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  1. No Access

    Article

    Sarcoma microenvironment cell states and ecosystems are associated with prognosis and predict response to immunotherapy

    Characterization of the diverse malignant and stromal cell states that make up soft tissue sarcomas and their correlation with patient outcomes has proven difficult using fixed clinical specimens. Here, we emp...

    Ajay Subramanian, Neda Nemat-Gorgani, Timothy J. Ellis-Caleo… in Nature Cancer (2024)

  2. No Access

    Article

    Inferring gene expression from cell-free DNA fragmentation profiles

    Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles fr...

    Mohammad Shahrokh Esfahani, Emily G. Hamilton, Mahya Mehrmohamadi… in Nature Biotechnology (2022)

  3. No Access

    Article

    Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA

    Circulating tumor-derived DNA (ctDNA) is an emerging biomarker for many cancers, but the limited sensitivity of current detection methods reduces its utility for diagnosing minimal residual disease. Here we de...

    David M. Kurtz, Joanne Soo, Lyron Co Ting Keh, Stefan Alig… in Nature Biotechnology (2021)

  4. No Access

    Article

    Circulating tumor DNA dynamics predict benefit from consolidation immunotherapy in locally advanced non-small-cell lung cancer

    Circulating tumor DNA (ctDNA) molecular residual disease (MRD) following curative-intent treatment strongly predicts recurrence in multiple tumor types, but whether further treatment can improve outcomes in pa...

    Everett J. Moding, Yufei Liu, Barzin Y. Nabet, Jacob J. Chabon… in Nature Cancer (2020)