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DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cancer Pharmacology and Computational Medicine.ORCID iD: 0000-0002-9615-5079
Karolinska Intstitutet.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
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2015 (English)In: Clinical Epigenetics, E-ISSN 1868-7083, Vol. 7, 11Article in journal (Refereed) Published
Abstract [en]


We present a method that utilizes DNA methylation profiling for prediction of the cytogenetic subtypes of acute lymphoblastic leukemia (ALL) cells from pediatric ALL patients. The primary aim of our study was to improve risk stratification of ALL patients into treatment groups using DNA methylation as a complement to current diagnostic methods. A secondary aim was to gain insight into the functional role of DNA methylation in ALL.


We used the methylation status of ~450,000 CpG sites in 546 well-characterized patients with T-ALL or seven recurrent B-cell precursor ALL subtypes to design and validate sensitive and accurate DNA methylation classifiers. After repeated cross-validation, a final classifier was derived that consisted of only 246 CpG sites. The mean sensitivity and specificity of the classifier across the known subtypes was 0.90 and 0.99, respectively. We then used DNA methylation classification to screen for subtype membership of 210 patients with undefined karyotype (normal or no result) or non-recurrent cytogenetic aberrations (‘other’ subtype). Nearly half (n = 106) of the patients lacking cytogenetic subgrouping displayed highly similar methylation profiles as the patients in the known recurrent groups. We verified the subtype of 20% of the newly classified patients by examination of diagnostic karyotypes, array-based copy number analysis, and detection of fusion genes by quantitative polymerase chain reaction (PCR) and RNA-sequencing (RNA-seq). Using RNA-seq data from ALL patients where cytogenetic subtype and DNA methylation classification did not agree, we discovered several novel fusion genes involving ETV6, RUNX1, and PAX5.


Our findings indicate that DNA methylation profiling contributes to the clarification of the heterogeneity in cytogenetically undefined ALL patient groups and could be implemented as a complementary method for diagnosis of ALL. The results of our study provide clues to the origin and development of leukemic transformation. The methylation status of the CpG sites constituting the classifiers also highlight relevant biological characteristics in otherwise unclassified ALL patients.

Place, publisher, year, edition, pages
2015. Vol. 7, 11
National Category
URN: urn:nbn:se:uu:diva-242351DOI: 10.1186/s13148-014-0039-zISI: 000350260800001PubMedID: 25729447OAI: oai:DiVA.org:uu-242351DiVA: diva2:783295
Swedish Foundation for Strategic Research , RBc08-008

De två sista författarna delar sistaförfattarskapet.

Available from: 2015-01-25 Created: 2015-01-25 Last updated: 2015-03-31Bibliographically approved
In thesis
1. Machine Learning Based Analysis of DNA Methylation Patterns in Pediatric Acute Leukemia
Open this publication in new window or tab >>Machine Learning Based Analysis of DNA Methylation Patterns in Pediatric Acute Leukemia
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
Maskininlärningsbaserad analys av DNA-metyleringsmönster i pediatrisk akut lymfatisk leukemi
Abstract [en]

Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer in the Nordic countries. Recent evidence indicate that DNA methylation (DNAm) play a central role in the development and progression of the disease.

DNAm profiles of a collection of ALL patient samples and a panel of non-leukemic reference samples were analyzed using the Infinium 450k methylation assay. State-of-the-art machine learning algorithms were used to search the large amounts of data produced for patterns predictive of future relapses, in vitro drug resistance, and cytogenetic subtypes, aiming at improving our understanding of the disease and ultimately improving treatment.

In paper I, the predictive modeling framework developed to perform the analyses of DNAm dataset was presented. It focused on uncompromising statistical rigor and computational efficiency, while allowing a high level of modeling flexibility and usability. In paper II, the DNAm landscape of ALL was comprehensively characterized, discovering widespread aberrant methylation at diagnosis strongly influenced by cytogenetic subtype. The aberrantly methylated regions were enriched for genes repressed by polycomb group proteins, repressively marked histones in healthy cells, and genes associated with embryonic development. A consistent trend of hypermethylation at relapse was also discovered. In paper III, a tool for DNAm-based subtyping was presented, validated using blinded samples and used to re-classify samples with incomplete phenotypic information. Using RNA-sequencing, previously undetected non-canonical aberrations were found in many re-classified samples. In paper IV, the relationship between DNAm and in vitro drug resistance was investigated and predictive signatures were obtained for seven of the eight therapeutic drugs studied. Interpretation was challenging due to poor correlation between DNAm and gene expression, further complicated by the discovery that random subsets of the array can yield comparable classification accuracy. Paper V presents a novel Bayesian method for multivariate density estimation with variable bandwidths. Simulations showed comparable performance to the current state-of-the-art methods and an advantage on skewed distributions.

In conclusion, the studies characterize the information contained in the aberrant DNAm patterns of ALL and assess its predictive capabilities for future relapses, in vitro drug sensitivity and subtyping. They also present three publicly available tools for the scientific community to use.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2015. 68 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1069
National Category
Bioinformatics (Computational Biology) Hematology Cancer and Oncology
urn:nbn:se:uu:diva-242544 (URN)978-91-554-9151-2 (ISBN)
Public defence
2015-03-13, Auditorium minus, Museum Gustavianum, Akademigatan 3, Uppsala, 14:00 (English)
Swedish Foundation for Strategic Research , RBc08-008
Available from: 2015-02-19 Created: 2015-01-27 Last updated: 2015-03-27Bibliographically approved

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Nordlund, JessicaBäcklin, ChristoferCavelier, LuciaDahlberg, JohanÖvernäs, ElinLarsson, RolfPalle, JosefineGustafsson, MatsLönnerholm, GudmarSyvänen, Ann-Christine
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Molecular MedicineCancer Pharmacology and Computational MedicineDepartment of Immunology, Genetics and PathologyPediatrics
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