Peer-Reviewed Publications

Below is a listing of peer-reviewed publications, book chapters and abstracts that supports GPS Cancer.

  1. Inferred immune-cell activity is an independent predictor of HER2 negative breast cancer prognosis and response to paclitaxel-based therapy in the GeparSepto trial. Fasching PA, Szeto C, Denkert C, Benz S, Weber K, Spilman P, Budczies J, Schneeweiss A, Stickeler E, Schmatloch S, Jackisch C, Karn T, Sinn HP, Warm M, van Mackelenbergh M, Rabizadeh S, Schem C, Heinmoeller E, Mueller V, Marme F, Soon-Shiong P, Nekljudova V, Untch M, Loibl S. Clin Cancer Res. 2023 Apr 4:CCR-22-2213. doi: 10.1158/1078-0432.CCR-22-2213. PMID: 37014668

  3. Safety, Feasibility, and Merits of Longitudinal Molecular Testing of Multiple Metastatic Sites to Inform mTNBC Patient Treatment in the Intensive Trial of Omics in Cancer. Burton KA, Mahen E, Konnick EQ, Blau S, Dorschner MO, Ramirez AB, Schmechel SC, Song C, Parulkar R, Parker S, Senecal FM, Pritchard CC, Mecham BH, Szeto C, Spilman P, Zhu J, Gadi VK, Ronen R, Stilwell J, Kaldjian E, Dutkowski J, Benz SC, Rabizadeh S, Soon-Shiong P, Blau CA. JCO Precis Oncol. 2022 Mar;6:e2100280. doi: 10.1200/PO.21.00280. PMID: 35294224

  5. Glycolytic expression in lower-grade glioma reveals an epigenetic association between IDH mutation status and PDL1/2 expression. Givechian KB, Garner C, Benz S, Rabizadeh S, Soon-Shiong P. Neurooncol Adv. 2020 Nov 27;3(1):vdaa162. doi: 10.1093/noajnl/vdaa162. eCollection 2021 Jan-Dec. PMID: 33532725

  7. Identification and validation of expressed HLA-binding breast cancer neoepitopes for potential use in individualized cancer therapy. Reimann H, Nguyen A, Sanborn JZ, Vaske CJ, Benz SC, Niazi K, Rabizadeh S, Spilman P, Mackensen A, Ruebner M, Hein A, Beckmann MW, van der Meijden ED, Bausenwein J, Kretschmann S, Griffioen M, Schlom J, Gulley JL, Lee KL, Hamilton DH, Soon-Shiong P, Fasching PA, Kremer AN. J Immunother Cancer. 2021 Jun;9(6):e002605. doi: 10.1136/jitc-2021-002605. PMID: 34172517

  9. Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples. Newton Y, Sedgewick AJ, Cisneros L, Golovato J, Johnson M, Szeto CW, Rabizadeh S, Sanborn JZ, Benz SC, Vaske C. Sci Rep. 2020 Oct 19;10(1):17597. doi: 10.1038/s41598-020-74483-1. PMID: 33077815

  11. A deep learning image-based intrinsic molecular subtype classifier of breast tumors reveals tumor heterogeneity that may affect survivalJaber MI, Song B, Taylor C, Vaske CJ, Benz SC, Rabizadeh S, Soon-Shiong P, Szeto CW. Breast Cancer Res. 2020 Jan 28;22(1):12. doi: 10.1186/s13058-020-1248-3. PMID: 31992350

  13. An immunogenic NSCLC microenvironment is associated with favorable survival in lung adenocarcinoma.Givechian KB, Garner C, Benz S, Song B, Rabizadeh S, Soon-Shiong P. Oncotarget. 2019 Mar 5;10(19):1840-1849. doi: 10.18632/oncotarget.26748. PMID: 30956762

  15. Deep Learning Implicitly Handles Tissue Specific Phenomena to Predict Tumor DNA Accessibility and Immune Activity.Wnuk K, Sudol J, Givechian KB, Soon-Shiong P, Rabizadeh S, Szeto C, Vaske C. iScience. 2019 Oct 25;20:119-136. doi: 10.1016/j.isci.2019.09.018. Epub 2019 Sep 14.
    PMID: 31563852

  17. Efficient Tumor Clearance and Diversified Immunity through Neoepitope Vaccines and Combinatorial Immunotherapy. Lee KL, Benz SC, Hicks KC, Nguyen A, Gameiro SR, Palena C, Sanborn JZ, Su Z, Ordentlich P, Rohlin L, Lee JH, Rabizadeh S, Soon-Shiong P, Niazi K, Schlom J, Hamilton DH. Cancer Immunol Res. 2019 Aug;7(8):1359-1370. doi: 10.1158/2326-6066.CIR-18-0620. Epub 2019 Jul 10. PMID: 31292145

  19. CAD/POLD2 gene expression is associated with poor overall survival and chemoresistance in bladder urothelial carcinoma. Givechian KB, Garner C, Garban H, Rabizadeh S, Soon-Shiong P. Oncotarget. 2018 Jul 3;9(51):29743-29752. doi: 10.18632/oncotarget.25701. eCollection 2018 Jul 3. PMID: 30038717

  21. Identification of an immune gene expression signature associated with favorable clinical features in Treg-enriched patient tumor samples. Givechian KB, Wnuk K, Garner C, Benz S, Garban H, Rabizadeh S, Niazi K, Soon-Shiong P. NPJ Genom Med. 2018 Jun 13;3:14. doi: 10.1038/s41525-018-0054-7. eCollection 2018. PMID: 29928512

  23. Comprehensive genomic transcriptomic tumor-normal gene panel analysis for enhanced precision in patients with lung cancer. Rabizadeh S, Garner C, Sanborn JZ, Benz SC, Reddy S, Soon-Shiong P.
    Oncotarget. 2018 Apr 10;9(27):19223-19232. doi: 10.18632/oncotarget.24973. eCollection 2018 Apr 10. PMID: 29721196

  25. Proof of the quantitative potential of immunofluorescence by mass spectrometry. Toki MI, Cecchi F, Hembrough T, Syrigos KN, Rimm DL. Lab Invest. 2017 Mar;97(3):329-324.

  27. MET tyrosine kinase receptor expression and amplification as prognostic biomarkers of survival in gastroesophageal adenocarcinoma. Catenacci DV, Ang A, Liao WL, Shen J, O’Day E, Loberg RD, Cecchi F, et al. Cancer. 2017 May;123(6):1061-1070.

  29. Quantitative proteomic analysis of HER2 expression in the selection of gastric cancer patients for trastuzumab treatment. An E, Ock CY, Kim TY, Lee KH, Han SW, Im SA, et al. Ann Oncol. 2017 Jan;28(1):110-115.

  31. Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM Andrew J. Sedgewick, Stephen C. Benz, Shahrooz Rabizadeh, Patrick Soon-Shiong, and Charles J. Vaske

  33. Quantification of Anaplastic Lymphoma Kinase Protein Expression in Non-Small Cell Lung Cancer Tissues from Patients Treated with Crizotinib. Hembrough T, Liao WL, Hartley CP, Ma PC, Velcheti V, Lanigan C et al. Clin Chem. 2016;62:252-261.

  35. Therapeutically induced changes in HER2, HER3, and EGFR protein expression for treatment guidance. Sellappan S, Blackler A, Liao W-L, O’Day E, Xu P, Thyparambil S, Cecchi F, Hembrough T, Catenacci DVT. JNCCN. 2016;14:503-507.

  37. High HER2 protein levels correlate with increased survival in breast cancer patients treated with anti-HER2 therapy. Nuciforo P, Thyparambil S, Aura C, Garrido-Castro A, Vilaro M, Peg V et al. Mol Oncol. 2016 Jan;10(1):138-47.

  39. Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination. Sanborn, JZ, Chung J, Purdom E, Wang, NJ, Kakavand, H, Wilmott JS, et al. (2015). PNAS.  2015;112:10995-11000.

  41. FOXM1 cistrome predicts breast cancer metastatic outcome better than FOXM1 expression levels or tumor proliferation index.  Yau C, Meyer L, Benz S, Vaske C, Scott G, Egan B, et al. Br Can Res Treat.  2015;154:23–32.

  43. Mass-spectrometry-based quantitation of Her2 in gastroesophageal tumor tissue: comparison to IHC and FISH. Catenacci DV, Liao WL, Zhao L, Whitcomb E, Henderson L, O’Day E et al. Gastric Cancer. 2016 Oct;19(4):1066-79.

  45. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.. Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR et al. N Engl J Med. 2015;372:2481-2498.

  47. Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome. Favero F, McGranahan N, Salm M, Birkbak NJ, Sanborn JZ, Benz SC et al. Ann Oncol. 2015;26:880-887.

  49. Application of tissue mesodissection to molecular cancer diagnostics. Krizman D, Adey N, Parry R. J Clin Pathol. 2015;68:166-9.

  51. Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53. Quigley D, Silwal-Pandit L, Dannenfelser R, Langerod A, Vollan HK, Vaske C et al. Mol Cancer Res. 2015;13:493-501.

  53. The molecular landscape of premenopausal breast cancer. Liao S, Hartmaier RJ, McGuire KP, Puhalla SL, Luthra S, Chandran UR et al. Breast Cancer Res. 2015;17:104.

  55. Multiple Hereditary Infundibulocystic Basal Cell Carcinoma Syndrome Associated With a Germline SUFU Mutation. Schulman JM, Oh DH, Sanborn JZ, Pincus L, McCalmont THCho RJ. JAMA Dermatol. 2015;1-5.

  57. Obstacles to precision oncology: confronting current factors affecting the successful introduction of biomarkers to the clinic. Prudkin LNuciforo P. Cell Oncol (Dordr). 2015;38:39-48.

  59. Characterization of HPV and host genome interactions in primary head and neck cancers. Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA et al. Proc Natl Acad Sci U S A. 2014;111:15544-15549.

  61. JARID1B is a luminal lineage-driving oncogene in breast cancer. Yamamoto S, Wu Z, Russnes HG, Takagi S, Peluffo G, Vaske C et al. Cancer Cell. 2014;25:762-777.

  63. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S et al. Cell. 2014;158:929-944.

  65. Absolute quantitation of Met using mass spectrometry for clinical application: assay precision, stability, and correlation with MET gene amplification in FFPE tumor tissue. Catenacci DV, Liao WL, Thyparambil S, Henderson L, Xu P, Zhao L et al. PLoS One. 2014;9:e100586.

  67. Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing. Lee MC, Lopez-Diaz FJ, Khan SY, Tariq MA, Dayn Y, Vaske CJ et al. Proc Natl Acad Sci U S A. 2014;111:E4726-4735.

  69. Targeting RPL39 and MLF2 reduces tumor initiation and metastasis in breast cancer by inhibiting nitric oxide synthase signaling. Dave B, Granados-Principal S, Zhu R, Benz S, Rabizadeh S, Soon-Shiong P et al. Proc Natl Acad Sci U S A. 2014;111:8838-8843.

  71. Combined MET inhibition and topoisomerase I inhibition block cell growth of small cell lung cancer. Rolle CE, Kanteti R, Surati M, Nandi S, Dhanasingh I, Yala S et al. Mol Cancer Ther. 2014;13:576-584.

  73. Comparative evaluation of strategies for quantifying signaling pathway proteins in Ewing sarcoma. Applebaum MA, Thomas DG, Hembrough T, Burrows J, Horvai AE, Lawlor ER et al. Appl Immunohistochem Mol Morphol. 2014;22:593-599.

  75. The Cancer Genome Atlas Pan-Cancer analysis project. Cancer Genome Atlas Research N, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA et al. Nat Genet. 2013;45:1113-1120.

  77. Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Sanborn JZ, Salama SR, Grifford M, Brennan CW, Mikkelsen T, Jhanwar S et al. Cancer Res. 2013;73:6036-6045.

  79. Application of selected reaction monitoring for multiplex quantification of clinically validated biomarkers in formalin-fixed, paraffin-embedded tumor tissue. Hembrough T, Thyparambil S, Liao WL, Darfler MM, Abdo J, Bengali KM et al. J Mol Diagn. 2013;15:454-465.

  81. A gene signature for late distant metastasis in breast cancer identifies a potential mechanism of late recurrences. Mittempergher L, Saghatchian M, Wolf DM, Michiels S, Canisius S, Dessen P et al. Mol Oncol. 2013;7:987-999.

  83. Integrated genomic characterization of endometrial carcinoma. Cancer Genome Atlas Research N, Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y et al. Nature. 2013;497:67-73.

  85. Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM. Sedgewick AJ, Benz SC, Rabizadeh S, Soon-Shiong PVaske CJ. Bioinformatics. 2013;29:i62-70.

  87. Modeling precision treatment of breast cancer. Daemen A, Griffith OL, Heiser LM, Wang NJ, Enache OM, Sanborn Z et al. Genome Biol. 2013;14:R110.

  89. Use of formalin-fixed, paraffin-embedded tissue for proteomic biomarker discovery. Krizman DB, Burrows J. Methods Mol Biol. 2013;1002:85-92.

  91. The somatic genomic landscape of glioblastoma. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR et al. Cell. 2013;155:462-477.

  93. The UCSC Interaction Browser: multidimensional data views in pathway context. Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D et al. Nucleic Acids Res. 2013;41:W218-224.

  95. Comprehensive genomic characterization of squamous cell lung cancers. Cancer Genome Atlas Research N. Nature. 2012;489:519-525.

  97. Comprehensive molecular characterization of human colon and rectal cancer Cancer Genome Atlas N. Nature. 2012;487:330-337.

  99. Comprehensive molecular portraits of human breast tumours. Cancer Genome Atlas N. Nature. 2012;490:61-70.

  101. Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells? Sadanandam A, Lal A, Benz SC, Eppenberger-Castori S, Scott G, Gray JW et al. Breast Cancer Res Treat. 2012;136:693-703.

  103. Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Kristensen VN, Vaske CJ, Ursini-Siegel J, Van Loo P, Nordgard SH, Sachidanandam R et al. Proc Natl Acad Sci U S A. 2012;109:2802-2807.

  105. Subtype and pathway specific responses to anticancer compounds in breast cancer. Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S et al. Proc Natl Acad Sci U S A. 2012;109:2724-2729.

  107. Selected Reaction Monitoring (SRM) Analysis of Epidermal Growth Factor Receptor (EGFR) in Formalin Fixed Tumor Tissue. Hembrough T, Thyparambil S, Liao WL, Darfler MM, Abdo J, Bengali KM et al. Clin Proteomics. 2012;9:5.

  109. Integrated genomic analyses of ovarian carcinoma. Cancer Genome Atlas Research N. Nature. 2011;474:609-615.

  111. Differential proteomic analysis of late-stage and recurrent breast cancer from formalin-fixed paraffin-embedded tissues. Bateman NW, Sun M, Bhargava R, Hood BL, Darfler MM, Kovatich AJ, Hooke JA, Krizman DB, et al. J Proteome Res.2011;10:1323-1332.

  113. Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma. Wang NJ, Sanborn Z, Arnett KL, Bayston LJ, Liao W, Proby CM, Leigh IM, Collisson EA, et al. Proc Natl Acad Sci U S A. 2011;108:17761-17766.

  115. The Integration of Biological Pathway Knowledge in Cancer Genomics: A review of existing computational approaches. Varadan V, Mittal P, Vaske C, Benz S. IEEE Signal Processing Magazine. 2011;29:35-50.

  117. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J et al. Bioinformatics. 2010;26:i237-245.

  119. mTRAQ-based quantification of potential endometrial carcinoma biomarkers from archived formalin-fixed paraffin-embedded tissues. DeSouza LV, Krakovska O, Darfler MM, Krizman DB, Romaschin AD, Colgan TJ, Siu KW. Proteomics.2010;10:3108-3116.

  121. LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis. Huang SK, Darfler MM, Nicholl MB, You J, Bemis KG, Tegeler TJ, Wang M, Wery JP, et al. PLoS One. 2009;4:e4430.

  123. Proteomic analysis of laser-captured paraffin-embedded tissues: a molecular portrait of head and neck cancer progression. Patel V, Hood BL, Molinolo AA, Lee NH, Conrads TP, Braisted JC, Krizman DB, Veenstra TD, et al. Clin Cancer Res. 2008;14:1002-1014.

  125. Quantitative Proteomic Analysis of Formalin Fixed Paraffin Embedded Oral HPV Lesions from HIV Patients. Jain MR, Liu T, Hu J, Darfler M, Fitzhugh V, Rinaggio J, Li H. Open Proteomics J. 2008;1:40-45.

  127. Application of a global proteomic approach to archival precursor lesions: deleted in malignant brain tumors 1 and tissue transglutaminase 2 are upregulated in pancreatic cancer precursors. Cheung W, Darfler MM, Alvarez H, Hood BL, Conrads TP, Habbe N, Krizman DB, Mollenhauer J, et al. Pancreatology. 2008;8:608-616.

  129. Liquid Tissue: proteomic profiling of formalin-fixed tissues. Prieto DA, Hood BL, Darfler MM, Guiel TG, Lucas DA, Conrads TP, Veenstra TD, Krizman DB. Biotechniques. 2005;Suppl:32-35.

  131. Proteomic analysis of formalin-fixed prostate cancer tissue. Hood BL, Darfler MM, Guiel TG, Furusato B, Lucas DA, Ringeisen BR, Sesterhenn IA, Conrads TP, et al. Mol Cell Proteomics. 2005;4:1741-1753.

  133. Printing of protein microarrays via a capillary-free fluid jetting mechanism. Barron JA, Young HD, Dlott DD, Darfler MM, Krizman DB, Ringeisen BR. Proteomics.2005;5:4138-4144.

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