Quantification of tumor-specific variants (TSVs) in cell-free DNA is rapidly evolving as a prognostic and predictive tool in patients with cancer. Currently, both variant allele frequency (VAF) and number of mutant molecules per mL plasma are used as units of measurement to report those TSVs. However, it is unknown to what extent both units of measurement agree and what are the factors underlying an existing disagreement. To study the agreement between VAF and mutant molecules in current clinical studies, we analyzed 1116 TSVs from 338 patients identified with next-generation sequencing (NGS) or digital droplet PCR (ddPCR). On different study cohorts, a Deming regression analysis was performed and its 95% prediction interval was used as surrogate for the limits of agreement between VAF and number of mutant molecules per mL and to identify outliers. VAF and number of mutant molecules per mL plasma yielded greater agreement when using ddPCR than NGS. In case of discordance between VAF and number of mutant molecules per mL, insufficient molecular coverage in NGS and high cell-free DNA concentration were the main responsible factors. We propose several optimization steps needed to bring monitoring of TSVs in cell-free DNA to its full potential.
Bibliographical noteFunding Information:
We thank Jean Helmijr for his extensive efforts in obtaining ddPCR results at the Laboratory of Translational Cancer Genomics, Erasmus MC Rotterdam. Finally, would like to express our sincere gratitude to all clinicians involved in patient recruitment and to all patients that participated in our studies.
Manouk K Bos – Research funding: Dutch Cancer Society (no. NKB‐EMCR‐2016‐108154). Maurice P. H. Jansen – Research funding: Dutch Cancer Society (no. NKB‐NKI‐2014‐7080). Lindsay Angus – Consulting honorarium: Merck; Speaking honorarium: Pfizer. Winand N.M. Dinjens – Consulting honorarium: Bristol‐Myers Squibb, Roche, Bayer, Astra Zeneca, Novartis. Marzia del Re – Speaker honoraria: Astellas, Astra Zeneca, Celgene, Novartis, Pfizer, Bio‐Rad, Janssen, Sanofi‐Aventis; Consulting honoraria: Ipsen, Janssen‐Cilag, Sanofi‐Aventis; Speaker's bureau: Celgene, Janssen, Sanofi; Travel support: Astra‐Zeneca, Celgene, Janssen, Bio‐Rad. Hendrikus Jan Dubbink– Supported by a grant from AstraZeneca; Consulting or Advisory Role: AstraZeneca. John W.M. Martens – Consulting honorarium: Novartis; Research funding: Cancer Genomics Netherlands (CGC.nl), funded by the Netherlands Organization for Scientific Research (NWO). Kazem Nasserinejad, Peggy Atmodimedjo, Evert de Jonge, Ron H.N. van Schaik, Stefan Sleijfer – No conflict of interest.
© 2020 The Authors. Molecular Oncology published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies