.2005.03.1021","article-title":"Select high-risk genetic features predict earlier progression following chemoimmunotherapy with fludarabine and rituximab in chronic lymphocytic leukemia: justification for risk-adapted therapy","volume":"24","author":"Byrd","year":"2006","journal-title":"J Clin Oncol"},{"issue":"3","key":"2020021109164302400_B13","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1182\/blood-2015-09-667675","article-title":"Fludarabine, cyclophosphamide, and rituximab treatment achieves long-term disease-free survival in IGHV-mutated chronic lymphocytic leukemia","volume":"127","author":"Thompson","year":"2016","journal-title":"Blood"},{"issue":"1","key":"2020021109164302400_B14","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/leu.2017.175","article-title":"Extended follow-up and impact of high-risk prognostic factors from the phase 3 RESONATE study in patients with previously treated CLL\/SLL","volume":"32","author":"Brown","year":"2018","journal-title":"Leukemia"},{"issue":"25","key":"2020021109164302400_B15","doi-asserted-by":"crossref","first-page":"2425","DOI":"10.1056\/NEJMoa1509388","article-title":"Ibrutinib as initial therapy for patients with chronic lymphocytic leukemia","volume":"373","author":"Burger","year":"2015","journal-title":"N Engl J Med"},{"issue":"3","key":"2020021109164302400_B16","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1056\/NEJMoa1400376","article-title":"Ibrutinib versus ofatumumab in previously treated chronic lymphoid leukemia","volume":"371","author":"Byrd","year":"2014","journal-title":"N Engl J Med"},{"issue":"17","key":"2020021109164302400_B17","doi-asserted-by":"crossref","first-page":"1910","DOI":"10.1182\/blood-2017-10-810044","article-title":"Single-agent ibrutinib in treatment-na\u00efve and relapsed\/refractory chronic lymphocytic leukemia: a 5-year experience","volume":"131","author":"O\u2019Brien","year":"2018","journal-title":"Blood"},{"issue":"13","key":"2020021109164302400_B18","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1200\/JCO.2016.70.2282","article-title":"BTKC481S-mediated resistance to ibrutinib in chronic lymphocytic leukemia","volume":"35","author":"Woyach","year":"2017","journal-title":"J Clin Oncol"},{"issue":"1","key":"2020021109164302400_B19","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1001\/jamaoncol.2014.218","article-title":"Etiology of ibrutinib therapy discontinuation and outcomes in patients with chronic lymphocytic leukemia","volume":"1","author":"Maddocks","year":"2015","journal-title":"JAMA Oncol"},{"issue":"26","key":"2020021109164302400_B20","doi-asserted-by":"crossref","first-page":"2517","DOI":"10.1056\/NEJMoa1812836","article-title":"Ibrutinib regimens versus chemoimmunotherapy in older patients with untreated CLL","volume":"379","author":"Woyach","year":"2018","journal-title":"N Engl J Med"},{"issue":"2","key":"2020021109164302400_B21","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/nrc1279","article-title":"The history of cancer epigenetics","volume":"4","author":"Feinberg","year":"2004","journal-title":"Nat Rev Cancer"},{"issue":"7","key":"2020021109164302400_B22","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/s41571-018-0004-4","article-title":"Analysis of DNA methylation in cancer: location revisited [published correction appears in Nat Rev Clin Oncol. 2018;15(7):467.]","volume":"15","author":"Koch","year":"2018","journal-title":"Nat Rev Clin Oncol"},{"issue":"11","key":"2020021109164302400_B23","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1038\/ng.2443","article-title":"Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia","volume":"44","author":"Kulis","year":"2012","journal-title":"Nat Genet"},{"issue":"3","key":"2020021109164302400_B24","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/leu.2014.252","article-title":"A B-cell epigenetic signature defines three biologic subgroups of chronic lymphocytic leukemia with clinical impact","volume":"29","author":"Queiros","year":"2015","journal-title":"Leukemia"},{"issue":"3","key":"2020021109164302400_B25","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1038\/ng.3488","article-title":"DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia","volume":"48","author":"Oakes","year":"2016","journal-title":"Nat Genet"},{"issue":"3","key":"2020021109164302400_B26","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1158\/2159-8290.CD-13-0349","article-title":"Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia","volume":"4","author":"Oakes","year":"2014","journal-title":"Cancer Discov"},{"issue":"6","key":"2020021109164302400_B27","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1038\/leu.2016.10","article-title":"Longitudinal copy number, whole exome and targeted deep sequencing of \u201cgood risk\u201d IGHV-mutated CLL patients with progressive disease","volume":"30","author":"Rose-Zerilli","year":"2016","journal-title":"Leukemia"},{"issue":"4","key":"2020021109164302400_B28","doi-asserted-by":"crossref","first-page":"e303","DOI":"10.1038\/bcj.2015.14","article-title":"Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development","volume":"5","author":"Smith","year":"2015","journal-title":"Blood Cancer J"},{"issue":"1","key":"2020021109164302400_B29","first-page":"E3","article-title":"DNA methylation analysis: choosing the right method","volume":"5","author":"Kurdyukov","year":"2016","journal-title":"Biology (Basel)"},{"issue":"2","key":"2020021109164302400_B30","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/j.jmoldx.2012.09.006","article-title":"Genomic variation by whole-genome SNP mapping arrays predicts time-to-event outcome in patients with chronic lymphocytic leukemia: a comparison of CLL and HapMap genotypes","volume":"15","author":"Schweighofer","year":"2013","journal-title":"J Mol Diagn"},{"issue":"1","key":"2020021109164302400_B31","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1172\/JCI93801","article-title":"Drug-perturbation-based stratification of blood cancer","volume":"128","author":"Dietrich","year":"2018","journal-title":"J Clin Invest"},{"issue":"7","key":"2020021109164302400_B32","doi-asserted-by":"crossref","first-page":"e41361","DOI":"10.1371\/journal.pone.0041361","article-title":"Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility","volume":"7","author":"Reinius","year":"2012","journal-title":"PLoS One"},{"issue":"20","key":"2020021109164302400_B33","doi-asserted-by":"crossref","first-page":"2483","DOI":"10.1200\/JCO.2011.39.3090","article-title":"Quantitative DNA methylation analysis identifies a single CpG dinucleotide important for ZAP-70 expression and predictive of prognosis in chronic lymphocytic leukemia","volume":"30","author":"Claus","year":"2012","journal-title":"J Clin Oncol"},{"issue":"7697","key":"2020021109164302400_B34","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/nature26000","article-title":"DNA methylation-based classification of central nervous system tumours","volume":"555","author":"Capper","year":"2018","journal-title":"Nature"},{"issue":"10","key":"2020021109164302400_B35","first-page":"1640","article-title":"The immunological profile of B-cell disorders and proposal of a scoring system for the diagnosis of CLL","volume":"8","author":"Matutes","year":"1994","journal-title":"Leukemia"},{"issue":"20","key":"2020021109164302400_B36","doi-asserted-by":"crossref","first-page":"3612","DOI":"10.1002\/cncr.29566","article-title":"Complex karyotype is a stronger predictor than del(17p) for an inferior outcome in relapsed or refractory chronic lymphocytic leukemia patients treated with ibrutinib-based regimens","volume":"121","author":"Thompson","year":"2015","journal-title":"Cancer"},{"issue":"6","key":"2020021109164302400_B37","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1080\/15592294.2016.1178432","article-title":"Prognostic impact of epigenetic classification in chronic lymphocytic leukemia: The case of subset #2","volume":"11","author":"Bhoi","year":"2016","journal-title":"Epigenetics"},{"issue":"19","key":"2020021109164302400_B38","doi-asserted-by":"crossref","first-page":"4467","DOI":"10.1182\/blood-2011-11-393694","article-title":"Stereotyped B-cell receptors in one-third of chronic lymphocytic leukemia: a molecular classification with implications for targeted therapies","volume":"119","author":"Agathangelidis","year":"2012","journal-title":"Blood"},{"issue":"20","key":"2020021109164302400_B39","doi-asserted-by":"crossref","first-page":"5048","DOI":"10.1158\/1078-0432.CCR-18-0133","article-title":"The light chain IgLV3-21 defines a new poor prognostic subgroup in chronic lymphocytic leukemia: results of a multicenter study","volume":"24","author":"Stamatopoulos","year":"2018","journal-title":"Clin Cancer Res"},{"issue":"10","key":"2020021109164302400_B40","doi-asserted-by":"crossref","first-page":"4047","DOI":"10.1182\/blood-2002-11-3479","article-title":"Mutated VH genes and preferential VH3-21 use define new subsets of mantle cell lymphoma","volume":"101","author":"Walsh","year":"2003","journal-title":"Blood"}],"container-title":["Blood"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/ashpublications.org\/blood\/article-pdf\/134\/8\/688\/1554215\/bloodbld2019000490.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/ashpublications.org\/blood\/article-pdf\/134\/8\/688\/1554215\/bloodbld2019000490.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,11]],"date-time":"2021-01-11T13:23:53Z","timestamp":1610371433000},"score":1,"resource":{"primary":{"URL":"https:\/\/ashpublications.org\/blood\/article\/134\/8\/688\/260758\/Developmental-subtypes-assessed-by-DNA"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,8,22]]},"references-count":40,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2019,8,22]]}},"URL":"https:\/\/doi.org\/10.1182\/blood.2019000490","relation":{},"ISSN":["0006-4971","1528-0020"],"issn-type":[{"value":"0006-4971","type":"print"},{"value":"1528-0020","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,22]]}}}