/ en Mon, 22 Sep 25 10:00:11 -0400 /news/new-ai-based-diagnostic-tool-uses-epigenomics-accelerate-acute-leukemia-diagnosis <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" class="datetime">September 22, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>By classifying acute leukemia samples based on methylation patterns, MARLIN reduces diagnosis time from days to hours.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Nicole Oliverio, Dana-Farber Cancer Institute </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" title="Monday, September 22, 2025 - 10:00" class="datetime">September 22, 2025</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodelong-storyfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=lBHJ2tK9 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="736" height="520"/> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=VMhZ1AdI 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="641" height="451"/> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=4lbYFPL7 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="706" height="417"/> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z 1x" media="all and (max-width: 539px)" type="image/jpeg" width="499" height="294"/> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z" alt="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." title="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." typeof="foaf:Image" /> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: NCI Visuals Online </div> <div class="media-caption__description"> Acute myeloid leukemia cells (red). </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous" /></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/2391/feed&title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/2391/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&body=/taxonomy/term/2391/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> <div class="block block-layout-builder block-field-blocknodelong-storyfield-content-paragraphs"> <div class="field field--name-field-content-paragraphs field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--text-with-sidebar text-with-sidebar"> <div class="field field--name-field-sidebar field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related people</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related programs</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/node/8831">Epigenomics Program</a></div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Researchers at Dana-Farber Cancer Institute and the Ó³»­´«Ã½ have developed an artificial intelligence-based diagnostic tool that could transform the way acute leukemia is identified and treated. The tool, called MARLIN (Methylation- and AI-guided Rapid Leukemia Subtype Inference), uses DNA methylation patterns and machine learning to classify acute leukemia with speed and accuracy. This tool has the potential to significantly improve patient care by allowing faster and more precise treatment decisions.</p> <p>Acute leukemia is an aggressive blood cancer that requires accurate diagnosis to guide treatment. Current diagnostic methods, which rely on a combination of molecular and cytogenetic tests, often take days or even weeks to complete. Built as a neural network, MARLIN, however, can provide results in as little as two hours from the time of biopsy. By providing rapid and detailed insights into leukemia subtypes, MARLIN could enable clinicians to make treatment decisions sooner and with more complete information.</p> <p>"Ultimately, we envision that methylation-based acute leukemia classifications will complement standard-of-care diagnostic tests to provide more comprehensive and timely information to pathologists, clinicians, and patients," said <a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a>, a computational biologist at Dana-Farber, an associate member in Ó³»­´«Ã½'s <a href="/node/8831">Epigenomics Program</a>, and co-senior author of the study. </p> <p>The findings were published in <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank"><em>Nature Genetics</em></a>.</p> <p>To develop MARLIN, the research team first created a large reference database of DNA methylation patterns from over 2,500 patient samples, representing a wide range of leukemia subtypes. This revealed 38 distinct methylation classes across disease subtypes in adults and children. "Our analysis confirms many established molecular categories in acute leukemia but also reveals new classes that are best seen through the lens of epigenetics," said Til Steinicke, co-first author of the study along with Salvatore Benfatto.</p> <p>Using this reference dataset, the team trained MARLIN to identify methylation classes in bone marrow and blood samples from patients with acute leukemia. When paired with long-read nanopore sequencing technology, which permits DNA methylation profiling from clinical samples, MARLIN demonstrated high accuracy for disease classification in both retrospective and prospective samples. "We adapted our machine learning approach to use very small amounts of data as input, which allowed us to quickly generate classifications after just a few minutes of sequencing," said Benfatto.</p> <p>In real-time tests, MARLIN correctly classified leukemia samples in under two hours from the time of biopsy receipt, a dramatic improvement over the timelines of current diagnostic workflows. "As our work continues, we hope MARLIN will greatly accelerate treatment planning, reduce medical complications, and ease patient worries in the future," said Evan Chen, a collaborator on the study and medical oncologist at Dana-Farber.</p> <p>The researchers also found that MARLIN could resolve diagnostic "blind spots" missed by conventional methods. For example, it successfully identified cryptic genetic events such as rearrangements involving the <em>DUX4</em> gene that are associated with favorable clinical outcomes. Additionally, MARLIN revealed novel predictive signatures, such as HOX-activated subgroups, which could inform future treatment strategies.</p> <p>"We believe that our framework paves the way for future developments in epigenetic classification of acute leukemia, machine learning-assisted diagnostics, and methylation-based predictive biomarkers of drug response," said Gabriel Griffin, a cancer researcher, Ó³»­´«Ã½ associate member, Dana-Farber pathologist, and co-senior author of the study.</p> <p>The researchers now aim to develop MARLIN into a tool that can be provided to patients in the clinic to accelerate disease classification, inform treatment selection in real-time, and generate a resource for the cancer research community to study the role of DNA methylation in leukemia.</p> <p><em>Adapted from <a href="https://www.dana-farber.org/newsroom/news-releases/2025/new-diagnostic-tool-developed-at-dana-farber-revolutionizes-acute-leukemia-diagnosis" target="_blank">a press release</a> issued by Dana-Farber Cancer Institute.</em><br>  </p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study came from the Evans MDS Center at Dana-Farber Cancer Institute and other sources.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Steinicke TL, Benfatto S, et al. <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank">Rapid epigenomic classification of acute leukemia</a>. <em>Nature Genetics</em>. Online September 22, 2025. DOI: 10.1038/s41588-025-02321-z.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/epigenomics" hreflang="en">Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/cancer" hreflang="en">Cancer</a></div> <div class="field__item"><a href="/broad-tags/artificial-intelligence" hreflang="en">Artificial intelligence</a></div> <div class="field__item"><a href="/broad-tags/machine-learning-0" hreflang="en">Machine Learning</a></div> </div> </div> </div> </div> </div> Mon, 22 Sep 2025 14:00:11 +0000 tulrich@broadinstitute.org 5559416 at /news/new-machine-learning-based-single-cell-search-engine-makes-cell-annotation-faster-more <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" class="datetime">September 22, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>By classifying acute leukemia samples based on methylation patterns, MARLIN reduces diagnosis time from days to hours.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Nicole Oliverio, Dana-Farber Cancer Institute </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" title="Monday, September 22, 2025 - 10:00" class="datetime">September 22, 2025</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodelong-storyfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=lBHJ2tK9 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="736" height="520"/> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=VMhZ1AdI 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="641" height="451"/> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=4lbYFPL7 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="706" height="417"/> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z 1x" media="all and (max-width: 539px)" type="image/jpeg" width="499" height="294"/> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z" alt="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." title="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." typeof="foaf:Image" /> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: NCI Visuals Online </div> <div class="media-caption__description"> Acute myeloid leukemia cells (red). </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous" /></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/2391/feed&title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/2391/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&body=/taxonomy/term/2391/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> <div class="block block-layout-builder block-field-blocknodelong-storyfield-content-paragraphs"> <div class="field field--name-field-content-paragraphs field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--text-with-sidebar text-with-sidebar"> <div class="field field--name-field-sidebar field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related people</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related programs</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/node/8831">Epigenomics Program</a></div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Researchers at Dana-Farber Cancer Institute and the Ó³»­´«Ã½ have developed an artificial intelligence-based diagnostic tool that could transform the way acute leukemia is identified and treated. The tool, called MARLIN (Methylation- and AI-guided Rapid Leukemia Subtype Inference), uses DNA methylation patterns and machine learning to classify acute leukemia with speed and accuracy. This tool has the potential to significantly improve patient care by allowing faster and more precise treatment decisions.</p> <p>Acute leukemia is an aggressive blood cancer that requires accurate diagnosis to guide treatment. Current diagnostic methods, which rely on a combination of molecular and cytogenetic tests, often take days or even weeks to complete. Built as a neural network, MARLIN, however, can provide results in as little as two hours from the time of biopsy. By providing rapid and detailed insights into leukemia subtypes, MARLIN could enable clinicians to make treatment decisions sooner and with more complete information.</p> <p>"Ultimately, we envision that methylation-based acute leukemia classifications will complement standard-of-care diagnostic tests to provide more comprehensive and timely information to pathologists, clinicians, and patients," said <a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a>, a computational biologist at Dana-Farber, an associate member in Ó³»­´«Ã½'s <a href="/node/8831">Epigenomics Program</a>, and co-senior author of the study. </p> <p>The findings were published in <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank"><em>Nature Genetics</em></a>.</p> <p>To develop MARLIN, the research team first created a large reference database of DNA methylation patterns from over 2,500 patient samples, representing a wide range of leukemia subtypes. This revealed 38 distinct methylation classes across disease subtypes in adults and children. "Our analysis confirms many established molecular categories in acute leukemia but also reveals new classes that are best seen through the lens of epigenetics," said Til Steinicke, co-first author of the study along with Salvatore Benfatto.</p> <p>Using this reference dataset, the team trained MARLIN to identify methylation classes in bone marrow and blood samples from patients with acute leukemia. When paired with long-read nanopore sequencing technology, which permits DNA methylation profiling from clinical samples, MARLIN demonstrated high accuracy for disease classification in both retrospective and prospective samples. "We adapted our machine learning approach to use very small amounts of data as input, which allowed us to quickly generate classifications after just a few minutes of sequencing," said Benfatto.</p> <p>In real-time tests, MARLIN correctly classified leukemia samples in under two hours from the time of biopsy receipt, a dramatic improvement over the timelines of current diagnostic workflows. "As our work continues, we hope MARLIN will greatly accelerate treatment planning, reduce medical complications, and ease patient worries in the future," said Evan Chen, a collaborator on the study and medical oncologist at Dana-Farber.</p> <p>The researchers also found that MARLIN could resolve diagnostic "blind spots" missed by conventional methods. For example, it successfully identified cryptic genetic events such as rearrangements involving the <em>DUX4</em> gene that are associated with favorable clinical outcomes. Additionally, MARLIN revealed novel predictive signatures, such as HOX-activated subgroups, which could inform future treatment strategies.</p> <p>"We believe that our framework paves the way for future developments in epigenetic classification of acute leukemia, machine learning-assisted diagnostics, and methylation-based predictive biomarkers of drug response," said Gabriel Griffin, a cancer researcher, Ó³»­´«Ã½ associate member, Dana-Farber pathologist, and co-senior author of the study.</p> <p>The researchers now aim to develop MARLIN into a tool that can be provided to patients in the clinic to accelerate disease classification, inform treatment selection in real-time, and generate a resource for the cancer research community to study the role of DNA methylation in leukemia.</p> <p><em>Adapted from <a href="https://www.dana-farber.org/newsroom/news-releases/2025/new-diagnostic-tool-developed-at-dana-farber-revolutionizes-acute-leukemia-diagnosis" target="_blank">a press release</a> issued by Dana-Farber Cancer Institute.</em><br>  </p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study came from the Evans MDS Center at Dana-Farber Cancer Institute and other sources.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Steinicke TL, Benfatto S, et al. <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank">Rapid epigenomic classification of acute leukemia</a>. <em>Nature Genetics</em>. Online September 22, 2025. DOI: 10.1038/s41588-025-02321-z.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/epigenomics" hreflang="en">Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/cancer" hreflang="en">Cancer</a></div> <div class="field__item"><a href="/broad-tags/artificial-intelligence" hreflang="en">Artificial intelligence</a></div> <div class="field__item"><a href="/broad-tags/machine-learning-0" hreflang="en">Machine Learning</a></div> </div> </div> </div> </div> </div> Mon, 28 Oct 2024 14:55:51 +0000 Corie Lok 5557581 at /news/machine-learning-guides-researchers-new-synthetic-genetic-switches <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" class="datetime">September 22, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>By classifying acute leukemia samples based on methylation patterns, MARLIN reduces diagnosis time from days to hours.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Nicole Oliverio, Dana-Farber Cancer Institute </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" title="Monday, September 22, 2025 - 10:00" class="datetime">September 22, 2025</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodelong-storyfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=lBHJ2tK9 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="736" height="520"/> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=VMhZ1AdI 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="641" height="451"/> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=4lbYFPL7 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="706" height="417"/> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z 1x" media="all and (max-width: 539px)" type="image/jpeg" width="499" height="294"/> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z" alt="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." title="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." typeof="foaf:Image" /> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: NCI Visuals Online </div> <div class="media-caption__description"> Acute myeloid leukemia cells (red). </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous" /></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/2391/feed&title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/2391/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&body=/taxonomy/term/2391/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> <div class="block block-layout-builder block-field-blocknodelong-storyfield-content-paragraphs"> <div class="field field--name-field-content-paragraphs field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--text-with-sidebar text-with-sidebar"> <div class="field field--name-field-sidebar field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related people</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related programs</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/node/8831">Epigenomics Program</a></div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Researchers at Dana-Farber Cancer Institute and the Ó³»­´«Ã½ have developed an artificial intelligence-based diagnostic tool that could transform the way acute leukemia is identified and treated. The tool, called MARLIN (Methylation- and AI-guided Rapid Leukemia Subtype Inference), uses DNA methylation patterns and machine learning to classify acute leukemia with speed and accuracy. This tool has the potential to significantly improve patient care by allowing faster and more precise treatment decisions.</p> <p>Acute leukemia is an aggressive blood cancer that requires accurate diagnosis to guide treatment. Current diagnostic methods, which rely on a combination of molecular and cytogenetic tests, often take days or even weeks to complete. Built as a neural network, MARLIN, however, can provide results in as little as two hours from the time of biopsy. By providing rapid and detailed insights into leukemia subtypes, MARLIN could enable clinicians to make treatment decisions sooner and with more complete information.</p> <p>"Ultimately, we envision that methylation-based acute leukemia classifications will complement standard-of-care diagnostic tests to provide more comprehensive and timely information to pathologists, clinicians, and patients," said <a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a>, a computational biologist at Dana-Farber, an associate member in Ó³»­´«Ã½'s <a href="/node/8831">Epigenomics Program</a>, and co-senior author of the study. </p> <p>The findings were published in <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank"><em>Nature Genetics</em></a>.</p> <p>To develop MARLIN, the research team first created a large reference database of DNA methylation patterns from over 2,500 patient samples, representing a wide range of leukemia subtypes. This revealed 38 distinct methylation classes across disease subtypes in adults and children. "Our analysis confirms many established molecular categories in acute leukemia but also reveals new classes that are best seen through the lens of epigenetics," said Til Steinicke, co-first author of the study along with Salvatore Benfatto.</p> <p>Using this reference dataset, the team trained MARLIN to identify methylation classes in bone marrow and blood samples from patients with acute leukemia. When paired with long-read nanopore sequencing technology, which permits DNA methylation profiling from clinical samples, MARLIN demonstrated high accuracy for disease classification in both retrospective and prospective samples. "We adapted our machine learning approach to use very small amounts of data as input, which allowed us to quickly generate classifications after just a few minutes of sequencing," said Benfatto.</p> <p>In real-time tests, MARLIN correctly classified leukemia samples in under two hours from the time of biopsy receipt, a dramatic improvement over the timelines of current diagnostic workflows. "As our work continues, we hope MARLIN will greatly accelerate treatment planning, reduce medical complications, and ease patient worries in the future," said Evan Chen, a collaborator on the study and medical oncologist at Dana-Farber.</p> <p>The researchers also found that MARLIN could resolve diagnostic "blind spots" missed by conventional methods. For example, it successfully identified cryptic genetic events such as rearrangements involving the <em>DUX4</em> gene that are associated with favorable clinical outcomes. Additionally, MARLIN revealed novel predictive signatures, such as HOX-activated subgroups, which could inform future treatment strategies.</p> <p>"We believe that our framework paves the way for future developments in epigenetic classification of acute leukemia, machine learning-assisted diagnostics, and methylation-based predictive biomarkers of drug response," said Gabriel Griffin, a cancer researcher, Ó³»­´«Ã½ associate member, Dana-Farber pathologist, and co-senior author of the study.</p> <p>The researchers now aim to develop MARLIN into a tool that can be provided to patients in the clinic to accelerate disease classification, inform treatment selection in real-time, and generate a resource for the cancer research community to study the role of DNA methylation in leukemia.</p> <p><em>Adapted from <a href="https://www.dana-farber.org/newsroom/news-releases/2025/new-diagnostic-tool-developed-at-dana-farber-revolutionizes-acute-leukemia-diagnosis" target="_blank">a press release</a> issued by Dana-Farber Cancer Institute.</em><br>  </p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study came from the Evans MDS Center at Dana-Farber Cancer Institute and other sources.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Steinicke TL, Benfatto S, et al. <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank">Rapid epigenomic classification of acute leukemia</a>. <em>Nature Genetics</em>. Online September 22, 2025. DOI: 10.1038/s41588-025-02321-z.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/epigenomics" hreflang="en">Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/cancer" hreflang="en">Cancer</a></div> <div class="field__item"><a href="/broad-tags/artificial-intelligence" hreflang="en">Artificial intelligence</a></div> <div class="field__item"><a href="/broad-tags/machine-learning-0" hreflang="en">Machine Learning</a></div> </div> </div> </div> </div> </div> Wed, 23 Oct 2024 15:05:19 +0000 tulrich@broadinstitute.org 5557621 at /news/researchers-identify-cheap-and-effective-biomarkers-dcis-tumor-stage <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" class="datetime">September 22, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>By classifying acute leukemia samples based on methylation patterns, MARLIN reduces diagnosis time from days to hours.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Nicole Oliverio, Dana-Farber Cancer Institute </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" title="Monday, September 22, 2025 - 10:00" class="datetime">September 22, 2025</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodelong-storyfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=lBHJ2tK9 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="736" height="520"/> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=VMhZ1AdI 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="641" height="451"/> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=4lbYFPL7 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="706" height="417"/> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z 1x" media="all and (max-width: 539px)" type="image/jpeg" width="499" height="294"/> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z" alt="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." title="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." typeof="foaf:Image" /> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: NCI Visuals Online </div> <div class="media-caption__description"> Acute myeloid leukemia cells (red). </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous" /></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/2391/feed&title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/2391/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&body=/taxonomy/term/2391/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> <div class="block block-layout-builder block-field-blocknodelong-storyfield-content-paragraphs"> <div class="field field--name-field-content-paragraphs field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--text-with-sidebar text-with-sidebar"> <div class="field field--name-field-sidebar field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related people</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related programs</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/node/8831">Epigenomics Program</a></div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Researchers at Dana-Farber Cancer Institute and the Ó³»­´«Ã½ have developed an artificial intelligence-based diagnostic tool that could transform the way acute leukemia is identified and treated. The tool, called MARLIN (Methylation- and AI-guided Rapid Leukemia Subtype Inference), uses DNA methylation patterns and machine learning to classify acute leukemia with speed and accuracy. This tool has the potential to significantly improve patient care by allowing faster and more precise treatment decisions.</p> <p>Acute leukemia is an aggressive blood cancer that requires accurate diagnosis to guide treatment. Current diagnostic methods, which rely on a combination of molecular and cytogenetic tests, often take days or even weeks to complete. Built as a neural network, MARLIN, however, can provide results in as little as two hours from the time of biopsy. By providing rapid and detailed insights into leukemia subtypes, MARLIN could enable clinicians to make treatment decisions sooner and with more complete information.</p> <p>"Ultimately, we envision that methylation-based acute leukemia classifications will complement standard-of-care diagnostic tests to provide more comprehensive and timely information to pathologists, clinicians, and patients," said <a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a>, a computational biologist at Dana-Farber, an associate member in Ó³»­´«Ã½'s <a href="/node/8831">Epigenomics Program</a>, and co-senior author of the study. </p> <p>The findings were published in <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank"><em>Nature Genetics</em></a>.</p> <p>To develop MARLIN, the research team first created a large reference database of DNA methylation patterns from over 2,500 patient samples, representing a wide range of leukemia subtypes. This revealed 38 distinct methylation classes across disease subtypes in adults and children. "Our analysis confirms many established molecular categories in acute leukemia but also reveals new classes that are best seen through the lens of epigenetics," said Til Steinicke, co-first author of the study along with Salvatore Benfatto.</p> <p>Using this reference dataset, the team trained MARLIN to identify methylation classes in bone marrow and blood samples from patients with acute leukemia. When paired with long-read nanopore sequencing technology, which permits DNA methylation profiling from clinical samples, MARLIN demonstrated high accuracy for disease classification in both retrospective and prospective samples. "We adapted our machine learning approach to use very small amounts of data as input, which allowed us to quickly generate classifications after just a few minutes of sequencing," said Benfatto.</p> <p>In real-time tests, MARLIN correctly classified leukemia samples in under two hours from the time of biopsy receipt, a dramatic improvement over the timelines of current diagnostic workflows. "As our work continues, we hope MARLIN will greatly accelerate treatment planning, reduce medical complications, and ease patient worries in the future," said Evan Chen, a collaborator on the study and medical oncologist at Dana-Farber.</p> <p>The researchers also found that MARLIN could resolve diagnostic "blind spots" missed by conventional methods. For example, it successfully identified cryptic genetic events such as rearrangements involving the <em>DUX4</em> gene that are associated with favorable clinical outcomes. Additionally, MARLIN revealed novel predictive signatures, such as HOX-activated subgroups, which could inform future treatment strategies.</p> <p>"We believe that our framework paves the way for future developments in epigenetic classification of acute leukemia, machine learning-assisted diagnostics, and methylation-based predictive biomarkers of drug response," said Gabriel Griffin, a cancer researcher, Ó³»­´«Ã½ associate member, Dana-Farber pathologist, and co-senior author of the study.</p> <p>The researchers now aim to develop MARLIN into a tool that can be provided to patients in the clinic to accelerate disease classification, inform treatment selection in real-time, and generate a resource for the cancer research community to study the role of DNA methylation in leukemia.</p> <p><em>Adapted from <a href="https://www.dana-farber.org/newsroom/news-releases/2025/new-diagnostic-tool-developed-at-dana-farber-revolutionizes-acute-leukemia-diagnosis" target="_blank">a press release</a> issued by Dana-Farber Cancer Institute.</em><br>  </p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study came from the Evans MDS Center at Dana-Farber Cancer Institute and other sources.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Steinicke TL, Benfatto S, et al. <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank">Rapid epigenomic classification of acute leukemia</a>. <em>Nature Genetics</em>. Online September 22, 2025. DOI: 10.1038/s41588-025-02321-z.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/epigenomics" hreflang="en">Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/cancer" hreflang="en">Cancer</a></div> <div class="field__item"><a href="/broad-tags/artificial-intelligence" hreflang="en">Artificial intelligence</a></div> <div class="field__item"><a href="/broad-tags/machine-learning-0" hreflang="en">Machine Learning</a></div> </div> </div> </div> </div> </div> Thu, 25 Jul 2024 16:05:54 +0000 tulrich@broadinstitute.org 5557156 at /news/de-risking-drug-discovery-predictive-ai <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" class="datetime">September 22, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>By classifying acute leukemia samples based on methylation patterns, MARLIN reduces diagnosis time from days to hours.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Nicole Oliverio, Dana-Farber Cancer Institute </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" title="Monday, September 22, 2025 - 10:00" class="datetime">September 22, 2025</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodelong-storyfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=lBHJ2tK9 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="736" height="520"/> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=VMhZ1AdI 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="641" height="451"/> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=4lbYFPL7 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="706" height="417"/> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z 1x" media="all and (max-width: 539px)" type="image/jpeg" width="499" height="294"/> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z" alt="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." title="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." typeof="foaf:Image" /> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: NCI Visuals Online </div> <div class="media-caption__description"> Acute myeloid leukemia cells (red). </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous" /></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/2391/feed&title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/2391/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&body=/taxonomy/term/2391/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> <div class="block block-layout-builder block-field-blocknodelong-storyfield-content-paragraphs"> <div class="field field--name-field-content-paragraphs field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--text-with-sidebar text-with-sidebar"> <div class="field field--name-field-sidebar field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related people</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related programs</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/node/8831">Epigenomics Program</a></div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Researchers at Dana-Farber Cancer Institute and the Ó³»­´«Ã½ have developed an artificial intelligence-based diagnostic tool that could transform the way acute leukemia is identified and treated. The tool, called MARLIN (Methylation- and AI-guided Rapid Leukemia Subtype Inference), uses DNA methylation patterns and machine learning to classify acute leukemia with speed and accuracy. This tool has the potential to significantly improve patient care by allowing faster and more precise treatment decisions.</p> <p>Acute leukemia is an aggressive blood cancer that requires accurate diagnosis to guide treatment. Current diagnostic methods, which rely on a combination of molecular and cytogenetic tests, often take days or even weeks to complete. Built as a neural network, MARLIN, however, can provide results in as little as two hours from the time of biopsy. By providing rapid and detailed insights into leukemia subtypes, MARLIN could enable clinicians to make treatment decisions sooner and with more complete information.</p> <p>"Ultimately, we envision that methylation-based acute leukemia classifications will complement standard-of-care diagnostic tests to provide more comprehensive and timely information to pathologists, clinicians, and patients," said <a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a>, a computational biologist at Dana-Farber, an associate member in Ó³»­´«Ã½'s <a href="/node/8831">Epigenomics Program</a>, and co-senior author of the study. </p> <p>The findings were published in <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank"><em>Nature Genetics</em></a>.</p> <p>To develop MARLIN, the research team first created a large reference database of DNA methylation patterns from over 2,500 patient samples, representing a wide range of leukemia subtypes. This revealed 38 distinct methylation classes across disease subtypes in adults and children. "Our analysis confirms many established molecular categories in acute leukemia but also reveals new classes that are best seen through the lens of epigenetics," said Til Steinicke, co-first author of the study along with Salvatore Benfatto.</p> <p>Using this reference dataset, the team trained MARLIN to identify methylation classes in bone marrow and blood samples from patients with acute leukemia. When paired with long-read nanopore sequencing technology, which permits DNA methylation profiling from clinical samples, MARLIN demonstrated high accuracy for disease classification in both retrospective and prospective samples. "We adapted our machine learning approach to use very small amounts of data as input, which allowed us to quickly generate classifications after just a few minutes of sequencing," said Benfatto.</p> <p>In real-time tests, MARLIN correctly classified leukemia samples in under two hours from the time of biopsy receipt, a dramatic improvement over the timelines of current diagnostic workflows. "As our work continues, we hope MARLIN will greatly accelerate treatment planning, reduce medical complications, and ease patient worries in the future," said Evan Chen, a collaborator on the study and medical oncologist at Dana-Farber.</p> <p>The researchers also found that MARLIN could resolve diagnostic "blind spots" missed by conventional methods. For example, it successfully identified cryptic genetic events such as rearrangements involving the <em>DUX4</em> gene that are associated with favorable clinical outcomes. Additionally, MARLIN revealed novel predictive signatures, such as HOX-activated subgroups, which could inform future treatment strategies.</p> <p>"We believe that our framework paves the way for future developments in epigenetic classification of acute leukemia, machine learning-assisted diagnostics, and methylation-based predictive biomarkers of drug response," said Gabriel Griffin, a cancer researcher, Ó³»­´«Ã½ associate member, Dana-Farber pathologist, and co-senior author of the study.</p> <p>The researchers now aim to develop MARLIN into a tool that can be provided to patients in the clinic to accelerate disease classification, inform treatment selection in real-time, and generate a resource for the cancer research community to study the role of DNA methylation in leukemia.</p> <p><em>Adapted from <a href="https://www.dana-farber.org/newsroom/news-releases/2025/new-diagnostic-tool-developed-at-dana-farber-revolutionizes-acute-leukemia-diagnosis" target="_blank">a press release</a> issued by Dana-Farber Cancer Institute.</em><br>  </p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study came from the Evans MDS Center at Dana-Farber Cancer Institute and other sources.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Steinicke TL, Benfatto S, et al. <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank">Rapid epigenomic classification of acute leukemia</a>. <em>Nature Genetics</em>. Online September 22, 2025. DOI: 10.1038/s41588-025-02321-z.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/epigenomics" hreflang="en">Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/cancer" hreflang="en">Cancer</a></div> <div class="field__item"><a href="/broad-tags/artificial-intelligence" hreflang="en">Artificial intelligence</a></div> <div class="field__item"><a href="/broad-tags/machine-learning-0" hreflang="en">Machine Learning</a></div> </div> </div> </div> </div> </div> Wed, 17 Jul 2024 19:00:47 +0000 tulrich@broadinstitute.org 5557131 at /news/study-reveals-links-between-blood-vessel-biology-and-heart-disease-risk <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> <span class="field field--name-uid field--type-entity-reference field--label-hidden"> <span>By Tom Ulrich</span> </span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" class="datetime">September 22, 2025</time> </span> <div class="hero-section container"> <div class="hero-section__row row"> <div class="hero-section__content hero-section__content_left col-6"> <div class="hero-section__breadcrumbs"> <div class="block block-system block-system-breadcrumb-block"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <h2 id="system-breadcrumb" class="visually-hidden">Breadcrumb</h2> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> </ol> </nav> </div> </div> <div class="hero-section__title"> <div class="block block-layout-builder block-field-blocknodelong-storytitle"> <span class="field field--name-title field--type-string field--label-hidden"><h1>New AI-based diagnostic tool uses epigenomics to accelerate acute leukemia diagnosis</h1> </span> </div> </div> <div class="hero-section__description"> <div class="block block-layout-builder block-field-blocknodelong-storybody"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>By classifying acute leukemia samples based on methylation patterns, MARLIN reduces diagnosis time from days to hours.</p> </div> </div> </div> <div class="hero-section__author"> <div class="block block-layout-builder block-extra-field-blocknodelong-storyextra-field-author-custom"> By Nicole Oliverio, Dana-Farber Cancer Institute </div> </div> <div class="hero-section__date"> <div class="block block-layout-builder block-field-blocknodelong-storycreated"> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2025-09-22T10:00:11-04:00" title="Monday, September 22, 2025 - 10:00" class="datetime">September 22, 2025</time> </span> </div> </div> </div> <div class="hero-section__right col-6"> <div class="hero-section__image"> <div class="block block-layout-builder block-field-blocknodelong-storyfield-image"> <div class="field field--name-field-image field--type-entity-reference field--label-hidden field__item"> <article class="media media--type-image media--view-mode-multiple-content-types-header"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <picture> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1921px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop_xl/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dbp0YNS- 1x" media="all and (min-width: 1601px) and (max-width: 1920px)" type="image/jpeg" width="754" height="503"/> <source srcset="/files/styles/multiple_ct_header_desktop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=lBHJ2tK9 1x" media="all and (min-width: 1340px) and (max-width: 1600px)" type="image/jpeg" width="736" height="520"/> <source srcset="/files/styles/multiple_ct_header_laptop/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=VMhZ1AdI 1x" media="all and (min-width: 800px) and (max-width: 1339px)" type="image/jpeg" width="641" height="451"/> <source srcset="/files/styles/multiple_ct_header_tablet/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=4lbYFPL7 1x" media="all and (min-width: 540px) and (max-width: 799px)" type="image/jpeg" width="706" height="417"/> <source srcset="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z 1x" media="all and (max-width: 539px)" type="image/jpeg" width="499" height="294"/> <img loading="eager" width="499" height="294" src="/files/styles/multiple_ct_header_phone/public/news/images/2019/AML_cells_in_red_nci-vol-2336-150.jpg?h=9994641b&itok=dg2-VY-Z" alt="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." title="A microscope image of cells from acute myeloid leukemia, a kind of cancer. The cancer cells are stained red." typeof="foaf:Image" /> </picture> </div> <div class="media-caption"> <div class="media-caption__credit"> Credit: NCI Visuals Online </div> <div class="media-caption__description"> Acute myeloid leukemia cells (red). </div> </div> </article> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block block-better-social-sharing-buttons block-social-sharing-buttons-block"> <div style="display: none"><link rel="preload" href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg" as="image" type="image/svg+xml" crossorigin="anonymous" /></div> <div class="social-sharing-buttons"> <a href="https://www.facebook.com/sharer/sharer.php?u=/taxonomy/term/2391/feed&title=" target="_blank" title="Share to Facebook" aria-label="Share to Facebook" class="social-sharing-buttons-button share-facebook" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#facebook" /> </svg> </a> <a href="https://twitter.com/intent/tweet?text=+/taxonomy/term/2391/feed" target="_blank" title="Share to X" aria-label="Share to X" class="social-sharing-buttons-button share-x" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#x" /> </svg> </a> <a href="mailto:?subject=&body=/taxonomy/term/2391/feed" title="Share to Email" aria-label="Share to Email" class="social-sharing-buttons-button share-email" target="_blank" rel="noopener"> <svg aria-hidden="true" width="32px" height="32px" style="border-radius:100%;"> <use href="/modules/contrib/better_social_sharing_buttons/assets/dist/sprites/social-icons--no-color.svg#email" /> </svg> </a> </div> </div> <div class="block block-layout-builder block-field-blocknodelong-storyfield-content-paragraphs"> <div class="field field--name-field-content-paragraphs field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--text-with-sidebar text-with-sidebar"> <div class="field field--name-field-sidebar field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related people</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a></div> </div> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--sidebar-menu sidebar-menu"> <div class="sidebar-menu__col"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Related programs</p> </div> <div class="field field--name-field-links field--type-link field--label-hidden field__items"> <div class="field__item"><a href="/node/8831">Epigenomics Program</a></div> </div> </div> </div> </div> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Researchers at Dana-Farber Cancer Institute and the Ó³»­´«Ã½ have developed an artificial intelligence-based diagnostic tool that could transform the way acute leukemia is identified and treated. The tool, called MARLIN (Methylation- and AI-guided Rapid Leukemia Subtype Inference), uses DNA methylation patterns and machine learning to classify acute leukemia with speed and accuracy. This tool has the potential to significantly improve patient care by allowing faster and more precise treatment decisions.</p> <p>Acute leukemia is an aggressive blood cancer that requires accurate diagnosis to guide treatment. Current diagnostic methods, which rely on a combination of molecular and cytogenetic tests, often take days or even weeks to complete. Built as a neural network, MARLIN, however, can provide results in as little as two hours from the time of biopsy. By providing rapid and detailed insights into leukemia subtypes, MARLIN could enable clinicians to make treatment decisions sooner and with more complete information.</p> <p>"Ultimately, we envision that methylation-based acute leukemia classifications will complement standard-of-care diagnostic tests to provide more comprehensive and timely information to pathologists, clinicians, and patients," said <a href="https://sites.broadinstitute.org/gro/people/volker-hovestadt-phd">Volker Hovestadt</a>, a computational biologist at Dana-Farber, an associate member in Ó³»­´«Ã½'s <a href="/node/8831">Epigenomics Program</a>, and co-senior author of the study. </p> <p>The findings were published in <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank"><em>Nature Genetics</em></a>.</p> <p>To develop MARLIN, the research team first created a large reference database of DNA methylation patterns from over 2,500 patient samples, representing a wide range of leukemia subtypes. This revealed 38 distinct methylation classes across disease subtypes in adults and children. "Our analysis confirms many established molecular categories in acute leukemia but also reveals new classes that are best seen through the lens of epigenetics," said Til Steinicke, co-first author of the study along with Salvatore Benfatto.</p> <p>Using this reference dataset, the team trained MARLIN to identify methylation classes in bone marrow and blood samples from patients with acute leukemia. When paired with long-read nanopore sequencing technology, which permits DNA methylation profiling from clinical samples, MARLIN demonstrated high accuracy for disease classification in both retrospective and prospective samples. "We adapted our machine learning approach to use very small amounts of data as input, which allowed us to quickly generate classifications after just a few minutes of sequencing," said Benfatto.</p> <p>In real-time tests, MARLIN correctly classified leukemia samples in under two hours from the time of biopsy receipt, a dramatic improvement over the timelines of current diagnostic workflows. "As our work continues, we hope MARLIN will greatly accelerate treatment planning, reduce medical complications, and ease patient worries in the future," said Evan Chen, a collaborator on the study and medical oncologist at Dana-Farber.</p> <p>The researchers also found that MARLIN could resolve diagnostic "blind spots" missed by conventional methods. For example, it successfully identified cryptic genetic events such as rearrangements involving the <em>DUX4</em> gene that are associated with favorable clinical outcomes. Additionally, MARLIN revealed novel predictive signatures, such as HOX-activated subgroups, which could inform future treatment strategies.</p> <p>"We believe that our framework paves the way for future developments in epigenetic classification of acute leukemia, machine learning-assisted diagnostics, and methylation-based predictive biomarkers of drug response," said Gabriel Griffin, a cancer researcher, Ó³»­´«Ã½ associate member, Dana-Farber pathologist, and co-senior author of the study.</p> <p>The researchers now aim to develop MARLIN into a tool that can be provided to patients in the clinic to accelerate disease classification, inform treatment selection in real-time, and generate a resource for the cancer research community to study the role of DNA methylation in leukemia.</p> <p><em>Adapted from <a href="https://www.dana-farber.org/newsroom/news-releases/2025/new-diagnostic-tool-developed-at-dana-farber-revolutionizes-acute-leukemia-diagnosis" target="_blank">a press release</a> issued by Dana-Farber Cancer Institute.</em><br>  </p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro paragraph--view-mode--default"> <div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Funding</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Support for this study came from the Evans MDS Center at Dana-Farber Cancer Institute and other sources.</p> </div> </div> </div> <div class="field__item"> <div class="paragraph paragraph--type--table-outro-row paragraph--view-mode--default"> <div class="clearfix text-formatted field field--name-field-heading field--type-text field--label-hidden field__item"><p>Paper cited</p> </div> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__item"><p>Steinicke TL, Benfatto S, et al. <a href="https://doi.org/10.1038/s41588-025-02321-z" target="_blank">Rapid epigenomic classification of acute leukemia</a>. <em>Nature Genetics</em>. Online September 22, 2025. DOI: 10.1038/s41588-025-02321-z.</p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="content-section container"> <div class="content-section__main"> <div class="block-node-broad-tags block block-layout-builder block-field-blocknodelong-storyfield-broad-tags"> <div class="block-node-broad-tags__row"> <div class="block-node-broad-tags__title">Tags:</div> <div class="field field--name-field-broad-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/broad-tags/epigenomics" hreflang="en">Epigenomics</a></div> <div class="field__item"><a href="/broad-tags/cancer" hreflang="en">Cancer</a></div> <div class="field__item"><a href="/broad-tags/artificial-intelligence" hreflang="en">Artificial intelligence</a></div> <div class="field__item"><a href="/broad-tags/machine-learning-0" hreflang="en">Machine Learning</a></div> </div> </div> </div> </div> </div> Wed, 07 Feb 2024 16:50:22 +0000 tulrich@broadinstitute.org 5556406 at