Philip S. Bernard, M.D.

Research Interests

  • Non-Coding RNAs for Cancer Classification, Detection, and Monitoring
  • DNA Alterations in Primary and Circulating Tumors
  • Identifying Predictive Biomarkers for Cancer Therapy Response

Labs

Lab Website

Languages

  • English

Academic Information

  • Departments: Pathology - Associate Professor
  • Divisions: Anatomic Pathology
  • Cancer Center Programs: Experimental Therapeutics

Board Certification

  • American Board of Pathology (Clinical Path)
  • National Board of Medical Examiners

Academic Office Information

  • (801) 581-5353
  • School of Medicine
    Pathology
    30 N 1900 E
    Salt Lake City, UT 84132

Email: phil.bernard@hci.utah.edu

Academic Bio

Philip Bernard, MD, is an associate professor of pathology at the University of Utah School of Medicine, medical director of the Molecular Oncology Dx, and a Huntsman Cancer Institute investigator. He is a member of the Experimental Therapeutics Program.

Bernard's research focuses on molecular classifications of solid tumors for prognosis and treatment. Using cutting-edge technology, his lab correlates clinical behavior of tumors with molecular features. His group was instrumental in the development of the PAM50 (Prosigna) breast cancer subtyping test for prognosis in early stage disease (link to ARUP CME on this topic). Along with expression profiling and DNA analyses of solid tumors, his lab is now investigating a variety of techniques to identify circulating biomarkers for screening and monitoring cancers.

Education History

Type School Degree
Residency University of Utah School of Medicine
Pathology
Resident
Research Fellow Carl T. Wittwer, MD, PhD
Pathology
Research Fellow
Professional Medical University of Utah
Medicine
M.D.
Undergraduate University of Utah
Biology
B.S.

Selected Publications

Journal Article

  1. Intrinsic subtypes from the PAM50 gene expression assay in a population-based breast cancer survivor cohort: prognostication of short- and long-term outcomes.Caan BJ, Sweeney C, Habel LA, Kwan ML, Kroenke CH, Weltzien EK, Quesenberry CP Jr, Castillo A, Factor RE, Kushi LH, Bernard PS (2014). Intrinsic subtypes from the PAM50 gene expression assay in a population-based breast cancer survivor cohort: prognostication of short- and long-term outcomes. Cancer Epidemiol Biomarkers Prev, 23(5), 725-34.
  2. Prognostic significance of progesterone receptor-positive tumor cells within immunohistochemically defined luminal A breast cancer.Prat A, Cheang MC, Martin M, Parker JS, Carrasco E, Caballero R, Tyldesley S, Gelmon K, Bernard PS, Nielsen TO, Perou CM (2013). Prognostic significance of progesterone receptor-positive tumor cells within immunohistochemically defined luminal A breast cancer. J Clin Oncol, 31(2), 203-9.
  3. A phase II study of UCN-01 in combination with irinotecan in patients with metastatic triple negative breast cancer.Ma CX, Ellis MJ, Petroni GR, Guo Z, Cai SR, Ryan CE, Craig Lockhart A, Naughton MJ, Pluard TJ, Brenin CM, Picus J, Creekmore AN, Mwandoro T, Yarde ER, Reed J, Ebbert M, Bernard PS, Watson M, Doyle LA, Dancey J, Piwnica-Worms H, Fracasso PM (2013). A phase II study of UCN-01 in combination with irinotecan in patients with metastatic triple negative breast cancer. Breast Cancer Res Treat, 137(2), 483-92.
  4. PAM50 proliferation score as a predictor of weekly paclitaxel benefit in breast cancer.Martin M, Prat A, Rodriguez-Lescure A, Caballero R, Ebbert MT, Munarriz B, Ruiz-Borrego M, Bastien RR, Crespo C, Davis C, Rodriguez CA, Lopez-Vega JM, Furio V, Garcia AM, Casas M, Ellis MJ, Berry DA, Pitcher BN, Harris L, Ruiz A, Winer E, Hudis C, Stijleman IJ, Tuck DP, Carrasco E, Perou CM, Bernard PS (2013). PAM50 proliferation score as a predictor of weekly paclitaxel benefit in breast cancer. Breast Cancer Res Treat, 138(2), 457-66.
  5. Prediction of lung cancer histological types by RT-qPCR gene expression in FFPE specimens.Wilkerson MD, Schallheim JM, Hayes DN, Roberts PJ, Bastien RR, Mullins M, Yin X, Miller CR, Thorne LB, Geiersbach KB, Muldrew KL, Funkhouser WK, Fan C, Hayward MC, Bayer S, Perou CM, Bernard PS (2013). Prediction of lung cancer histological types by RT-qPCR gene expression in FFPE specimens. J Mol Diagn, 15(4), 485-97.
  6. A survey of immunohistochemical biomarkers for basal-like breast cancer against a gene expression profile gold standard.Won JR, Gao D, Chow C, Cheng J, Lau SY, Ellis MJ, Perou CM, Bernard PS, Nielsen TO (2013). A survey of immunohistochemical biomarkers for basal-like breast cancer against a gene expression profile gold standard. Mod Pathol, 26(11), 1438-50.
  7. TRIM29 functions as a tumor suppressor in nontumorigenic breast cells and invasive ER+ breast cancer.Liu J, Welm B, Boucher KM, Ebbert MT, Bernard PS (2012). TRIM29 functions as a tumor suppressor in nontumorigenic breast cells and invasive ER+ breast cancer. Am J Pathol, 180(2), 839-47.
  8. Responsiveness of intrinsic subtypes to adjuvant anthracycline substitution in the NCIC.CTG MA.5 randomized trial.Cheang MC, Voduc KD, Tu D, Jiang S, Leung S, Chia SK, Shepherd LE, Levine MN, Pritchard KI, Davies S, Stijleman IJ, Davis C, Ebbert MT, Parker JS, Ellis MJ, Bernard PS, Perou CM, Nielsen TO (2012). Responsiveness of intrinsic subtypes to adjuvant anthracycline substitution in the NCIC.CTG MA.5 randomized trial. Clin Cancer Res, 18(8), 2402-12.
  9. Agreement in risk prediction between the 21-gene recurrence score assay (Oncotype DX(R)) and the PAM50 breast cancer intrinsic Classifier in early-stage estrogen receptor-positive breast cancer.Kelly CM, Bernard PS, Krishnamurthy S, Wang B, Ebbert MT, Bastien RR, Boucher KM, Young E, Iwamoto T, Pusztai L (2012). Agreement in risk prediction between the 21-gene recurrence score assay (Oncotype DX(R)) and the PAM50 breast cancer intrinsic Classifier in early-stage estrogen receptor-positive breast cancer. Oncologist, 17(4), 492-8.
  10. Concordance among gene expression-based predictors for ER-positive breast cancer treated with adjuvant tamoxifen.Prat A, Parker JS, Fan C, Cheang MC, Miller LD, Bergh J, Chia SK, Bernard PS, Nielsen TO, Ellis MJ, Carey LA, Perou CM (2012). Concordance among gene expression-based predictors for ER-positive breast cancer treated with adjuvant tamoxifen. Ann Oncol, 23(11), 2866-73.
  11. Differential pathogenesis of lung adenocarcinoma subtypes involving sequence mutations, copy number, chromosomal instability, and methylation.Wilkerson MD, Yin X, Walter V, Zhao N, Cabanski CR, Hayward MC, Miller CR, Socinski MA, Parsons AM, Thorne LB, Haithcock BE, Veeramachaneni NK, Funkhouser WK, Randell SH, Bernard PS, Perou CM, Hayes DN (2012). Differential pathogenesis of lung adenocarcinoma subtypes involving sequence mutations, copy number, chromosomal instability, and methylation. PLoS One, 7(5), e36530.
  12. TBCRC 001: randomized phase II study of cetuximab in combination with carboplatin in stage IV triple-negative breast cancer.Carey LA, Rugo HS, Marcom PK, Mayer EL, Esteva FJ, Ma CX, Liu MC, Storniolo AM, Rimawi MF, Forero-Torres A, Wolff AC, Hobday TJ, Ivanova A, Chiu WK, Ferraro M, Burrows E, Bernard PS, Hoadley KA, Perou CM, Winer EP (2012). TBCRC 001: randomized phase II study of cetuximab in combination with carboplatin in stage IV triple-negative breast cancer. J Clin Oncol, 30(21), 2615-23.
  13. A 50-gene intrinsic subtype classifier for prognosis and prediction of benefit from adjuvant tamoxifen.Chia SK, Bramwell VH, Tu D, Shepherd LE, Jiang S, Vickery T, Mardis E, Leung S, Ung K, Pritchard KI, Parker JS, Bernard PS, Perou CM, Ellis MJ, Nielsen TO (2012). A 50-gene intrinsic subtype classifier for prognosis and prediction of benefit from adjuvant tamoxifen. Clin Cancer Res, 18(16), 4465-72.
  14. PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers.Bastien RR, Rodriguez-Lescure A, Ebbert MT, Prat A, Munarriz B, Rowe L, Miller P, Ruiz-Borrego M, Anderson D, Lyons B, Alvarez I, Dowell T, Wall D, Segui MA, Barley L, Boucher KM, Alba E, Pappas L, Davis CA, Aranda I, Fauron C, Stijleman IJ, Palacios J, Anton A, Carrasco E, Caballero R, Ellis MJ, Nielsen TO, Perou CM, Astill M, Bernard PS, Martin M (2012). PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers. BMC Med Genomics, 5, 44.
  15. Targeting the PyMT Oncogene to Diverse Mammary Cell Populations Enhances Tumor Heterogeneity and Generates Rare Breast Cancer Subtypes.Smith BA, Shelton DN, Kieffer C, Milash B, Usary J, Perou CM, Bernard PS, Welm BE (2012). Targeting the PyMT Oncogene to Diverse Mammary Cell Populations Enhances Tumor Heterogeneity and Generates Rare Breast Cancer Subtypes. Genes Cancer, 3(9-10), 550-63.
  16. High quality and quantity Genome-wide germline genotypes from FFPE normal tissue.Cannon-Albright LA, Cooper KG, Georgelas A, Bernard PS (2011). High quality and quantity Genome-wide germline genotypes from FFPE normal tissue. BMC Res Notes, 4, 159.
  17. Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomes.DeRose YS, Wang G, Lin YC, Bernard PS, Buys SS, Ebbert MT, Factor R, Matsen C, Milash BA, Nelson E, Neumayer L, Randall RL, Stijleman IJ, Welm BE, Welm AL (2011). Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomes. Nat Med, 17(11), 1514-20.
  18. Characterization of uncertainty in the classification of multivariate assays: application to PAM50 centroid-based genomic predictors for breast cancer treatment plans.Ebbert MT, Bastien RR, Boucher KM, Martin M, Carrasco E, Caballero R, Stijleman IJ, Bernard PS, Facelli JC (2011). Characterization of uncertainty in the classification of multivariate assays: application to PAM50 centroid-based genomic predictors for breast cancer treatment plans. J Clin Bioinforma, 1, 37.
  19. Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types.Wilkerson MD, Yin X, Hoadley KA, Liu Y, Hayward MC, Cabanski CR, Muldrew K, Miller CR, Randell SH, Socinski MA, Parsons AM, Funkhouser WK, Lee CB, Roberts PJ, Thorne L, Bernard PS, Perou CM, Hayes DN (2010). Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types. Clin Cancer Res, 16(19), 4864-75.
  20. Phase II study of bortezomib and pegylated liposomal doxorubicin in the treatment of metastatic breast cancer.Irvin WJ Jr, Orlowski RZ, Chiu WK, Carey LA, Collichio FA, Bernard PS, Stijleman IJ, Perou C, Ivanova A, Dees EC (2010). Phase II study of bortezomib and pegylated liposomal doxorubicin in the treatment of metastatic breast cancer. Clin Breast Cancer, 10(6), 465-70.
  21. A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer.Nielsen TO, Parker JS, Leung S, Voduc D, Ebbert M, Vickery T, Davies SR, Snider J, Stijleman IJ, Reed J, Cheang MC, Mardis ER, Perou CM, Bernard PS, Ellis MJ (2010). A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clin Cancer Res, 16(21), 5222-32.
  22. Supervised risk predictor of breast cancer based on intrinsic subtypes.Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PS (2009). Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol, 27(8), 1160-7.
  23. Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer.Cheang MC, Chia SK, Voduc D, Gao D, Leung S, Snider J, Watson M, Davies S, Bernard PS, Parker JS, Perou CM, Ellis MJ, Nielsen TO (2009). Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. J Natl Cancer Inst, 101(10), 736-50.
  24. Distribution of molecular breast cancer subtypes in middle eastern-saudi arabian women: a pilot study.Al-Tamimi DM, Bernard PS, Shawarby MA, Al-Amri AM, Hadi MA (2009). Distribution of molecular breast cancer subtypes in middle eastern-saudi arabian women: a pilot study. Ultrastruct Pathol, 33(4), 141-50.

Letter

  1. Clinical implementation of the intrinsic subtypes of breast cancer.Perou CM, Parker JS, Prat A, Ellis MJ, Bernard PS (2010). Clinical implementation of the intrinsic subtypes of breast cancer [Letter to the editor]. Lancet Oncol, 11(8), 718-9; author reply 720-1.

Video