Abstract LB-77: Measurement of tumor-specific chromosomal rearrangements in serial blood samples to monitor breast cancer burden and detect occult metastasis.
Authors: Olsson Eleonor , Winter Christof , George Anthony , Chen Yilun , Tang Man-Hung Eric , Dahlgren Malin , Schulz Ralph , Fernö Mårten , Rose Carsten , Howlin Jillian , Ingvar Christian , Rydén Lisa , Borg Åke , Gruvberger-Saal Sofia K. , Jernström Helena , Saal Lao H. 
Published: August 2014

Malignant cells release into the blood circulation their naked DNA, a potential biomarker containing tumor-specific chromosomal rearrangements. These tumor-derived rearrangements can be detected and quantified in cell-free blood plasma for information on minimal residual disease, treatment response, and detection of occult metastasis. Advances in high-throughput sequencing now allows for timely and affordable enumeration of tumor-specific chromosomal rearrangements in tumor types that have no pathognomonic DNA changes, such as breast cancer. We investigated whether individualized tumor-specific chromosomal rearrangements could meet clinical sensitivity and specificity criteria to serve as robust breast cancer biomarkers in serial blood plasma samples. To this end, we studied a retrospective cohort of 35 patients with early breast cancer for which frozen primary tumor specimens were available and blood plasma samples had been biobanked at diagnosis (prior to surgery) and at regular time intervals during the clinical course. Nine patients were relapse-free at 7-years follow-up and 26 patients had metastatic disease detected clinically between 1.1 to 5.7 years after diagnosis. HiSeq paired-end sequencing of the primary tumor DNA to 1.8 to 8-fold genome coverage (average 3.9x) identified 27 to 417 chromosomal rearrangements per tumor (average 134). For rearrangements confirmed to be somatic, droplet digital PCR (ddPCR) assays were designed for their quantification in the DNA isolated from cell-free blood plasma. Tumor and matched normal DNA were used as positive and negative controls. In the ddPCR analysis of 15 patients thus far, monitoring 2 to 6 rearrangements per patient, our method exhibits 100% sensitivity and 100% specificity for post-surgical molecular detection of tumor-specific rearranged DNA in the plasma from patients with and without confirmed clinical recurrence. Furthermore, the time-point of our molecular detection of recurrent disease preceded symptoms and clinical detection in nearly all patients (an average lead time of 9 months; range 0 to 28 months). Our results demonstrate that identification of tumor-specific chromosomal rearrangements and subsequent serial analysis of genomic aberrations in blood is a highly sensitive and specific method for monitoring tumor burden and relapse in early breast cancer. Given that the cost of such analyses is comparable to medical procedures such as CT scans, our approach shows great promise as a clinical test for routine cancer management.

Citation Format: Eleonor Olsson, Christof Winter, Anthony George, Yilun Chen, Man-Hung Eric Tang, Malin Dahlgren, Ralph Schulz, Mårten Fernö, Carsten Rose, Jillian Howlin, Christian Ingvar, Lisa Rydén, Åke Borg, Sofia K. Gruvberger-Saal, Helena Jernström, Lao H. Saal. Measurement of tumor-specific chromosomal rearrangements in serial blood samples to monitor breast cancer burden and detect occult metastasis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-77. doi:10.1158/1538-7445.AM2013-LB-77