title: Targeted deep DNA methylation analysis of circulating cell-free DNA in plasma using massively parallel semiconductor sequencing.
abstract: OBJECTIVE
  To set up a targeted methylation analysis using semiconductor sequencing and evaluate the potential for studying methylation in circulating cell-free DNA (cfDNA).
  
  
  METHODS
  Methylation of VIM, FBLN1, LTBP2, HINT2, h19 and IGF2 was analyzed in plasma cfDNA and white blood cell DNA obtained from eight hepatocellular carcinoma patients and eight controls using Ion Torrent™ PGM sequencer.
  
  
  RESULTS
  h19 and IGF2 showed consistent methylation levels and methylation was detected for VIM and FBLN1, whereas LTBP2 and HINT2 did not show methylation for target regions. VIM gene promoter methylation was higher in HCC cfDNA than in cfDNA of controls or white blood cell DNA.
  
  
  CONCLUSIONS
  Semiconductor sequencing is a suitable method for analyzing methylation profiles in cfDNA. Furthermore, differences in cfDNA methylation can be detected between controls and hepatocellular carcinoma cases, even though due to the small sample set these results need further validation.
authors.affiliation: International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France.|Instituto Nacional de Cancerología, México DF, Mexico.|Unidad de Biomedicina, FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), México DF, Mexico.
authors.forename: Felipe
authors.initials: F
authors.lastname: Vaca-Paniagua
authors.affiliation: International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France.|Instituto de Ciencias Básicas y Medicina Experimental del Hospital Italiano de Buenos Aires. Potosí 450, C1199ACL, Buenos Aires, Argentina.
authors.forename: Javier
authors.initials: J
authors.lastname: Oliver
authors.affiliation: International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France.|UCB BioPharma SPRL, Chemin du Foriest 1, B-1420 Braine L'Alleud, Belgium.
authors.forename: Andre
authors.initials: A
authors.lastname: Nogueira da Costa
authors.affiliation: Croix-Rousse Hospital, 103 grande place de la Croix-Rousse, 69004 Lyon, France.|Centre de Recherche en Cancérologie de Lyon (CRCL) UMR INSERM 1052, 151 Cours Albert Thomas, 69424 Lyon Cedex 03, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Merle
authors.affiliation: International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France.
authors.forename: James
authors.initials: J
authors.lastname: McKay
authors.affiliation: International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France.
authors.forename: Zdenko
authors.initials: Z
authors.lastname: Herceg
authors.affiliation: International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France.
authors.forename: Reetta
authors.initials: R
authors.lastname: Holmila
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics; D004247:DNA / Q000097:blood; D019175:DNA Methylation; D018392:Genomic Imprinting; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation / Q000379:methods*; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics; D011401:Promoter Regions, Genetic; D012666:Semiconductors; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods*
chemical_list: D004247:DNA
keywords: cfDNA; early cancer detection; hepatocellular carcinoma; methylation; next-generation sequencing