Real-time genomic characterization of advanced pancreatic cancer to enable precision medicine

Aguirre, A. J., Nowak, J. A., Camarda, N. D., Moffitt, R. A., Ghazani, A. A., Hazar-Rethinam, M., Raghavan, S., Kim, J., Brais, L. K., Ragon, D., Welch, M. W., Reilly, E., McCabe, D., Marini, L., Anderka, K., Helvie, K., Oliver, N., Babic, A., Da Silva, A., Nadres, B., Van Seventer, E. E., Shahzade, H. A., St Pierre, J. P., Burke, K. P., Clancy, T. E., Cleary, J. M., Doyle, L. A., Jajoo, K., McCleary, N. J., Meyerhardt, J. A., Murphy, J. E., Ng, K., Patel, A. K., Perez, K., Rosenthal, M. H., Rubinson, D. A., Ryou, M., Shapiro, G. I., Sicinska, E., Silverman, S. G., Nagy, R. J., Lanman, R. B., Knoerzer, D., Welsch, D. J., Yurgelun, M. B., Fuchs, C. S., Garraway, L. A., Getz, G., Hornick, J. L., Johnson, B. E., Kulke, M. H., Mayer, R. J., Miller, J. W., Shyn, P. B., Tuveson, D. A., Wagle, N., Yeh, J. J., Hahn, W. C., Corcoran, R. B., Carter, S. L., Wolpin, B. M. (June 2018) Real-time genomic characterization of advanced pancreatic cancer to enable precision medicine. Cancer Discov, 8 (9). pp. 1096-1111. ISSN 2159-8274

URL: https://www.ncbi.nlm.nih.gov/pubmed/29903880
DOI: 10.1158/2159-8290.cd-18-0275

Abstract

Clinically relevant subtypes exist for pancreatic ductal adenocarcinoma (PDAC), but molecular characterization is not yet standard in clinical care. We implemented a biopsy protocol to perform time-sensitive whole exome sequencing and RNA-sequencing for patients with advanced PDAC. Therapeutically relevant genomic alterations were identified in 48% (34/71) and pathogenic/likely pathogenic germline alterations in 18% (13/71) of patients. Overall, 30% (21/71) of enrolled patients experienced a change in clinical management as a result of genomic data. Twenty-six patients had germline and/or somatic alterations in DNA-damage repair genes, and 5 additional patients had mutational signatures of homologous recombination deficiency but no identified causal genomic alteration. Two patients had oncogenic in-frame BRAF deletions, and we report the first clinical evidence that this alteration confers sensitivity to MAP-kinase pathway inhibition. Moreover, we identified tumor/stroma gene expression signatures with clinical relevance. Collectively, these data demonstrate the feasibility and value of real-time genomic characterization of advanced PDAC.

Item Type: Paper
Subjects: bioinformatics
diseases & disorders > cancer
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
diseases & disorders
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
diseases & disorders > neoplasms
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA repair
diseases & disorders > cancer > drugs and therapies
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
diseases & disorders > cancer > cancer types > pancreatic cancer
diseases & disorders > cancer > drugs and therapies > precision medicine
diseases & disorders > cancer > cancer types
CSHL Authors:
Communities: CSHL labs > Tuveson lab
CSHL Cancer Center Program > Cellular Communication in Cancer Program
Depositing User: Matt Covey
Date: 14 June 2018
Date Deposited: 20 Jun 2018 21:16
Last Modified: 06 Feb 2024 20:35
PMCID: PMC6192263
Related URLs:
URI: https://repository.cshl.edu/id/eprint/36746

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