Abstract PR05: Analysis of ctDNA using the mFastSeqS and plasma–Seq methods for screening and therapy monitoring in prostate cancer patients
Authors: Belic Jelena , Heitzer Ellen , Ulz Peter , Auer Martina , Fischereder Katja , Bauernhofer Thomas , Geigl Jochen B. , Speicher Michael R. 
Published: May 2016

Abstract
Background: Prostate cancer is the most common malignancy in males. Prostate cancer progression can be inhibited by androgen-deprivation therapy, but nearly all patients eventually develop castration-resistance prostate cancer (CRPC). In the management of prostate cancer treatment, there are still unsolved questions as to how patients can best be matched to targeted therapies in accordance with the characteristics of their tumor genome. Recent progress in the analysis of cell-free circulating tumor DNA (ctDNA) now allows for the monitoring of tumor genomes by non-invasive means. Therefore, there is an unmet need to develop methods which will allow cost-effective pre-screening and therapy monitoring.
Methods: We analyzed a total of 71 metastatic prostate cancer patients with our recently published plasma-Seq method in order to establish genome-wide copy number aberrations (CNAs). Furthermore, we used a targeted resequencing approach to screen for mutations in a set of 58 cancer-associated genes and for the presence of TMPRSS-ERG fusions. In order to assess the amount of ctDNA in plasma, we used a modified FAST-Seq (mFAST-Seq) approach in a subset of samples. Follow-up samples were available from a total of 30 patients, which enabled us to monitor the constantly changing tumor genomes.
Results: Using plasma-Seq, we observed a variety of copy number changes characteristic of prostate cancer, i.e. 8q gains as well as losses at 3p, 8p, 10q, 13q, 17p and 21q in 67% of patients. AR gene amplifications were found in 70% of metastatic castration-resistant patients. Furthermore, when analyzing follow-up samples, we observed the occurrence of novel copy number aberrations and clonal shifts in one-third of the patients. In one extreme case we observed the loss of an AR focal amplification, which was accompanied by shifts in mutant allele frequencies for TP53 and EP300 mutations from 76.9% to 94.8% and from 14.4% to undetectable levels, respectively, after switching to cytotoxic chemotherapy. In a subset of samples (n=61), we performed mFAST-SeqS in order to estimate the ctDNA content and to identify samples with a ctDNA content of 10% or more. For samples that did not show any CNAs after plasma-Seq, a low amount of ctDNA (&lt; 10%) was also confirmed by mFAST-SeqS. In all other samples (ctDNA &gt; 10%), we observed highly consistent results (r=0.667) for plasma-Seq and mFastSeqS copy number profiles.
Conclusion: Plasma-Seq serves as a non-invasive method for monitoring a patient's response to therapy and may identify the occurrence of novel changes associated with resistance to a given therapy. The mFastSeqS approach has the advantage that no prior knowledge about the genetic composition of tumor samples is needed for the identification of plasma DNA samples with more than 10% of ctDNA content. Plasma DNA analyses may evolve to become a novel tool for the monitoring of patients with cancer and for the development of personalized medicine.
This abstract is also presented as Poster 28.
Citation Format: Jelena Belic, Ellen Heitzer, Peter Ulz, Martina Auer, Katja Fischereder, Thomas Bauernhofer, Jochen B. Geigl, Michael R. Speicher. Analysis of ctDNA using the mFastSeqS and plasma–Seq methods for screening and therapy monitoring in prostate cancer patients. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr PR05.