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Cancer treatment monitoring using cell-free DNA fragmentomes

Author

Listed:
  • 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.
    NYU Langone Health Perlmutter Comprehensive Cancer Center)

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

Suggested Citation

  • 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 P, 2024. "Cancer treatment monitoring using cell-free DNA fragmentomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53017-7
    DOI: 10.1038/s41467-024-53017-7
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    References listed on IDEAS

    as
    1. Viktor A. Adalsteinsson & Gavin Ha & Samuel S. Freeman & Atish D. Choudhury & Daniel G. Stover & Heather A. Parsons & Gregory Gydush & Sarah C. Reed & Denisse Rotem & Justin Rhoades & Denis Loginov & , 2017. "Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors," Nature Communications, Nature, vol. 8(1), pages 1-13, December.
    2. Alessandro Leal & Nicole C. T. van Grieken & Doreen N. Palsgrove & Jillian Phallen & Jamie E. Medina & Carolyn Hruban & Mark A. M. Broeckaert & Valsamo Anagnostou & Vilmos Adleff & Daniel C. Bruhm & J, 2020. "White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    3. Dimitrios Mathios & Jakob Sidenius Johansen & Stephen Cristiano & Jamie E. Medina & Jillian Phallen & Klaus R. Larsen & Daniel C. Bruhm & Noushin Niknafs & Leonardo Ferreira & Vilmos Adleff & Jia Yuee, 2021. "Detection and characterization of lung cancer using cell-free DNA fragmentomes," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    4. Stephen Cristiano & Alessandro Leal & Jillian Phallen & Jacob Fiksel & Vilmos Adleff & Daniel C. Bruhm & Sarah Østrup Jensen & Jamie E. Medina & Carolyn Hruban & James R. White & Doreen N. Palsgrove &, 2019. "Genome-wide cell-free DNA fragmentation in patients with cancer," Nature, Nature, vol. 570(7761), pages 385-389, June.
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