Novel methylated biomarkers and a robust assay to detect circulating tumor dna in metastatic breast cancer

Mary Jo Fackler, Zoila Lopez Bujanda, Christopher Umbricht, Wei Wen Teo, Soonweng Cho, Zhe Zhang, Kala Visvanathan, Stacie Jeter, Pedram Argani, Chenguang Wang, Jaclyn P. Lyman, Marina De Brot, James N. Ingle, Judy C Boughey, Kandace McGuire, Tari A. King, Lisa A. Carey, Leslie Cope, Antonio C. Wolff, Saraswati Sukumar

Research output: Contribution to journalArticle

81 Citations (Scopus)

Abstract

The ability to consistently detect cell-free tumor-specific DNA in peripheral blood of patients with metastatic breast cancer provides the opportunity to detect changes in tumor burden and to monitor response to treatment. We developed cMethDNA, a quantitative multiplexed methylation-specific PCR assay for a panel of ten genes, consisting of novel and known breast cancer hypermethylated markers identified by mining our previously reported study of DNA methylation patterns in breast tissue (103 cancer, 21 normal on the Illumina Human- Methylation27 Beadchip) and then validating the 10-gene panel in The Cancer Genome Atlas project breast cancer methylome database. For cMethDNA, a fixed physiologic level (50 copies) of artificially constructed, standard nonhuman reference DNA specific for each gene is introduced in a constant volume of serum (300 mL) before purification of the DNA, facilitating a sensitive, specific, robust, and quantitative assay of tumor DNA, with broad dynamic range. Cancer-specific methylated DNA was detected in training (28 normal, 24 cancer) and test (27 normal, 33 cancer) sets of recurrent stage IV patient sera with a sensitivity of 91% and a specificity of 96% in the test set. In a pilot study, cMethDNA assay faithfully reflected patient response to chemotherapy (N = 29). A core methylation signature present in the primary breast cancer was retained in serum and metastatic tissues collected at autopsy two to 11 years after diagnosis of the disease. Together, our data suggest that the cMethDNA assay can detect advanced breast cancer, and monitor tumor burden and treatment response in women with metastatic breast cancer.

Original languageEnglish (US)
Pages (from-to)2160-2170
Number of pages11
JournalCancer Research
Volume74
Issue number8
DOIs
StatePublished - Apr 15 2014

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Biomarkers
Breast Neoplasms
Neoplasms
DNA
Tumor Burden
Methylation
Serum
Genes
Atlases
DNA Methylation
Autopsy
Breast
Genome
Databases
Drug Therapy
Polymerase Chain Reaction
Therapeutics

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Fackler, M. J., Bujanda, Z. L., Umbricht, C., Teo, W. W., Cho, S., Zhang, Z., ... Sukumar, S. (2014). Novel methylated biomarkers and a robust assay to detect circulating tumor dna in metastatic breast cancer. Cancer Research, 74(8), 2160-2170. https://doi.org/10.1158/0008-5472.CAN-13-3392

Novel methylated biomarkers and a robust assay to detect circulating tumor dna in metastatic breast cancer. / Fackler, Mary Jo; Bujanda, Zoila Lopez; Umbricht, Christopher; Teo, Wei Wen; Cho, Soonweng; Zhang, Zhe; Visvanathan, Kala; Jeter, Stacie; Argani, Pedram; Wang, Chenguang; Lyman, Jaclyn P.; De Brot, Marina; Ingle, James N.; Boughey, Judy C; McGuire, Kandace; King, Tari A.; Carey, Lisa A.; Cope, Leslie; Wolff, Antonio C.; Sukumar, Saraswati.

In: Cancer Research, Vol. 74, No. 8, 15.04.2014, p. 2160-2170.

Research output: Contribution to journalArticle

Fackler, MJ, Bujanda, ZL, Umbricht, C, Teo, WW, Cho, S, Zhang, Z, Visvanathan, K, Jeter, S, Argani, P, Wang, C, Lyman, JP, De Brot, M, Ingle, JN, Boughey, JC, McGuire, K, King, TA, Carey, LA, Cope, L, Wolff, AC & Sukumar, S 2014, 'Novel methylated biomarkers and a robust assay to detect circulating tumor dna in metastatic breast cancer', Cancer Research, vol. 74, no. 8, pp. 2160-2170. https://doi.org/10.1158/0008-5472.CAN-13-3392
Fackler, Mary Jo ; Bujanda, Zoila Lopez ; Umbricht, Christopher ; Teo, Wei Wen ; Cho, Soonweng ; Zhang, Zhe ; Visvanathan, Kala ; Jeter, Stacie ; Argani, Pedram ; Wang, Chenguang ; Lyman, Jaclyn P. ; De Brot, Marina ; Ingle, James N. ; Boughey, Judy C ; McGuire, Kandace ; King, Tari A. ; Carey, Lisa A. ; Cope, Leslie ; Wolff, Antonio C. ; Sukumar, Saraswati. / Novel methylated biomarkers and a robust assay to detect circulating tumor dna in metastatic breast cancer. In: Cancer Research. 2014 ; Vol. 74, No. 8. pp. 2160-2170.
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