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Division of Clinical Chemistry

Email dchan@jhmi.edu
Phone (410) 955-2674

Daniel W. Chan, Ph.D., DABCC, FACB

Professor of Pathology, Oncology, Radiology and Urology
Director, Clinical Chemistry Division
Co-Director of Pathology Core Laboratories
Director, Center for Biomarker Discovery and Translation

The focus of my research is cancer proteomics. In 2000, I founded the Center for Biomarker Discovery and Translation. The focus of the Center is to discover and translate proteomics cancer biomarkers using mass spectrometry, protein microarrays and immunoassays. Our team developed the test OVA1 which is based on 5 proteomic biomarkers for ovarian cancer. In 2009, this test became the 1st FDA cleared proteomic in vitro diagnostic multivariate index assay (IVDMIA). I am the principal investigator (PI) of the Biomarker Reference Laboratory (BRL) for the National Cancer Institute (NCI) Early Detection Research Network (EDRN) and the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC). We were instrumental in the development of public-private partnerships leading to the clinical study, publication and FDA approval in 2012 of two new prostate cancer tests - proPSA (phi) with Beckman Coulter Inc. and PCA3 (PROGENSA) with Gen-probe (Hologic, Inc). I was one of founders of the USHUPO (Human Proteomics Organization) society. Currently, I am the Editor-in-Chief of Clinical Proteomics. At this year's HUPO world congress in Madrid, Spain, my research was recognized and awarded the inaugural "Translational Proteomics Award" for outstanding achievement in proteomics.

Füzéry AK, Levin J, Chan MM and Chan DW. Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges. Clin Proteomics 2013, 10:13.

Sartori DA and Chan DW. Biomarkers in prostate cancer: what's new? Curr Opin Oncol 2014, 26(3): 259-64.

Li, D and Chan DW. Proteomic cancer biomarkers from discovery to approval: it's worth the effort. Expert Rev Proteomics 2014, 11(2):135-6.

Serum fucosylated prostate-specific antigen (PSA) improves the differentiation of aggressive from non-aggressive prostate cancers. Li QK, Chen L, Ao MH, Chiu JH, Zhang Z, Zhang H, Chan DW. Theranostics. 2015 Jan 1;5(3):267-76

Email wclarke@jhmi.edu
Phone (410) 502-7692

Related Websites

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William Clarke, Ph.D.

Primary Appointment in Pathology
Member, Graduate Program in Biochemistry, Cellular and Molecular Biology

My research interests primarily involve the development of analytical methods for drug analysis. This includes the development and implementation of tandem mass spectrometry and high resolution-accurate mass (HRAM) mass spectrometry method for measurement of multiple drugs in a single sample, as well as investigation of alternative matrices for drug testing. In addition, I am interested in the application of pharmacokinetic measurements, along with pharmacogenetic testing, to clinical management of patients. Active projects in our lab include pharmacokinetic monitoring of antidepressants and mood-stabilizing drugs in bariatric surgery patients, pharmacokinetic evaluation of antidepressant drugs in pregnant women with mood disorders, and qualitative screening for antiretroviral drugs and substances of abuse in various HIV Prevention Clinical Trials. We are also investigating ways to improve the robustness and throughput of LC-MS methods in the clinical laboratory by evaluation of newly developed technologies and alternative approaches to LC-MS method development.

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Email mmarzin1@jhmi.edu
Phone (443) 287-7516
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Mark A. Marzinke, Ph.D.

Primary Appointment in Pathology; Secondary Appointment in Medicine; Associate Director, Clinical Pharmacology Analytical Laboratory (Division of Clinical Pharmacology)

My primary research focuses are in the development and validation of analytical methods for the assessment of phenotype-genotype and pharmacokinetic-pharmacodynamic (PK-PD) relationships. Specifically, my interests lie in the clinical application of molecular testing for targeted pharmacogenetic analysis using a variety of techniques, including high-resolution melting (HRM) curve discrimination of genetic polymorphisms, and probe-based quantitative PCR techniques to identify genetic aberrations, to direct drug treatment. Additionally, my work is focused on the quantification or qualitative identification of small molecules, including anti-retroviral agents and pain management medications in a variety of specimen sources to assess PK-PD relationships. Our group utilizes mass spectrometry in a variety of ways, including the development, bioanalytical validation and utilization of liquid chromatographic-tandem mass spectrometric (LC-MS/MS) and high-resolution accurate mass (HRAM) spectrometric methods for analyte identification and quantification. Other research interests include laboratory automation and workflow and process improvement initiatives.

Marzinke MA, Choi CH, Chen L, Shih IM, Chan DW, Zhang H. Proteomic Analysis of Temporally Stimulated Ovarian Cancer Cells for Biomarker Discovery. Mol Cell Proteomics 2013; 12(2): 356-368.

Marzinke MA, Clarke W, Wang L, Cummings V, Liu TY, Piwowar-Manning E, Breaud A, Griffith S, Buchbinder S, Shoptaw S, Del Rio C, Magnus M, Mannheimer S, Fields SD, Mayer KH, Wheeler DP, Koblin BA, Eshleman SH, Fogel JM. Nondisclosure of HIV Status in a Clinical Trial Setting: Antiretroviral Drug Screening Can Help Distinguish Between Newly Diagnosed and Previously Diagnosed HIV Infection. Clin Infect Dis. 2014 Jan;58(1):117-20. PMID: 24092804.

Seserko LA, Emory JF, Hendrix CW, Marzinke MA. The development and validation of an UHPLC-MS/MS method for the rapid quantification of the antiretroviral agent dapivirine in human plasma. Bioanalysis. 2013; 5(22):2771-83. PMID: 24256358.

Petrides AK, Clarke W, Marzinke MA. Application and utility of pharmacogenetics in the clinical laboratory. J Analyt Molecul Tech. 2014; 1(1): 15.

Marzinke MA, Breaud A, Parsons TL, Cohen MS, Piwowar-Manning E, Eshleman SH, Clarke W. The development and validation of a method using high-resolution mass spectrometry (HRMS) for the qualitative detection of antiretroviral agents in human blood. Clin Chim Acta, 2014; 433C: 157-168.

Email lsokoll@jhmi.edu
Phone (410) 955-2673
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Lori Sokoll, Ph.D.

Primary Appointment in Pathology; Secondary Appointments in Oncology and Urology

My primary research interest is the investigation of serum tumor markers for the early detection, diagnosis, staging, and monitoring of cancer. Our focus is to develop new tumor markers and to develop new applications for existing markers in order to increase their clinical utility. We are primarily studying markers for prostate cancer and breast cancer. Other research interests include immunoassay automation and intraoperative hormone measurements.


Email zzhang7@jhmi.edu
Phone (410) 502-7871
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Zhen Zhang, Ph.D.

Primary Appointment in Pathology

My research interests are in the development and application of bioinformatics tools for clinical diagnosis. What used to be considered as a single diagnosis may actually consist of a number of different phenotypes with distinguished disease pathways and varying genomic and proteomics expression patterns. I am interested in deriving new mathematical and computational algorithms to identify such patterns for biomarker discovery and use them to establish predictive models for the diagnosis and management of diseases. Currently, our effort is focused on tumor marker discovery using high throughput proteomics approaches.

Zhang Z., Barnhill S.D., Zhang H., Xu F., Yu Y., Jacobs I., Woolas R.P., Berchuck A., Madyastha K.R., Bast R.C. Jr. Combination of multiple serum markers using an artificial neural network to improve specificity in discriminating malignant from benign pelvic masses. Gynecol Oncol. 1999; 73(1):56-61.

Li J, Zhang Z., Rosenzweig J., Wang Y., Chan D.W. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin. Chem., 2002 Aug;48(8):1296-1304.

Zhang Z. Combining Multiple Biomarkers in Clinical Diagnostics - A review of Methods and Issues. In: Diamandis E.P., Fritsche H.A., Lilja H.,Chan D.W., Schwartz M.K., eds. Tumor Markers: Physiology, Pathobiology, Technology and Clinical Applications. AACC Press, Washington, DC, 2002.

Buckhaults P., Zhang Z., Chen Y.C., Wang T.L., St Croix B., Saha S., Bardelli A., Morin P.J., Polyak K., Hruban R.H., Velculescu V.E., Shih IeM. Identifying tumor origin using a gene expression-based classification map. Cancer Res. 2003; 63(14):4144-9.

Zhang Z., Bast R.C. Jr, Yu Y., Li J., Sokoll L.J., Rai A.J., Rosenzweig J.M., Cameron B., Wang Y.Y., Meng X.Y., Berchuck A., Van Haaften-Day C., Hacker N.F., de Bruijn H.W., van der Zee A.G., Jacobs I.J., Fung E.T., Chan D.W. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res. 2004; 64(16):5882-90.

Email hzhang32@jhmi.edu
Phone (410) 502-8149

Related Websites
Biomarker Center


Human Cancer Proteome Project

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Hui Zhang, Ph.D.

Professor of Pathology;
Director of Mass Spectrometry Core Facility, Center for Biomarker Discovery and Translation

My research interests are centered on understanding functions of proteins and protein modifications using high-throughput proteomic technologies. Currently, projects in the lab focus on understanding structures and functions of proteins and protein glycosylation in biology and human diseases. Researchers in the group developed integrated proteomic, glycoproteomic, and glycomic technologies for comprehensive glycoprotein characterization. These technologies enable the identification and quantification of glycoproteins, glycosites, glycans associated with each glycosite and their occupancies. The group participates in several research programs including Early Detection Research Network (EDRN), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and Programs of Excellence in Glycosciences (PEG).

Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou J, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha S-W, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Choi C, Monroe ME, Thomas S, Moore RJ, ,Yu K-H, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih I-M, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD, and the CPTAC investigators. Deep proteogenomic characterization of human ovarian cancer. Cell. 2016; 166: 755-765.

Sun S, Shah P, Toghi Eshghi S, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Hoti NU, Zhang Z, Chan DW, Zhang H*. Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides. Nature Biotechnology. 2016; 34: 84-88.

Shah P, Wang X, Yang W, Toghi Eshghi S, Sun S, Hoti N, Pasay J, Rubin A, Zhang H*. Integrated proteomic and glycoproteomic analyses of prostate cancer cells reveals glycoprotein alteration in protein abundance and glycosylation. Molecular & Cellular Proteomics. 2015; 14: 2753-2763.

Toghi Eshghi S, Shah P, Yang W, Li X, Zhang H*. GPQuest: A Spectral Library Matching Algorithm for Site-Specific Assignment of Spectra from Tandem Mass Spectrometric Analysis of Intact Glycopeptides. Analytical Chemistry. 2015; 87: 5181-5188.

Zhang, H., Li, X. J., Martin, D. B., and Aebersold, R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nature Biotechnology (2003) 21:660.

Zhang, H., Zha, X., Tan, Y., Hornbeck, P. V., Mastrangelo, A. J., Alessi, D. R., Polakiewicz, R. D., and Comb, M. J. Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs. Journal of Biological Chemistry (2002) 277:39379.

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