title: Methylome analysis identifies a Wilms tumor epigenetic biomarker detectable in blood.
abstract: BACKGROUND
  Wilms tumor is the most common pediatric renal malignancy and there is a clinical need for a molecular biomarker to assess treatment response and predict relapse. The known mutated genes in this tumor type show low mutation frequencies, whereas aberrant methylation at 11p15 is by far the most common aberration. We therefore analyzed the epigenome, rather than the genome, to identify ubiquitous tumor-specific biomarkers.
  
  
  RESULTS
  Methylome analysis of matched normal kidney and Wilms tumor identifies 309 preliminary methylation variable positions which we translate into three differentially methylated regions (DMR) for use as tumor-specific biomarkers. Using two novel algorithms we show that these three DMRs are not confounded by cell type composition. We further show that these DMRs are not methylated in embryonic blastema but are intermediately methylated in Wilms tumor precursor lesions. We validate the biomarker DMRs using two independent sample sets of normal kidney and Wilms tumor and seven Wilms tumor histological subtypes, achieving 100% and 98% correct classification, respectively. As proof-of-principle for clinical utility, we successfully use biomarker DMR-2 in a pilot analysis of cell-free circulating DNA to monitor tumor response during treatment in ten patients.
  
  
  CONCLUSIONS
  These findings define the most common methylated regions in Wilms tumor known to date which are not associated with their embryonic origin or precursor stage. We show that this tumor-specific methylated DNA is released into the blood circulation where it can be detected non-invasively showing potential for clinical utility.
authors.forename: Jocelyn
authors.initials: J
authors.lastname: Charlton
authors.forename: Richard D
authors.initials: RD
authors.lastname: Williams
authors.forename: Mark
authors.initials: M
authors.lastname: Weeks
authors.forename: Neil J
authors.initials: NJ
authors.lastname: Sebire
authors.forename: Sergey
authors.initials: S
authors.lastname: Popov
authors.forename: Gordan
authors.initials: G
authors.lastname: Vujanic
authors.forename: William
authors.initials: W
authors.lastname: Mifsud
authors.forename: Marisa
authors.initials: M
authors.lastname: Alcaide-German
authors.forename: Lee M
authors.initials: LM
authors.lastname: Butcher
authors.forename: Stephan
authors.initials: S
authors.lastname: Beck
authors.forename: Kathy
authors.initials: K
authors.lastname: Pritchard-Jones
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000097:blood* / Q000235:genetics*; D002474:Cell-Free System; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D015894:Genome, Human; D006801:Humans; D007680:Kidney Neoplasms / Q000097:blood / Q000235:genetics* / Q000473:pathology; D010865:Pilot Projects; D009396:Wilms Tumor / Q000097:blood / Q000235:genetics* / Q000473:pathology
chemical_list: D014408:Biomarkers, Tumor