Peer-Reviewed Publications (2005-2016)

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

  1. 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
  2. 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.
  3. 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.
  4. 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. 2015;e-published ahead of print.
  5. 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.
  6. 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.
  7. 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. 2015;
  8. 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.
  9. 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.
  10. Application of tissue mesodissection to molecular cancer diagnostics. Krizman D, Adey N, Parry R. J Clin Pathol. 2015;68:166-9.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. Use of formalin-fixed, paraffin-embedded tissue for proteomic biomarker discovery. Krizman DB, Burrows J. Methods Mol Biol. 2013;1002:85-92.
  31. 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.
  32. 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.
  33. Comprehensive genomic characterization of squamous cell lung cancers. Cancer Genome Atlas Research N. Nature. 2012;489:519-525.
  34. Comprehensive molecular characterization of human colon and rectal cancer Cancer Genome Atlas N. Nature. 2012;487:330-337.
  35. Comprehensive molecular portraits of human breast tumours. Cancer Genome Atlas N. Nature. 2012;490:61-70.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. Integrated genomic analyses of ovarian carcinoma. Cancer Genome Atlas Research N. Nature. 2011;474:609-615.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.
  52. 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.

Selected Abstracts (2014-2016)

  1. High-throughput identification of neoepitopes for the development of patient-specific cancer immunotherapies. Nguyen A, Sanborn JZ, Vaske CJ, Rabizadeh S, Niazi K, Soon-Shiong P, Benz SC. American Association for Cancer Research Annual Meeting. 2016 (abstr 4512).
  2. Targeted proteomic analysis for personalized treatment of muscle invasive bladder cancer. Cecchi F, Thyparambil S, Blackler A, Hembrough T, Rabizadeh S, Soon-Shiong P, Frierson H, Theodorescu D. American Association for Cancer Research Annual Meeting. 2016 (abstr 449).
  3. Targeted proteomic analysis of hepatocellular carcinoma and its histologic mimickers. Cecchi F, Ku N, Wang H, Blackler A, Hembrough T, Rabizadeh S, Soon-Shiong P, Huang J. American Association for Cancer Research Annual Meeting. 2016 (abstr 4935).
  4. Quantitative HER2 protein expression analysis in multiple cancer indications. Sellappan S, Schwartz S, Cecchi F, Blackler A, Soon-Shiong P, Rabizadeh S, Hembrough T. 14th International Congress on Targeted Anticancer Therapies. 2016 (abstr P5.2).
  5. KRAS gene amplification to define a distinct molecular subgroup of gastroesophageal adenocarcinoma. Henderson L, Xu P, O'Day E, Cecchi F, Blackler A, Liao W-L, Hembrough TA, Catenacci DVT. J Clin Oncol. 2016;34 (suppl 4S; abstr 74)
  6. Integrating whole genome sequencing data with RNAseq, pathway analysis, and quantitative proteomics to determine prognosis after standard adjuvant treatment with trastuzumab and chemotherapy in primary breast cancer patients. Benz SC, Rabizadeh S, Cecchi F, Beckman MW, Brucker SY, Hartmann A, Golovato J, Hembrough T, Janni W, Rack B, Sanborn JZ, Schneeweiss A, Vaske CJ, Soon-Shiong P, Fasching PA. San Antonio Breast Cancer Symposium 2015 (abstr P6-04-14)
  7. Quantitative HER family proteins assessment as prognostic and predictive biomarkers in the EGF30008 clinical trial. Nuciforo P, Thyparambil S, Galvá n P, Vilaro M, Jimenez J, Liao W-L, Cecchi F, Blackler A, Press MF, Gagnon R, Ellis C, Hembrough T, Johnston S, Prat A.  San Antonio Breast Cancer Symposium 2015 (abstr P3-07-08).
  8. Evaluation of MET using FISH, IHC, or mass spectrometry as a prognostic biomarker in patients with gastroesophageal cancer. Catenacci D, Shen J, Liao WL, Oliner K, Ang A, Loberg R, O'Day E, Xu P, Henderson L, Cecchi F, Burrows J, Hembrough T, Ruzzo A, Graziano F. European Cancer Congress 2015 (abstr 2397).
  9. Integrating whole exome sequencing data with RNAseq and quantitative proteomics to better inform clinical treatment decisions in patients with metastatic triple negative breast cancer. Soon-Shiong P, Rabizadeh S, Benz S, Cecchi F, Hembrough T, Mahen E, Burton K, Song C, Senecal F, Schmechel S, Pritchard C, Dorschner M, Blau S, Blau A. San Antonio Breast Cancer Symposium 2015 (abstr P6-05-08).
  10. Protein expression by genetic mutations identified in gene panels (hotspots) and efficacy of targeted treatments. Benz SC, Rabizadeh R, Sanborn JZ, Vaske CJ, Palmer GA, Soon-Shiong P, J Clin Oncol. 2015;33 (suppl; abstr 11005).
  11. Genomics, transcriptomics, and proteomics in the clinical setting: Integrating whole genome and RNA sequencing with quantitative proteomics to better inform clinical treatment selection. Rabizadeh S, Benz SC, Burrows J, Hembrough TA, Sanborn JZ, Vaske CJ, Soon-Shiong P. J Clin Oncol 33, 2015 (suppl; abstr 11093).
  12. An EMT-like gene expression profile differentiates helical from kinase domain PIK3CA mutations. Yau C, Garay J, Benz S, Gray J, Park B, Benz CC. Cancer Res. 2015; 75 (suppl; abstr 1084).
  13. Whole genome sequencing and quantitative proteomics reveal HPV integration and HER2 overexpression in a patient with cervical cancer: Comprehensive omics analysis driving clinical treatment decisions. Benz S, Sanborn JZ, Hensley NS, Hembrough T, Vaske CJ, Burrows J, Rabizadeh S, Royston I, Soon-Shiong P. AACR Precision Medicine Series. 2015; abstr.
  14. Proteomic analysis of primary and metastatic breast cancers and expression of the folate receptor as a potential drug target. Hembrough TA, Cecchi F, Blackler A, Thyparambil SP, Burrows J, O'Shaughnessy J. J Clin Oncol 33, 2015 (suppl; abstr 1045).
  15. Quantitative measurement of HER2 levels by multiplexed mass spectrometry to predict survival in gastric cancer patients treated with trastuzumab. Ock C-Y, An E, Oh D-Y, Kim T-Y, Lee K-H, Han S-W, Im S-A, Kim T-Y, Liao W-L, Cecchi F, Blackler A, Thyparambil SP, Hoos WA, Kim WH, Burrows J, Hembrough TA, Bang Y-J. J Clin Oncol 2015; 33 (suppl; abstr 4050).
  16. HER2 quantification by mass spectrometry compared to IHC or ISH in predicting clinical benefit from anti-HER2 therapy in HER2-positive breast cancer (BC).Nuciforo P, Aura C, Thyparambil SP, Vilaro M, Garrido-Castro AC, Peg V, Jimenez J, Hoos WA, Burrows J, Hembrough TA, Perez-Garcia JM, Cortes J, Scaltriti M. J Clin Oncol 33, 2015 (suppl; abstr 605).
  17. Clinical implication of mass-spectrometry-based selected reaction monitoring (SRM) assay in non-small cell lung cancer (NSCLC) patients exhibiting ALK gene rearrangement. An HJ, An E, Liao W-L, Kang JH, Burrows J, Hembrough TA, Kim T-J. J Clin Oncol 2015; 33 (suppl; abstr e22145).
  18. Quantitative Mass Spectrometry Proteomics Identifies FRalpha and GARFT as Predictive Biomarkers in NSCLC Patients Treated With Pemetrexed.  Alshehri AA, An E, Cecchi F, Hembrough T, Ma PC,  Smolkin M, Wen S, Monga M. 16th World Conference on Lung Cancer. 2015 (abstr 106).
  19. Clinical Survey of actionable proteins in multiple indications using multiplex mass spectrometry.  Cecchi F, Blackler A, Jordan H, Stocum M, Darfler M, Hembrough T, Burrows J. Ann Oncol 2015;26 (suppl 2).
  20. ChemoPlex SRM assay predicts response to specific chemotherapeutic agents in NSCLC.  An E, Kim T-J, Monga M, Bengali K, Drilea A, Reilly J, Darfler M, Burrows J, Hembrough T. Cancer Research 2015;75 (suppl; abstr 566).
  21. Clinical Survey of 19 actionable proteins in multiple indications using multiplex mass spectrometry. Cecchi F, Blackler A, Jordan H, Darfler M, Hembrough T, Stocum M, Burrows J. Cancer Research 2015;75 (suppl; abstr 3395).
  22. Development of a mass spectrometry based antibody-drug conjugate biomarker panel. Blackler A, Liao W-L, Thyparambil S, An E, Cecchi F, Darfler M, Hembrough T, Burrows J. Cancer Research 2015;75 (suppl; abstr 3398).
  23. Development and clinical validation of a quantitative mass spectrometric assay for immuno-oncology targets in FFPE samples. Thyparambil SP, Cecchi F, An E, Liao W-L, Burrows J, Hembrough T, Catenacci D. Cancer Research 2015;75 (suppl; abstr 3398).
  24. Her2 expression in gastroesophageal cancer (GEC) FFPE tissue using mass spectrometry (MS) and correlation with HER2 gene amplification. Catenacci D, Zhao L, Whitcomb E, Henderson L, O'Day E, Xu P, Xiao S-Y, Lee SM, Liao W-L, Thyparambil SP, Uzzell J, Darfler M, Krizman D, Burrows J, Hembrough TA; J Clin Oncol 2015;33 (suppl 3; abstr 82).
  25. Correlation of high levels of HER2 measured by multiplex mass spectrometry with increased overall survival in patients treated with anti-HER2-based therapy. Nuciforo P, Thyparambil SP, Garrido-Castro AC, Peg V, Prudkin L, Jimenez J, Hoos WA, Burrows J, Hembrough TA, Perez-Garcia JM, Cortes J, Scaltriti M. J Clin Oncol 2014;32:5s (suppl; abstr 649).
  26. Escape of EML4-ALK NSCLC to early phase precision therapy through TGFβ2-HOX-bioenergetics reprogramming. Yin L, Zhang W, Shi I, Feng Y, Choi H, Bagai RK, Makishima H, Lanigan C, Cicenia J, Gildea T, Liao W-L, Hembrough TA, Burrows J, Tubbs RR, Lindner D, Almeida F, Maciejewski JP, Ma PC. J Clin Oncol 2014;32 (suppl; abstr e19044).
  27. A comprehensive analysis of molecular profiles across over 10,000 tumor and germ-line exomes across more than 20 tumor types: Novel mechanisms and targets for clinical treatment.  Rabizadeh S, Benz SC, Sanborn JZ, Vaske CJ, Soon-Shiong P. J Clin Oncol 2014;32 (suppl; abstr 11031).
  28. Multi-omic profiling to predict response to gemcitabine/ carboplatin (GC) plus iniparib (BSI-201) as neoadjuvant therapy for triple-negative (TN) and BRCA1/2 mutation-associated breast cancer using a pathway-based approach. Vinayak S, Benz SC, Vaske CJ, Telli ML, Ford JM. Cancer Res 2014;24 (suppl; abstr 2826).
  29. Differential pathway activation associated with domain-specific PIK3CA mutations. Yau C, Benz S, Vaske C, Ng S, Stuart J, Benz CC. Cancer Res 2014;74 (suppl; abstr 4165)

Book Chapters

Focus on Personalized Molecular Based Medicine. Van der Ploeg L, Mishra B, Eitner C, Burrows J, Tombler T, Poponin V, Knauer D, Ichetovkin I, et al. In: Lenz H-J ed. Biomarkers in Oncology. Springer; 2012.

Quantitative SRM Analysis of EGFR Pathway Proteins in FFPE Tissue. Krizman DB, Burrows J. In: Kato H, Nakamura K, Nishimura T eds. Clinical Proteomics-Clinical Biomarker Aims to Personalized Medicine. Publishing Inc; 2012.

Analysis of Formalin Fixed Tissue for Cancer Biomarker Discovery. Krizman DB. In: T Veenstra ed. Methods in Molecular Biology: Proteomics for Biomarker Discovery. Humana Press; 2012