Evidence map›Paper›PMID 40730747›Full record

ArticleNature communications2025

Epigenomic diagnosis and prognosis of Acute Myeloid Leukemia.

Francisco Marchi, Vivek M Shastri, Richard J Marrero, Nam H K Nguyen, Antonella Öttl, Ann-Kathrin Schade, Marieke Landwehr, Olga Krali, Jessica Nordlund, Matin Ghavami and 19 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

29 authors.

Francisco MarchiPharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA.ORCID http://orcid.org/0000-0002-7318-9137
Vivek M ShastriPharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA.ORCID http://orcid.org/0009-0003-1105-1575
Richard J MarreroPharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA.ORCID http://orcid.org/0000-0002-0789-1075
Nam H K NguyenPharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA.ORCID http://orcid.org/0000-0003-3036-4748
Antonella ÖttlPharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA.
Ann-Kathrin SchadePharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA.
Marieke LandwehrPharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA.
Olga KraliDepartment of Medical Sciences, Molecular Precision Medicine, Uppsala University, Uppsala, Sweden.ORCID http://orcid.org/0000-0002-6436-9531
Jessica NordlundDepartment of Medical Sciences, Molecular Precision Medicine, Uppsala University, Uppsala, Sweden.ORCID http://orcid.org/0000-0001-8699-9959
Matin GhavamiDepartment of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA.
Fernando SckaffPharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA.
Vikash K MansinghkaDepartment of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
Xueyuan CaoDepartment of Health Promotion and Disease Prevention, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-4396-7460
William SlaytonDepartment of Pediatrics Hematology, University of Florida, Gainesville, FL, USA.
Petr StarostikUniversity of Florida Health Cancer Center, Gainesville, FL, USA.
Christopher R CogleUniversity of Florida Health Cancer Center, Gainesville, FL, USA.
Raul C RibeiroDepartment of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-9956-5647
Jeffrey E RubnitzDepartment of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Jeffery KlcoDepartment of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.ORCID http://orcid.org/0000-0003-2961-6960
Abdelrahman ElsayedDepartment of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA.
Alan S GamisHematology/Oncology/BMT, Children's Mercy Kansas City, Kansas City, MO, USA.
Timothy J TricheDepartment of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.ORCID http://orcid.org/0000-0001-5665-946X
Rhonda RiesTranslational Science and Therapeutics, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-3702-7923
E Anders KolbLeukemia & Lymphoma Society, Washington D.C., USA.
Richard AplencDepartment of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
Todd AlonzoUniversity of Southern California Keck School of Med, Los Angeles, CA, USA.
Stanley PoundsDepartment of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-9167-2114
Soheil MeshinchiTranslational Science and Therapeutics, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-6276-4423
Jatinder K LambaPharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA. jatinderklamba@ufl.edu.ORCID http://orcid.org/0000-0003-0411-0007

Funding

NCTN BIQSFP ANBL1531 (NRT)U10CA180886 · NCI · PUBLIC HEALTH INSTITUTE · PI Douglas S. Hawkins · 2014 to 2026
$390.6M
COG FOREIGN ACCRUALU10CA098543 · NCI · NATIONAL CHILDHOOD CANCER FOUNDATION · PI ADAMSON, PETER C. · 2003 to 2013
$335.5M
COG SDMC - Statistics CoreU10CA180899 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI TODD A ALONZO · 2014 to 2026
$132.8M
Children's Oncology Group Statistics &Data Center GrantU10CA098413 · NCI · UNIVERSITY OF NEBRASKA MEDICAL CENTER · PI DEVIDAS, MEENAKSHI · 2003 to 2013
$67.5M
University of Florida Health Cancer Center Support GrantP30CA247796 · NCI · UNIVERSITY OF FLORIDA · PI Alison Ivey · 2023 to 2026
$10.9M
Pharmacogenomics of Ara-C in AMLR01CA132946 · NCI · UNIVERSITY OF MINNESOTA · PI LAMBA, JATINDER K., POUNDS, STANLEY BARRETT · 2008 to 2025
$5.3M
Integrated Systems Biology of Pediatric AMLR01CA270120 · NCI · UNIVERSITY OF FLORIDA · PI Jatinder K. Lamba, Stanley Barrett Pounds · 2023 to 2026
$2.7M
American Cancer Society (American Cancer Society, Inc.) SAP 21-061-01NCI NIH HHS P30 CA247796NCI NIH HHS R01 CA132946NCI NIH HHS R01 CA270120NCI NIH HHS U10 CA098413NCI NIH HHS U10 CA098543NCI NIH HHS U10 CA180886NCI NIH HHS U10 CA180899U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R01CA132946U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R01CA270120
6 · The paper itself

Abstract

Despite the critical role of DNA methylation, clinical implementations harnessing its promise have not been described in acute myeloid leukemia. Utilizing DNA methylation from 3314 leukemia patient samples across 11 harmonized cohorts, we describe the Acute Leukemia Methylome Atlas, which includes robust models capable of accurately predicting AML subtypes. A genome-wide prognostic model as well as a targeted panel of 38 CpGs significantly predict five-year survival in our pediatric and adult test cohorts. To accelerate rapid clinical utility, we develop a specimen-to-result protocol that uses long-read nanopore sequencing and machine learning to characterize patients' whole genomes and epigenomes. Clinical validation on patient samples confirms high concordance between epigenomic signatures and genomic lesions, though uniquely rare karyotypes remained challenging due to limited available training data. These results unveil the potential for increased affordability, speed, and accuracy for patients in need of complex molecular diagnosis and prognosis.

Indexed as

EpigenomicsLeukemia, Myeloid, AcuteAdolescentAdultChildChild, PreschoolCohort StudiesCpG IslandsDNA MethylationEpigenesis, GeneticFemaleHumansMachine LearningMaleMiddle AgedPrognosis

Identifiers

PMID40730747
PMCPMC12307604

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.