Liquid Biopsy in Germ Cell Tumors

Theoretical framework: Testicular germ cell tumors (TGCT) are characterized by frequent chromosomal anomalies such as gain of chromosome 12p and low rates of somatic mutations. Cell-free circulating tumor DNA (ctDNA) has been investigated in some cancers but only a few studies explored the presence of ctDNA in TGCT. The consistent gain of genetic material from chromosome 12p makes TGCT patients to ideal candidates for liquid biopsy investigations. We have analyzed three pre-chemo samples with our plasma-Seq approach and applied the ichorCNA algorithm to call for somatic copy number alterations (SCNA) and estimate the tumor fraction. Besides the frequently observed chromosome 12p gain, a variety of other SCNA were detected indicating that shallow whole genome sequencing (sWGS) is a suitable approach to analyze ctDNA in TGCT. Only 60% of TGCT patients express the classical markers alpha fetoprotein (AFP) and beta (human chorionic gonadotropin) HCG. Biomarkers to monitor patients who don't express the classical markers are of great need.

Hypotheses: We postulate that tumor-specific aberrations can be detected non-invasively in plasma DNA from patients with metastatic TGCT and serve as a diagnostic tool. Furthermore, we will investigate if the change of ctDNA during curative treatment can be used as monitoring tool and allows risk classification in comparison to conventional markers and the novel micro RNA biomarker miR-371a-3p (prognostic value of ctDNA).

Methods: For ctDNA and micro RNA analysis, blood samples will be drawn from patients before orchiectomy, before chemotherapy start, prior to the second cycle of chemotherapy, after completion of treatment and in case of relapse. In order to identify SCNA and to estimate the tumor content in plasma we will employ sWGS and analyze the data with the ichorCNA algorithm for a detection of SCNA. Since TGCT have low rates of somatic mutations, orchiectomy samples from patients with disease recurrence and plasma samples at time of recurrence will also be compared with the Biomodal platform which allows analysis of genetic as well as epigenetic changes.