A two-gene blood test for methylated DNA sensitive for colorectal cancer.
BACKGROUND
Specific genes are methylated with high frequency in colorectal neoplasia, and may leak into blood. Detection of multiple methylated DNA biomarkers in blood may improve assay sensitivity for colorectal cancer (CRC) relative to a single marker. We undertook a case-control study evaluating the presence of two methylation DNA markers, BCAT1 and IKZF1, in circulation to determine if they were complementary for detection of CRC.


METHODS
Methylation-specific PCR assays were developed to measure the level of methylated BCAT1 and IKZF1 in DNA extracted from plasma obtained from colonoscopy-confirmed 144 healthy controls and 74 CRC cases.


RESULTS
DNA yields ranged from 2 to 730 ng/mL plasma (mean 18.6ng/mL; 95% CI 11-26 ng/mL) and did not correlate with gender, age or CRC status. Methylated BCAT1 and IKZF1 DNA were detected in respectively 48 (65%) and 50 (68%) of the 74 cancers. In contrast, only 5 (4%) and 7 (5%) controls were positive for BCAT1 and IKZF1 DNA methylation, respectively. A two-gene classifier model ("either or" rule) improved segregation of CRC from controls, with 57 of 74 cancers (77%) compared to only 11 of 144 (7.6%) controls being positive for BCAT1 and/or IKZF1 DNA methylation. Increasing levels of methylated DNA were observed as CRC stage progressed.


CONCLUSIONS
Detection of methylated BCAT1 and/or IKZF1 DNA in plasma may have clinical application as a novel blood test for CRC. Combining the results from the two methylation-specific PCR assays improved CRC detection with minimal change in specificity. Further validation of this two-gene blood test with a view to application in screening is now indicated.
Clinical Genomics Proprietary Limited, Sydney, Australia.
Susanne K
SK
Pedersen
Clinical Genomics Proprietary Limited, Sydney, Australia.
Rohan T
RT
Baker
Clinical Genomics Proprietary Limited, Sydney, Australia.
Aidan
A
McEvoy
Clinical Genomics Proprietary Limited, Sydney, Australia.
David H
DH
Murray
Clinical Genomics Proprietary Limited, Sydney, Australia.
Melissa
M
Thomas
Food & Nutrition Flagship, Commonwealth Scientific and Industrial Research Organisation, Sydney, Australia.
Peter L
PL
Molloy
Food & Nutrition Flagship, Commonwealth Scientific and Industrial Research Organisation, Sydney, Australia.
Sue
S
Mitchell
Food & Nutrition Flagship, Commonwealth Scientific and Industrial Research Organisation, Sydney, Australia.
Trevor
T
Lockett
Flinders Centre for Innovation in Cancer, Flinders University of South Australia, Adelaide, Australia.
Graeme P
GP
Young
Clinical Genomics Proprietary Limited, Sydney, Australia.
Lawrence C
LC
LaPointe
D014408:Biomarkers, Tumor / Q000235:genetics*; D015179:Colorectal Neoplasms / Q000098:blood supply* / Q000175:diagnosis / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D006801:Humans; D051740:Ikaros Transcription Factor / Q000235:genetics; D008297:Male; D009367:Neoplasm Staging; D000637:Transaminases / Q000235:genetics
D014408:Biomarkers, Tumor; C497239:IKZF1 protein, human; D051740:Ikaros Transcription Factor; C490590:BCAT1 protein, human; D000637:Transaminases