title: Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour.
abstract: BACKGROUND
  Patients with breast cancer have an increased risk of developing subsequent breast cancers. It is important to distinguish whether these tumours are de novo or recurrences of the primary tumour in order to guide the appropriate therapy. Our aim was to investigate the use of DNA methylation profiling and array comparative genomic hybridization (aCGH) to determine whether the second tumour is clonally related to the first tumour.
  
  
  METHODS
  Methylation-sensitive high-resolution melting was used to screen promoter methylation in a panel of 13 genes reported as methylated in breast cancer (RASSF1A, TWIST1, APC, WIF1, MGMT, MAL, CDH13, RARβ, BRCA1, CDH1, CDKN2A, TP73, and GSTP1) in 29 tumour pairs (16 ipsilateral and 13 contralateral). Using the methylation profile of these genes, we employed a Bayesian and an empirical statistical approach to estimate clonal relationship. Copy number alterations were analysed using aCGH on the same set of tumour pairs.
  
  
  RESULTS
  There is a higher probability of the second tumour being recurrent in ipsilateral tumours compared with contralateral tumours (38 % versus 8 %; p <0.05) based on the methylation profile. Using previously reported recurrence rates as Bayesian prior probabilities, we classified 69 % of ipsilateral and 15 % of contralateral tumours as recurrent. The inferred clonal relationship results of the tumour pairs were generally concordant between methylation profiling and aCGH.
  
  
  CONCLUSIONS
  Our results show that DNA methylation profiling as well as aCGH have potential as diagnostic tools in improving the clinical decisions to differentiate recurrences from a second de novo tumour.
authors.affiliation: Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, VIC, 3002, Australia. khua011@gmail.com.|Department of Pathology and Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3010, Australia. khua011@gmail.com.
authors.forename: Katie T
authors.initials: KT
authors.lastname: Huang
authors.affiliation: Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, VIC, 3002, Australia. Thomas.Mikeska@onjcri.org.au.|Department of Pathology and Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3010, Australia. Thomas.Mikeska@onjcri.org.au.|Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Studley Road, Heidelberg, VIC, 3084, Australia. Thomas.Mikeska@onjcri.org.au.
authors.forename: Thomas
authors.initials: T
authors.lastname: Mikeska
authors.affiliation: Bioinformatics, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, VIC, 3002, Australia. Jason.Li@petermac.org.
authors.forename: Jason
authors.initials: J
authors.lastname: Li
authors.affiliation: Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, VIC, 3002, Australia. Elena.Takano@petermac.org.
authors.forename: Elena A
authors.initials: EA
authors.lastname: Takano
authors.affiliation: South Eastern Area Laboratory Service (SEALS), St. George Hospital, Gary Street, Kogarah, NSW, 2217, Australia. Ewan.millar@sesiahs.health.nsw.gov.au.|The Kinghorn Cancer Centre & Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia. Ewan.millar@sesiahs.health.nsw.gov.au.|School of Medicine and Health Sciences, University of Western Sydney, Narellan Road, Campbelltown, NSW, 2560, Australia. Ewan.millar@sesiahs.health.nsw.gov.au.|Faculty of Medicine, University of NSW, High Street, Kensington, NSW, 2052, Australia. Ewan.millar@sesiahs.health.nsw.gov.au.
authors.forename: Ewan K A
authors.initials: EK
authors.lastname: Millar
authors.affiliation: The Kinghorn Cancer Centre & Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia. Peter.graham@sesiahs.health.nsw.gov.au.|School of Medicine and Health Sciences, University of Western Sydney, Narellan Road, Campbelltown, NSW, 2560, Australia. Peter.graham@sesiahs.health.nsw.gov.au.
authors.forename: Peter H
authors.initials: PH
authors.lastname: Graham
authors.affiliation: VBCRC Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, VIC, 3002, Australia. Samantha.Boyle@petermac.org.
authors.forename: Samantha E
authors.initials: SE
authors.lastname: Boyle
authors.affiliation: Department of Pathology and Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3010, Australia. Ian.campbell@petermac.org.|VBCRC Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, VIC, 3002, Australia. Ian.campbell@petermac.org.
authors.forename: Ian G
authors.initials: IG
authors.lastname: Campbell
authors.affiliation: Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. Terry@wehi.edu.au.
authors.forename: Terence P
authors.initials: TP
authors.lastname: Speed
authors.affiliation: Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, VIC, 3002, Australia. alex.dobrovic@onjcri.org.au.|Department of Pathology and Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3010, Australia. alex.dobrovic@onjcri.org.au.|Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Studley Road, Heidelberg, VIC, 3084, Australia. alex.dobrovic@onjcri.org.au.|School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3084, Australia. alex.dobrovic@onjcri.org.au.
authors.forename: Alexander
authors.initials: A
authors.lastname: Dobrovic
authors.affiliation: Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, VIC, 3002, Australia. Stephen.Fox@petermac.org.|Department of Pathology and Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3010, Australia. Stephen.Fox@petermac.org.
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Fox
mesh_terms: D000328:Adult; D000368:Aged; D001499:Bayes Theorem; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology*; D060965:Clonal Evolution / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D019295:Computational Biology; D056915:DNA Copy Number Variations; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D006801:Humans; D008875:Middle Aged; D009364:Neoplasm Recurrence, Local; D016609:Neoplasms, Second Primary / Q000235:genetics* / Q000473:pathology*; D011401:Promoter Regions, Genetic; D047368:Tumor Burden