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  1. Article

    Open Access

    Quantification of cerebrospinal fluid tumor DNA in lung cancer patients with suspected leptomeningeal carcinomatosis

    Cerebrospinal fluid tumor-derived DNA (CSF-tDNA) analysis is a promising approach for monitoring the neoplastic processes of the central nervous system. We applied a lung cancer-specific sequencing panel (CAPP...

    Tej D. Azad, Shigeki Nanjo, Michael C. **, Jacob J. Chabon… in npj Precision Oncology (2024)

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  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

    Integrating genomic features for non-invasive early lung cancer detection

    Radiologic screening of high-risk adults reduces lung-cancer-related mortality1,2; however, a small minority of eligible individuals undergo such screening in the United States3,4. The availability of blood-based...

    Jacob J. Chabon, Emily G. Hamilton, David M. Kurtz, Mohammad S. Esfahani… in Nature (2020)

  5. 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)

  6. No Access

    Article

    Evolution and clinical impact of co-occurring genetic alterations in advanced-stage EGFR-mutant lung cancers

    Analysis of a large cohort of EGFR-mutant lung cancer cell-free DNA samples along with longitudinal samples from a patient with EGFR-mutant lung cancer identifies pathways that inhibit EGFR-inhibitor response. Co...

    Collin M Blakely, Thomas B K Watkins, Wei Wu, Beatrice Gini… in Nature Genetics (2017)

  7. Article

    Open Access

    Correction: Corrigendum: Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients

    Nature Communications 7: Article number: 11815 (2016); Published 10 June 2016; Updated 14 November 2016 Previous work by Del Re et al. describing the emergence of KRAS mutations following treatment of non-smal...

    Jacob J. Chabon, Andrew D. Simmons, Alexander F. Lovejoy… in Nature Communications (2016)

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  8. Article

    Open Access

    Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients

    Circulating tumour DNA (ctDNA) analysis facilitates studies of tumour heterogeneity. Here we employ CAPP-Seq ctDNA analysis to study resistance mechanisms in 43 non-small cell lung cancer (NSCLC) patients trea...

    Jacob J. Chabon, Andrew D. Simmons, Alexander F. Lovejoy… in Nature Communications (2016)

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  9. No Access

    Article

    Integrated digital error suppression for improved detection of circulating tumor DNA

    Circulating tumor DNA is detected with high sensitivity and specificity using molecular barcoding and in silico error correction.

    Aaron M Newman, Alexander F Lovejoy, Daniel M Klass, David M Kurtz… in Nature Biotechnology (2016)