Cancer treatment monitoring using cell-free DNA fragmentomes

Iris van ’t Erve, Bahar Alipanahi, Keith Lumbard, Zachary L. Skidmore, Lorenzo Rinaldi, Laurel K. Millberg, Jacob Carey, Bryan Chesnick, Stephen Cristiano, Carter Portwood, Tony Wu, Erica Peters, Karen Bolhuis, Cornelis J. A. Punt, Jennifer Tom, Peter B. Bach, Nicholas C. Dracopoli, Gerrit A. Meijer, Robert B. Scharpf, Victor E. Velculescu, Remond J. A. Fijneman () and Alessandro Leal ()
Additional contact information
Iris van ’t Erve: Netherlands Cancer Institute
Bahar Alipanahi: Inc.
Keith Lumbard: Inc.
Zachary L. Skidmore: Inc.
Lorenzo Rinaldi: Inc.
Laurel K. Millberg: Inc.
Jacob Carey: Inc.
Bryan Chesnick: Inc.
Stephen Cristiano: Inc.
Carter Portwood: Inc.
Tony Wu: Inc.
Erica Peters: Inc.
Karen Bolhuis: University of Amsterdam
Cornelis J. A. Punt: University Medical Center Utrecht
Jennifer Tom: Inc.
Peter B. Bach: Inc.
Nicholas C. Dracopoli: Inc.
Gerrit A. Meijer: Netherlands Cancer Institute
Robert B. Scharpf: Johns Hopkins University School of Medicine
Victor E. Velculescu: Johns Hopkins University School of Medicine
Remond J. A. Fijneman: Netherlands Cancer Institute
Alessandro Leal: Inc.

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract Circulating cell-free DNA (cfDNA) assays for monitoring individuals with cancer typically rely on prior identification of tumor-specific mutations. Here, we develop a tumor-independent and mutation-independent approach (DELFI-tumor fraction, DELFI-TF) using low-coverage whole genome sequencing to determine the cfDNA tumor fraction and validate the method in two independent cohorts of patients with colorectal or lung cancer. DELFI-TF scores strongly correlate with circulating tumor DNA levels (ctDNA) (r = 0.90, p

Date: 2024
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DOI: 10.1038/s41467-024-53017-7

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