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DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia.

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Authors
Nordlund, Jessica
Bäcklin, Christofer L
Zachariadis, Vasilios
Cavelier, Lucia
Dahlberg, Johan
Öfverholm, Ingegerd
Barbany, Gisela
Nordgren, Ann
Övernäs, Elin
Abrahamsson, Jonas
Flaegstad, Trond
Heyman, Mats M
Jónsson, Ólafur G
Kanerva, Jukka
Larsson, Rolf
Palle, Josefine
Schmiegelow, Kjeld
Gustafsson, Mats G
Lönnerholm, Gudmar
Forestier, Erik
Syvänen, Ann-Christine
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Issue Date
2015

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Clin Epigenetics 2015, 7 (1):11
Abstract
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.
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To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access.
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http://dx.doi.org/10.1186/s13148-014-0039-z
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343276/
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Archived with thanks to Clinical epigenetics
openAccess
ae974a485f413a2113503eed53cd6c53
10.1186/s13148-014-0039-z
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