Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia

BMC Bioinformatics
Erdogan TaskesenJeroen de Ridder

Abstract

Acute Myeloid Leukemia (AML) is characterized by various cytogenetic and molecular abnormalities. Detection of these abnormalities is important in the risk-classification of patients but requires laborious experimentation. Various studies showed that gene expression profiles (GEP), and the gene signatures derived from GEP, can be used for the prediction of subtypes in AML. Similarly, successful prediction was also achieved by exploiting DNA-methylation profiles (DMP). There are, however, no studies that compared classification accuracy and performance between GEP and DMP, neither are there studies that integrated both types of data to determine whether predictive power can be improved. Here, we used 344 well-characterized AML samples for which both gene expression and DNA-methylation profiles are available. We created three different classification strategies including early, late and no integration of these datasets and used them to predict AML subtypes using a logistic regression model with Lasso regularization. We illustrate that both gene expression and DNA-methylation profiles contain distinct patterns that contribute to discriminating AML subtypes and that an integration strategy can exploit these patterns to achieve syne...Continue Reading

References

Jan 21, 1997·Proceedings of the National Academy of Sciences of the United States of America·D E ZhangD G Tenen
Feb 13, 2003·Nucleic Acids Research·Rafael A IrizarryTerence P Speed
Dec 25, 2003·Bioinformatics·Jelle J GoemanHans C van Houwelingen
Apr 16, 2004·The New England Journal of Medicine·Peter J M ValkRuud Delwel
Apr 9, 2005·Bioinformatics·Lodewyk F A WesselsLaura J van't Veer
Aug 18, 2006·Nucleic Acids Research·Chun-Chi LiuJeremy J W Chen
Jan 30, 2007·Nature Reviews. Immunology·Frank Rosenbauer, Daniel G Tenen
May 3, 2008·The New England Journal of Medicine·Richard F SchlenkUNKNOWN German-Austrian Acute Myeloid Leukemia Study Group
Nov 8, 2008·PLoS Computational Biology·Eunjung LeeDoheon Lee
Jan 15, 2014·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Antonio PalumboRobert Z Orlowski

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Citations

Mar 8, 2018·Journal of the National Cancer Institute·Pauline DepuydtKatleen De Preter
Oct 13, 2019·American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons·Lijie HanJie Peng
Mar 19, 2020·Molecular Genetics and Genomics : MGG·Noor Pratap Singh, P K Vinod
Feb 6, 2017·Journal of Hematology & Oncology·Yan LiLi Yu
Oct 12, 2018·BMC Bioinformatics·Jie LiuJuan Pablo Lewinger
Dec 6, 2020·FEBS Open Bio·Lili YinQing Yang
Apr 2, 2021·Biotechnology Advances·Parminder S ReelEmily Jefferson

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Datasets Mentioned

BETA
GSE14468

Methods Mentioned

BETA
chip

Software Mentioned

GEP
RMA

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