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Publications

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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.
Cancer Epidemiol Biomarkers Prev. 2014 Apr 17.

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Intrinsic Subtypes from PAM50 Gene Expression Assay in a Population-Based Breast Cancer Cohort: Differences by Age, Race, and Tumor Characteristics.
Sweeney C, Bernard PS, Factor RE, Kwan ML, Habel LA, Quesenberry CP Jr, Shakespear K, Weltzien EK, Stijleman IJ, Davis CA, Ebbert MT, Castillo A, Kushi LH, Caan BJ.
Cancer Epidemiol Biomarkers Prev. 2014 Apr 17.

Race and breast cancer survival by intrinsic subtype based on PAM50 gene expression.
Kroenke CH, Sweeney C, Kwan ML, Quesenberry CP, Weltzien EK, Habel LA, Castillo A, Bernard PS, Factor RE, Kushi LH, Caan BJ.
Breast Cancer Res Treat. 2014 Apr;144(3):689-99.

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.
Mod Pathol. 2013 Nov;26(11):1438-50.

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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.
J Mol Diagn. 2013 Jul;15(4):485-97.

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PAM50 proliferation score as a predictor of weekly paclitaxel benefit in breast cancer.
Martín M, Prat A, Rodríguez-Lescure A, Caballero R, Ebbert MT, Munárriz B, Ruiz-Borrego M, Bastien RR, Crespo C, Davis C, Rodríguez CA, López-Vega JM, Furió V, García 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.
Breast Cancer Res Treat. 2013 Apr;138(2):457-66.

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Prognostic significance of progesterone receptor-positive tumor cells within immunohistochemically defined luminal A breast cancer.
Prat A, Cheang MC, Martín M, Parker JS, Carrasco E, Caballero R, Tyldesley S, Gelmon K, Bernard PS, Nielsen TO, Perou CM.
J Clin Oncol. 2013 Jan 10;31(2):203-9.

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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.
Ann Oncol. 2012 Nov;23(11):2866-73.

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PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers.
Bastien RR, Rodríguez-Lescure Á, Ebbert MT, Prat A, Munárriz B, Rowe L, Miller P, Ruiz-Borrego M, Anderson D, Lyons B, Álvarez I, Dowell T, Wall D, Seguí MÁ, Barley L, Boucher KM, Alba E, Pappas L, Davis CA, Aranda I, Fauron C, Stijleman IJ, Palacios J, Antón A, Carrasco E, Caballero R, Ellis MJ, Nielsen TO, Perou CM, Astill M, Bernard PS, Martín M.
BMC Med Genomics. 2012 Oct 4;5:44.

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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.
Genes Cancer. 2012 Sep;3(9-10):550-63.

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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.
Clin Cancer Res. 2012 Aug 15;18(16):4465-72.

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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.
Clin Cancer Res. 2012 Apr 15;18(8):2402-12.

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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.
Am J Pathol. 2012 Feb;180(2):839-47.

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Agreement in risk prediction between the 21-gene recurrence score assay (Oncotype DX®) 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.
Oncologist. 2012;17(4):492-8.

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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.
PLoS One. 2012;7(5):e36530.

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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, Martín M, Carrasco E, Caballero R, Stijleman IJ, Bernard PS, Facelli JC.
J Clin Bioinforma. 2011 Dec 23;1:37.

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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.
Nat Med. 2011 Oct 23;17(11):1514-20.

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High quality and quantity Genome-wide germline genotypes from FFPE normal tissue.
Cannon-Albright LA, Cooper KG, Georgelas A, Bernard PS.
BMC Res Notes. 2011 May 26;4:159.

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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.
Clin Cancer Res. 2010 Nov 1;16(21):5222-32.

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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.
Clin Cancer Res. 2010 Oct 1;16(19):4864-75.

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

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.
Ultrastruct Pathol. 2009 Jul-Aug;33(4):141-50.

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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.
J Clin Oncol. 2009 Mar 10;27(8):1160-7.

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