Abstract 1587: Targeted sequencing of prostate cancer circulating tumor cells in comparison with matched cell free DNA and prostate tumors
Authors: Hu Brian , Liu Stephen , Xu Yucheng , Dempsey Paul , Strauss William , Wentzel Kristopher , Xu Tong , Pinski Jacek , Dorff Tanya , Winer-Jones Jessamine , Quinn David I. , Goldkorn Amir 
Published: August 2015

Abstract
Introduction: Precision oncology care is predicated upon detecting actionable genomic aberrations. Obtaining tissue that accurately reflects the genomic landscape of prostate cancer (PCa) is a challenge, though circulating tumor cells (CTCs) represent a promising tissue source. We demonstrate the feasibility of high throughput targeted sequencing of CTCs across multiple PCa disease states and compare the genomic variation among different cancer substrates (CTCs, cell free DNA [cfDNA], primary tumors, metastasis) in matched patient samples.
Methods: Under IRB approval, 7.5ml of peripheral blood was obtained from healthy controls and patients with PCa. CTCs were enriched using LiquidBiopsy® (Cynvenio Biosystems), a CLIA-certified immunoaffinity-based microfluidic platform. CTCs were defined as EpCAM+CK+DAPI+CD45. Amplicon libraries covering 50 cancer genes were generated (AmpliSeq 2.0, Life Technology) and sequenced on an Ion Proton System. Somatic single nucleotide variants (SSNV), occurring in &gt;1% of DNA in a sample, were identified based on their presence in CTCs and absence from WBC. When available, matched cfDNA, primary tumors and metastatic tissue were sequenced in parallel.
Results: Peripheral blood was collected from healthy controls (n = 31) and PCa patients (n = 26) at various disease states: localized (n = 2), biochemical recurrence (n = 4), metastatic hormone sensitive (n = 16), and castration resistant (n = 4). In patients with PCa, the median PSA was 3.32 ng/dl (range &lt;0.03-1531) and CTCs were identified in 26 of 26 (100%) patients with a median CTC count of 46 cells/7.5 ml (range 15-518). Six of 26 (23%) CTC samples from PCa patients had SSNV detected at 18 loci. Matched tissue was available in 17 of the 26 PCa patients: cfDNA (n = 14), primary tumor (n = 3), primary tumor and metastasis (n = 1). Five of 14 (36%) cfDNA samples had SSNVs detected at 16 loci; 2 of 3 (67%) primary tumors had SSNVs detected at 2 loci; and 1 of 1 (100%) metastasis had SSNVs detected at 4 loci. Of the 17 patients with matched tissue samples, SSNV concordance was seen in only one case. No SSNVs were detected in the control patients.
Conclusion: Targeted sequencing of CTCs was feasible across the spectrum of PCa and SSNVs identified in CTCs were not concordant with SSNVs in matched cfDNA or tumor DNA, likely reflecting cellular heterogeneity, clonal evolution, and tissue-specific extraction methodologies. Expanded matched sample cohorts are needed to elucidate how these DNA sources - used alone or in combination - can best inform clinical decisions in prostate cancer.
Citation Format: Brian Hu, Stephen Liu, Yucheng Xu, Paul Dempsey, William Strauss, Kristopher Wentzel, Tong Xu, Jacek Pinski, Tanya Dorff, Jessamine Winer-Jones, David I. Quinn, Amir Goldkorn. Targeted sequencing of prostate cancer circulating tumor cells in comparison with matched cell free DNA and prostate tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1587. doi:10.1158/1538-7445.AM2015-1587