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
Jan 13, 2000·Histopathology·N L HarrisC D Bloomfield
Jan 23, 2003·Bioinformatics·B M BolstadT P Speed
Feb 13, 2003·Nucleic Acids Research·Rafael A IrizarryTerence P Speed
Aug 20, 2003·Biostatistics·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
Aug 3, 2007·Blood·Bas J WoutersRuud Delwel
May 3, 2008·The New England Journal of Medicine·Richard F SchlenkUNKNOWN German-Austrian Acute Myeloid Leukemia Study Group
Oct 8, 2008·Haematologica·Roel G W VerhaakPeter J M Valk
Nov 8, 2008·PLoS Computational Biology·Eunjung LeeDoheon Lee
Mar 12, 2009·Methods in Molecular Biology·Maria E FigueroaJohn M Greally
Jan 12, 2010·Cancer Cell·Maria E FigueroaAri Melnick
Jun 8, 2010·BMC Genomics·Francesca OrsoDaniela Taverna
Aug 3, 2010·Nature Biotechnology·Leming ShiUNKNOWN MAQC Consortium
Dec 24, 2010·Blood·Erdogan TaskesenKonstanze Döhner
Sep 24, 2011·Genome Research·Qing XiongTerrence S Furey
Jul 19, 2012·PloS One·Martin H van VlietLodewyk F A Wessels
Jan 15, 2014·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Antonio PalumboRobert Z Orlowski
Citations
Apr 26, 2016·Scientific Reports·Erdogan TaskesenMarcel J T Reinders
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
Jan 18, 2019·JCO Clinical Cancer Informatics·Neeraja M KrishnanBinay Panda
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 11, 2016·Cancer Informatics·Christopher J WalshClaudia C Dos Santos
Oct 12, 2018·BMC Bioinformatics·Jie LiuJuan Pablo Lewinger
Dec 8, 2017·BMC Bioinformatics·Kang K YanHerbert Pang
Aug 11, 2020·Journal of Oncology·Qingrong SunMaode Lai
Oct 11, 2020·Cancers·Ludovic GabellierJérôme Moreaux
Dec 6, 2020·FEBS Open Bio·Lili YinQing Yang
Apr 25, 2020·Cancer Cell·Cristina Di GenuaClaus Nerlov
Apr 2, 2021·Biotechnology Advances·Parminder S ReelEmily Jefferson