title: Validation of DNA methylation to predict outcome in acute myeloid leukemia by use of xMELP.
abstract: BACKGROUND
  Epigenetic dysregulation involving alterations in DNA methylation is a hallmark of various types of cancer, including acute myeloid leukemia (AML). Although specific cancer types and clinical aggressiveness of tumors can be determined by DNA methylation status, the assessment of DNA methylation at multiple loci is not routinely performed in the clinical laboratory.
  
  
  METHODS
  We recently described a novel microsphere-based assay for multiplex evaluation of DNA methylation. In the current study, we validated and used an improved assay [termed expedited microsphere HpaII small fragment Enrichment by Ligation-mediated PCR (xMELP)] that can be performed with appropriate clinical turnaround time.
  
  
  RESULTS
  Using the xMELP assay in conjunction with a new 17-locus random forest classifier that has been trained using 344 AML samples, we were able to segregate an independent cohort of 70 primary AML patients into methylation-determined subgroups with significantly distinct mortality risk (P = 0.009). We also evaluated precision, QC parameters, and preanalytic variables of the xMELP assay and determined the sensitivity of the random forest classifier score to failure at 1 or more loci.
  
  
  CONCLUSIONS
  Our results demonstrate that xMELP performance is suitable for implementation in the clinical laboratory and predicts AML outcome in an independent patient cohort.
authors.affiliation: Department of Pathology, Children's Hospital of Philadelphia; Department of Pathology and Laboratory Medicine.
authors.forename: Gerald B W
authors.initials: GB
authors.lastname: Wertheim
authors.affiliation: Department of Pathology, Children's Hospital of Philadelphia;
authors.forename: Catherine
authors.initials: C
authors.lastname: Smith
authors.affiliation: Division of Hematology and Oncology, and.
authors.forename: Marlise
authors.initials: M
authors.lastname: Luskin
authors.affiliation: Division of Hematology and Oncology, and.
authors.forename: Alison
authors.initials: A
authors.lastname: Rager
authors.affiliation: Department of Pathology, University of Michigan Medical School, Ann Arbor, MI.
authors.forename: Maria E
authors.initials: ME
authors.lastname: Figueroa
authors.affiliation: Division of Hematology and Oncology, and Abramson Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA;
authors.forename: Martin
authors.initials: M
authors.lastname: Carroll
authors.affiliation: Department of Pathology and Laboratory Medicine, srmaster@mail.med.upenn.edu.
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Master
mesh_terms: D015331:Cohort Studies; D004247:DNA / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D018572:Disease-Free Survival; D044127:Epigenesis, Genetic; D006801:Humans; D053208:Kaplan-Meier Estimate; D015470:Leukemia, Myeloid, Acute / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D015999:Multivariate Analysis; D016133:Polymerase Chain Reaction / Q000379:methods*; D011379:Prognosis; D015203:Reproducibility of Results
chemical_list: D004247:DNA