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Updated: Feb 21, 2026
Testing Targeted Therapies in Cancer using Structural DNA Alteration Analysis and Patient-Derived Xenografts
Published on: July 25, 2020
Impact of Circulating Tumor DNA and Copy-Number Alterations on Clinical Outcome in Relapsed/Refractory Germ Cell
Milena Urbini1, Thomas F Eleveld2, Maurizio Polano3
1Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy.
Purpose:
High-dose chemotherapy (HDCT) is one of the salvage therapy options for patients with relapsed/refractory germ cell tumors (rGCT) after failure of first-line chemotherapy. We aimed to identify circulating biomarkers predicting clinical response and outcome of HDCT.
Methods:
Baseline and on-treatment plasma samples from 69 HDCT-treated and 26 conventional-dose chemotherapy (CDCT)-treated GCT patients were analyzed by shallow whole-genome sequencing. Tumor fraction (TF) and copy-number alterations (CNAs) were determined using ichorCNA, compared with miR-371a-3p levels, and correlated with progression-free survival (PFS) and overall survival (OS). CNA profiles from external tissue GCT cohorts were used for validation.
Results:
TF was detectable in 75.4% of baseline plasma of HDCT patients. High TF was strongly associated with worse OS in HDCT-treated nonseminomas (P = .021). This was confirmed in the CDCT cohort (P = .039), where shorter median OS was observed in high-TF patients compared with the HDCT cohort. Conversely, miR-371a-3p levels were not prognostic. Plasma CNA profiling confirmed the high frequency of chromosome 3p gain in rGCT cases and revealed other alterations linked to poor HDCT outcomes, including 9q and 11q gains and 6q loss. These CNAs were enriched in a cluster predominantly composed of GCT with extra-embryonic histology (yolk sac and choriocarcinoma). Unsupervised clustering of CNA profile of plasma identified 13 patients in this high-risk cluster, who had significantly worse PFS and OS compared with other rGCT cases.
Conclusion:
Analysis of cell free DNA provides valuable prognostic information in rGCTs. High baseline TF and specific CNA patterns linked to extra-embryonic histology identify patients at higher risk of poor outcomes. HDCT seems to be more effective than CDCT in high-TF patients. These minimally invasive biomarkers could refine risk stratification and guide selection of salvage therapies in rGCTs.
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