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  • Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors.

    AUTHORS: Reeser JW, Martin D, Miya J, Kautto EA, Lyon E, Zhu E, Wing MR, Smith A, Reeder M, Samorodnitsky E, Parks H, Naik KR, Gozgit J, Nowacki N, Davies KD, Varella-Garcia M, Yu L, Freud AG, Coleman J, Aisner DL, Roychowdhury S
    JOURNAL: J Mol Diagn, 2017

    Kinase gene fusions are important drivers of oncogenic transformation and can be inhibited with targeted therapies. Clinical grade diagnostics using RNA sequencing to detect gene rearrangements in solid tumors are limited, and the few that are available require prior... Read More

  • Landscape of Microsatellite Instability Across 39 Cancer Types.

    AUTHORS: Bonneville R, Krook MA, Kautto EA, Miya J, Wing MR, Chen HZ, Reeser JW, Yu L, Roychowdhury S
    JOURNAL: JCO Precis Oncol, 2017

    Purpose: Microsatellite instability (MSI) is a pattern of hypermutation that occurs at genomic microsatellites and is caused by defects in the mismatch repair system. Mismatch repair deficiency that leads to MSI has been well described in several types of human... 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

  • Microsatellite Instability Occurs in a Subset of Follicular Thyroid Cancers.

    AUTHORS: Genutis LK, Tomsic J, Bundschuh RA, Brock PL, Williams MD, Roychowdhury S, Reeser JW, Frankel WL, Alsomali M, Routbort MJ, Broaddus RR, Wakely PE Jr, Phay JE, Walker CJ, de la Chapelle A
    JOURNAL: Thyroid, 2019

    BACKGROUND: Inactivation of DNA mismatch repair (MMR) and the resulting microsatellite instability (MSI) are frequently observed in endometrial, stomach, and colorectal cancers, as well as more rarely in other solid tumor types. The prevalence of MSI in thyroid cancer... Read More

  • Inflammation-Induced Oxidative Stress Mediates Gene Fusion Formation in Prostate Cancer.

    AUTHORS: Mani RS, Amin MA, Li X, Kalyana-Sundaram S, Veeneman BA, Wang L, Ghosh A, Aslam A, Ramanand SG, Rabquer BJ, Kimura W, Tran M, Cao X, Roychowdhury S, Dhanasekaran SM, Palanisamy N, Sadek HA, Kapur P, Koch AE, Chinnaiyan AM
    JOURNAL: Cell Rep, 2016

    Approximately 50% of prostate cancers are associated with gene fusions of the androgen-regulated gene TMPRSS2 to the oncogenic erythroblast transformation-specific (ETS) transcription factor ERG. The three-dimensional proximity of TMPRSS2 and ERG genes, in combination... Read More

  • Somatic cancer variant curation and harmonization through consensus minimum variant level data.

    AUTHORS: Ritter DI, Roychowdhury S, Roy A, Rao S, Landrum MJ, Sonkin D, Shekar M, Davis CF, Hart RK, Micheel C, Weaver M, Van Allen EM, Parsons DW, McLeod HL, Watson MS, Plon SE, Kulkarni S, Madhavan S, ClinGen Somatic Cancer Working Group
    JOURNAL: Genome Med, 2016

    BACKGROUND: To truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic Working Group (WG) of the Clinical Genome Resource (ClinGen), in cooperation with ClinVar and... Read More

  • Translating cancer genomes and transcriptomes for precision oncology.

    AUTHORS: Roychowdhury S, Chinnaiyan AM
    JOURNAL: CA Cancer J Clin, 2016

    Understanding the molecular landscape of cancer has facilitated the development of diagnostic, prognostic, and predictive biomarkers for clinical oncology. Developments in next-generation DNA sequencing technologies have increased the speed and reduced the cost of... Read More

  • Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations.

    AUTHORS: Martin DP, Miya J, Reeser JW, Roychowdhury S
    JOURNAL: J Vis Exp, 2016

    RNA sequencing (RNAseq) is a versatile method that can be utilized to detect and characterize gene expression, mutations, gene fusions, and noncoding RNAs. Standard RNAseq requires 30 - 100 million sequencing reads and can include multiple RNA products such as mRNA... Read More

  • Genomic characterization of metastatic ultra-hypermutated interdigitating dendritic cell sarcoma through rapid research autopsy.

    AUTHORS: Chen HZ, Bonneville R, Yu L, Wing MR, Reeser JW, Krook MA, Miya J, Samorodnitsky E, Smith A, Martin D, Dao T, Guo Q, Liebner D, Freud AG, Allenby P, Roychowdhury S
    JOURNAL: Oncotarget, 2019

    Interdigitating dendritic cell sarcoma (IDCS) is an extremely rare cancer of dendritic cell origin that lacks a standardized treatment approach. Here, we performed genomic characterization of metastatic IDCS through whole exome sequencing (WES) of tumor tissues... Read More

  • Rapid Research Autopsy: Piecing the Puzzle of Tumor Heterogeneity.

    AUTHORS: Krook MA, Chen HZ, Bonneville R, Allenby P, Roychowdhury S
    JOURNAL: Trends Cancer, 2019

    Tumor heterogeneity decreases the effectiveness of anticancer therapies and is an important topic in translational cancer research, given its relevance in clinical oncology. Here, we discuss how rapid research autopsy of cancer patients can elucidate... Read More

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