title: Evaluation of Methylation Biomarkers for Detection of Circulating Tumor DNA and Application to Colorectal Cancer.
abstract: Solid tumors shed DNA into circulation, and there is growing evidence that the detection of circulating tumor DNA (ctDNA) has broad clinical utility, including monitoring of disease, prognosis, response to chemotherapy and tracking tumor heterogeneity. The appearance of ctDNA in the circulating cell-free DNA (ccfDNA) isolated from plasma or serum is commonly detected by identifying tumor-specific features such as insertions, deletions, mutations and/or aberrant methylation. Methylation is a normal cell regulatory event, and since the majority of ccfDNA is derived from white blood cells (WBC), it is important that tumour-specific DNA methylation markers show rare to no methylation events in WBC DNA. We have used a novel approach for assessment of low levels of DNA methylation in WBC DNA. DNA methylation in 29 previously identified regions (residing in 17 genes) was analyzed in WBC DNA and eight differentially-methylated regions (DMRs) were taken through to testing in clinical samples using methylation specific PCR assays. DMRs residing in four genes,BCAT1,GRASP,IKZF1andIRF4, exhibited low positivity, 3.5% to 7%, in the plasma of colonoscopy-confirmed healthy subjects, with the sensitivity for detection of ctDNA in colonoscopy-confirmed patients with colorectal cancer being 65%, 54.5%, 67.6% and 59% respectively.
authors.affiliation: CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia. smitch7@gmail.com.
authors.forename: Susan M
authors.initials: SM
authors.lastname: Mitchell
authors.affiliation: CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia. thu.ho@csiro.au.
authors.forename: Thu
authors.initials: T
authors.lastname: Ho
authors.affiliation: CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia. glenn.brown@csiro.au.
authors.forename: Glenn S
authors.initials: GS
authors.lastname: Brown
authors.affiliation: Clinical Genomics Pty Ltd., North Ryde, NSW 2113, Australia. rohan@geneticsignatures.com.
authors.forename: Rohan T
authors.initials: RT
authors.lastname: Baker
authors.affiliation: Clinical Genomics Pty Ltd., North Ryde, NSW 2113, Australia. thomas_mel@hotmail.com.
authors.forename: Melissa L
authors.initials: ML
authors.lastname: Thomas
authors.affiliation: Clinical Genomics Pty Ltd., North Ryde, NSW 2113, Australia. aidan.mcevoy@clinicalgenomics.com.
authors.forename: Aidan
authors.initials: A
authors.lastname: McEvoy
authors.affiliation: CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia. zheng-zhou.xu@csiroalumni.org.au.
authors.forename: Zheng-Zhou
authors.initials: ZZ
authors.lastname: Xu
authors.affiliation: CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia. jason.ross@csiro.au.
authors.forename: Jason P
authors.initials: JP
authors.lastname: Ross
authors.affiliation: CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia. trevor.lockett@csiro.au.
authors.forename: Trevor J
authors.initials: TJ
authors.lastname: Lockett
authors.affiliation: Flinders Centre for Innovation in Cancer, Flinders University of South Australia, GPO Box 2100, Adelaide, SA 5001, Australia. graeme.young@flinders.edu.au.
authors.forename: Graeme P
authors.initials: GP
authors.lastname: Young
authors.affiliation: Clinical Genomics Pty Ltd., North Ryde, NSW 2113, Australia. larry@clinicalgenomics.com.
authors.forename: Lawrence C
authors.initials: LC
authors.lastname: LaPointe
authors.affiliation: Clinical Genomics Pty Ltd., North Ryde, NSW 2113, Australia. susanne.pedersen@clinicalgenomics.com.
authors.forename: Susanne K
authors.initials: SK
authors.lastname: Pedersen
authors.affiliation: CSIRO Food and Nutrition, P.O. Box 52, North Ryde, NSW 1670, Australia. peter.molloy@csiro.au.
authors.forename: Peter L
authors.initials: PL
authors.lastname: Molloy
keywords: BCAT1; GRASP; IKZF1; IRF4 SDC2; SEPT9; biomarkers; circulating tumor DNA; colorectal cancer; epigenetics; hypermethylation; liquid biopsy; plasma