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  • Akt Activation Mediates Acquired Resistance to Fibroblast Growth Factor Receptor Inhibitor BGJ398.

    AUTHORS: Datta J, Damodaran S, Parks H, Ocrainiciuc C, Miya J, Yu L, Gardner EP, Samorodnitsky E, Wing MR, Bhatt D, Hays J, Reeser JW, Roychowdhury S
    JOURNAL: Mol Cancer Ther, 2017

    Activation of FGFR signaling through mutations, amplifications, or fusions involving Read More

  • Cancer Driver Log (CanDL): Catalog of Potentially Actionable Cancer Mutations.

    AUTHORS: Damodaran S, Miya J, Kautto E, Zhu E, Samorodnitsky E, Datta J, Reeser JW, Roychowdhury S
    JOURNAL: J Mol Diagn, 2015

    Massively parallel sequencing technologies have enabled characterization of genomic alterations across multiple tumor types. Efforts have focused on identifying driver mutations because they represent potential targets for therapy. However, because of the presence of... Read More

  • Integrative Clinical Sequencing in the Management of Refractory or Relapsed Cancer in Youth.

    AUTHORS: Mody RJ, Wu YM, Lonigro RJ, Cao X, Roychowdhury S, Vats P, Frank KM, Prensner JR, Asangani I, Palanisamy N, Dillman JR, Rabah RM, Kunju LP, Everett J, Raymond VM, Ning Y, Su F, Wang R, Stoffel EM, Innis JW, Roberts JS, Robertson PL, Yanik G, Chamdin A, Connelly JA, Choi S, Harris AC, Kitko C, Rao RJ, Levine JE, Castle VP, Hutchinson RJ, Talpaz M, Robinson DR, Chinnaiyan AM
    JOURNAL: JAMA, 2015

    IMPORTANCE: Cancer is caused by a diverse array of somatic and germline genomic aberrations. Advances in genomic sequencing technologies have improved the ability to detect these molecular aberrations with greater sensitivity. However, integrating them into clinical... Read More

  • Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing.

    AUTHORS: Samorodnitsky E, Jewell BM, Hagopian R, Miya J, Wing MR, Lyon E, Damodaran S, Bhatt D, Reeser JW, Datta J, Roychowdhury S
    JOURNAL: Hum Mutat, 2015

    Next-generation sequencing has aided characterization of genomic variation. While whole-genome sequencing may capture all possible mutations, whole-exome sequencing remains cost-effective and captures most phenotype-altering mutations. Initial strategies for exome... Read More

  • Analytic validation and real-time clinical application of an amplicon-based targeted gene panel for advanced cancer.

    AUTHORS: Wing MR, Reeser JW, Smith AM, Reeder M, Martin D, Jewell BM, Datta J, Miya J, Monk JP, Mortazavi A, Otterson GA, Goldberg RM, VanDeusen JB, Cole S, Dittmar K, Jaiswal S, Kinzie M, Waikhom S, Freud AG, Zhou XP, Chen W, Bhatt D, Roychowdhury S
    JOURNAL: Oncotarget, 2017

    Multiplex somatic testing has emerged as a strategy to test patients with advanced cancer. We demonstrate our analytic validation approach for a gene hotspot panel and real-time prospective clinical application for any cancer type. The TruSight Tumor 26 assay... Read More

  • Trametinib for the treatment of IGHV4-34, MAP2K1-mutant variant hairy cell leukemia.

    AUTHORS: Andritsos LA, Grieselhuber NR, Anghelina M, Rogers KA, Roychowdhury S, Reeser JW, Timmers CD, Freud AG, Blachly JS, Lucas DM, Lozanski G, Jones JA, Williams K, Oakes C, Jones D, Grever MR
    JOURNAL: Leuk Lymphoma, 2018

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  • Beyond Seed and Soil: Understanding and Targeting Metastatic Prostate Cancer; Report From the 2016 Coffey-Holden Prostate Cancer Academy Meeting.

    AUTHORS: Miyahira AK, Roychowdhury S, Goswami S, Ippolito JE, Priceman SJ, Pritchard CC, Sfanos KS, Subudhi SK, Simons JW, Pienta KJ, Soule HR
    JOURNAL: Prostate, 2017

    INTRODUCTION: The 2016 Coffey-Holden Prostate Cancer Academy (CHPCA) Meeting, "Beyond Seed and Soil: Understanding and Targeting Metastatic Prostate Cancer," was held from June 23 to June 26, 2016, in Coronado, California.METHODS: For the 4th year in a row, the... Read More

  • Comparison of custom capture for targeted next-generation DNA sequencing.

    AUTHORS: Samorodnitsky E, Datta J, Jewell BM, Hagopian R, Miya J, Wing MR, Damodaran S, Lippus JM, Reeser JW, Bhatt D, Timmers CD, Roychowdhury S
    JOURNAL: J Mol Diagn, 2015

    Targeted, capture-based DNA sequencing is a cost-effective method to focus sequencing on a coding region or other customized region of the genome. There are multiple targeted sequencing methods available, but none has been systematically investigated and compared. We... Read More

  • Clinical tumor sequencing: opportunities and challenges for precision cancer medicine.

    AUTHORS: Damodaran S, Berger MF, Roychowdhury S
    JOURNAL: Am Soc Clin Oncol Educ Book, 2015

    Advances in tumor genome sequencing have enabled discovery of actionable alterations leading to novel therapies. Currently, there are approved targeted therapies across various tumors that can be matched to genomic alterations, such as point mutations, gene... Read More

  • Implementing precision cancer medicine in the genomic era.

    AUTHORS: Chen HZ, Bonneville R, Roychowdhury S
    JOURNAL: Semin Cancer Biol, 2019

    The utilization of genomic data to direct treatment for cancer patients represents the central tenet in precision oncology, in which a patient is matched to a specific drug or therapy based on the genetic drivers detected in his or her tumor rather than the tumor's... Read More

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