Nature Communications (Jan 2024)

A Machine Learning-Driven Virtual Biopsy System For Kidney Transplant Patients

  • Daniel Yoo,
  • Gillian Divard,
  • Marc Raynaud,
  • Aaron Cohen,
  • Tom D. Mone,
  • John Thomas Rosenthal,
  • Andrew J. Bentall,
  • Mark D. Stegall,
  • Maarten Naesens,
  • Huanxi Zhang,
  • Changxi Wang,
  • Juliette Gueguen,
  • Nassim Kamar,
  • Antoine Bouquegneau,
  • Ibrahim Batal,
  • Shana M. Coley,
  • John S. Gill,
  • Federico Oppenheimer,
  • Erika De Sousa-Amorim,
  • Dirk R. J. Kuypers,
  • Antoine Durrbach,
  • Daniel Seron,
  • Marion Rabant,
  • Jean-Paul Duong Van Huyen,
  • Patricia Campbell,
  • Soroush Shojai,
  • Michael Mengel,
  • Oriol Bestard,
  • Nikolina Basic-Jukic,
  • Ivana Jurić,
  • Peter Boor,
  • Lynn D. Cornell,
  • Mariam P. Alexander,
  • P. Toby Coates,
  • Christophe Legendre,
  • Peter P. Reese,
  • Carmen Lefaucheur,
  • Olivier Aubert,
  • Alexandre Loupy

DOI
https://doi.org/10.1038/s41467-023-44595-z
Journal volume & issue
Vol. 15, no. 1
pp. 1 – 12

Abstract

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Abstract In kidney transplantation, day-zero biopsies are used to assess organ quality and discriminate between donor-inherited lesions and those acquired post-transplantation. However, many centers do not perform such biopsies since they are invasive, costly and may delay the transplant procedure. We aim to generate a non-invasive virtual biopsy system using routinely collected donor parameters. Using 14,032 day-zero kidney biopsies from 17 international centers, we develop a virtual biopsy system. 11 basic donor parameters are used to predict four Banff kidney lesions: arteriosclerosis, arteriolar hyalinosis, interstitial fibrosis and tubular atrophy, and the percentage of renal sclerotic glomeruli. Six machine learning models are aggregated into an ensemble model. The virtual biopsy system shows good performance in the internal and external validation sets. We confirm the generalizability of the system in various scenarios. This system could assist physicians in assessing organ quality, optimizing allograft allocation together with discriminating between donor derived and acquired lesions post-transplantation.