Faculty
Michael J. Becich, MD, PhD
Research Interests
• Translational Bioinformatics
• Pathology Informatics
• Oncology Informatics
• Tissue Banking Informatics
• Research Resource Development
• Personalized Medicine
Appointments and Positions
Current Research Projects and Collaborations
Sarcoidosis and A1AT Genomics & Informatics Coordinating Center (SAGIC) Alpha-1 antitrypsin deficiency (A1AT), an autosomal recessive genetic disease that is associated with a variable risk of COPD, and Sarcoidosis, a systemic disease characterized by the formation of granulomatous lesions especially in the lungs, liver, skin, and lymph nodes that leads to a dramatically heterogeneous set of clinical manifestations, differ in etiology and clinical presentation but share a variable and unpredictable course. To improve disease classification, facilitate biomarker discovery and accelerate advent of novel therapy an integrative approach that combines the results of clinical studies with molecular phenotyping results is required. SAGIC will facilitate this process by addressing the following objectives for the NHLBI Genomic Research in A1AT and Sarcoidosis (GRADS) program: 1) Coordination of Clinical Centers activities that include patient recruitment and phenotyping and biospecimen collection. 2) Performance of transcriptome and microbiome analyses of the samples obtained by the Clinical Centers, 3) Data analysis and integration, 4) Dataset preparation for deposit in the NHLBI BioLINCC repository. The objectives will be addressed through two research projects. Project 1: A1AT microbiome - will address the hypothesis that shifts in the lung microbiome determine the extent of lung involvement in A1AT and that they are reflected in mRNA and microRNA changes in surrogate tissues, and Project 2: Novel molecular phenotypes in Sarcoidosis - will address the hypothesis that systemic inflammation as reflected in gene expression changes in PBMC is indicative of disease extent, microbiome shifts and granuloma molecular networks. 4/1/2012-3/31/16
Cancer Informatics Services The University of Pittsburgh Cancer Institute (UPCI) is a multidisciplinary cancer research center with programs in basic research, translational research and clinical investigations. Dr. Becich directs the Cancer Informatics Services (CIS). The CIS has been continuously funded as part of the Cancer Center Support Grant (CCSG) funding at UPCI for 6 years and the CCSG grant has been in place for 22 years.
SPORE in Skin Cancer: Translational research such as that proposed in the Melanoma and Skin SPORE (MSCP) has a spectrum of needs that benefit from software solutions, including data warehousing, analysis tools and clinical information management. It is critical that this resource be supported and integrated into NCI’s research mission. The Informatics Core (Core D) of the MSCP is composed of the following integrated services:
1) Clinical Trials Management Application (CTMA) – collects, manages, and aggregates all data to support the clinical trials of the MSCP and UPCI with integration to the Cancer Registry, Tissue Banking Information Systems and our Research Data Warehouse (RDW).
2) Registry Information and Honest Broker Services (RIS/HBS) – collects and manages all clinical and outcomes annotation of patients who contribute their cancer tissues to our MSCP translational research efforts. HBS provides a de-identification service which is critical for HIPAA compliant research information data sharing and analysis.
3) Research Data Warehouse (RDW) – translate our clinical data collection from our oncology EMR, laboratory and radiology information systems, cancer registry, tissue bank and immunophenotyping core into an i2b2 database instance.
4) Cohort Discovery and Disease Modeling – utilize the clinical and demographic data from RDW into our analytical tool, Megascope, to allow for deep cohort identification and information modeling of disease biomarkers and outcomes to enable translational clinical research.
5) Bioinformatics Analysis – biomarker data derived from the MSCP projects and those from the Career Development Program (CDP) and Research Development Program (RDP) will require sophisticated bioinformatics analysis.
MSCP will be increasingly reliant on developing robust research information services to more effectively support the translation of innovation from the laboratory to the bedside and to utilize critical clinical and outcomes data in the clinic to guide discovery at the bench. Ms. Saul and Dr. Becich will co-direct this core. Both are also involved in the Biomedical Informatics Core of the Clinical and Translational Science Institute at the University of Pittsburgh as well as the Cancer Informatics Core of the Cancer Center Support Grant (CCSG). This additional level of integration with NIH Roadmap Initiatives and the NCI CCSG program is a key strength of the Informatics Core of the MSCP at UPCI. University of Pittsburgh and the University of Pittsburgh Cancer Institute (UPCI) 2008-2013
CDC Expansion of the National Mesothelioma Virtual Registry and Tissue Bank: The purpose of the National Mesothelioma Virtual Bank (NMVB) for Translational Research is to maximize the effectiveness of data and biospecimen collection and sharing for mesothelioma research nationally. The NMVB will continue to serve as a resource that will allow researchers real time access to clinical data associated with blood, DNA and tissue specimens from the registry, thus expanding scientific discovery and effective treatments to benefit the Mesothelioma clinical and translational research and patient communities. Our specific aims are: 1) To expand the NMVB to Mt. Sinai School of Medicine. We will continue to collect patients’ clinical data and enroll them in the biospecimen bank at the original NMVB partners: New York University (NYU), the University of Pennsylvania (Penn), the University of Pittsburgh (Pitt). At all sites we will collect biological samples including (but not limited to) biopsy material (fixed or frozen), blood, serum and white blood cells (for DNA). This will include continuing to accrue prospective cases, retrospective cases and case controls. 2) To expand the NMVB collection sites to the University of Hawaii Cancer Center and the University of California San Francisco through the “SPIRiT of Collaboration” and to facilitate translational research from funded investigators by the Meso Foundation and proposed Mesothelioma SPORE. 3) We will document and continually evaluate the usefulness of the NMVB to the scientific community and measure its impact in studies that address the etiology, mechanisms, diagnosis and treatment of malignant mesothelioma. The advantages of this approach which we call “The SPIRiT of Collaboration” is that it will begin to couple funding sources from the CDC NIOSH to the NCI (through the Meso SPORE) and NCRR (through the CTSA program). This effort will serve as a model for multi-agency funding of synergistic efforts. The NIH Roadmap stresses the importance of collaborative networks of researchers and the sharing of biospecimen resources and the National Mesothelioma Virtual Bank program of NIOSH/CDC clearly aims to facilitate that vision. University of Pennsylvania and New York University 2008-2016
NMVB website - http://www.mesotissue.org/
NMVB database for cohort disccovery - https://www.data.nmvb.org/mvb/
Clinical and Translational Science Award (CTSA) Biomedical Informatics Core for the Clinical and Translational Science Institute (CTSI) at Pittsburgh: Codirector of CTSI, Member of CTSA Steering Committee and Operations Committee, 38 funded CTSA sites 2006-2016
CTSI's Biomedical Informatics Core seeks to integrate informatics in all phases of the research lifecycle by offering assistance in obtaining data, consulting about software solutions, and deploying novel tools that address the needs of those conducting clinical and translational studies.
The Biomedical Informatics Core offers researchers at Pitt the following software and services:
The Text Information Extraction System (TIES)
The Text Information Extraction System (TIES)is the name given to the Cancer Text Information Extraction System (caTIES)production system at the University of Pittsburgh. It is a slightly customized version of caTIES that is freely available for download from the caTIES website.
The TIES system provides researchers with an intuitive user interface for finding patient cases and clinical data in a repository of more than 1.6 million UPMC de-identified pathology reports and to order the associated tissue for IRB-approved studies. A powerful charts builder allows researchers to create bar and pie charts categorized by age, gender, collection year or concepts like diagnosis or organ. Researchers can save the charts as image files to use later in publications or grants. Similar to tagging on sites like Flickr, researchers can now tag a set of reports with a descriptive name and then restrict searches within a particular set of tagged reports. TIES supports case sets, order management, and honest broker features to help manage tissue and data requests.
For more information about TIES, including information on how to request a TIES account, or to view the TIES User Manual or TIES Software Demos, visit the TIES website.
Digital Vita
Digital Vita is web-based social networking software that helps users identify potential research collaborators by using information about faculty members' research interests and publications. Users create an online profile in Digital Vita, and the system manages all of the data in each faculty member’s Curriculum Vitae (CV), providing an easy user interface for creating a paper or electronic CV and NIH biosketch. For more information on Digital Vita, visit the Find Colleagues/Digital Vita Page, or log into the network at the Digital Vita Website.
Center for Assistance in Research using eRecord (CARe)
The Center for Assistance in Research using eRecord (CARe)provides centralized assistance for researchers to access and extract data from UPMC electronic health records, for research purposes. CARe facilitates the safe, secure, and compliant transfer of data from the multiple electronic medical record systems that comprise UPMC eRecord.
Consulting
The staff of the Biomedical Informatics Core is available to help investigators identify the appropriate software for storing research data or the appropriate methodology for design or evaluation of software to be developed for a grant. While we do not develop software for individual research projects, we can often direct researchers to other resources on campus. To request a consulting session, email Girish Chavan at chavang@upmc.edu.
Helpdesk support
The Biomedical Informatics Core provides helpdesk support for Digital Vita, TIES, and various software applications used by the Clinical & Translational Resource Centers that comprise the Clinical Resources and Research Facilities and Networks.
Recent Publications
Bartholow TL, Chandran UR, Becich MJ, Parwani AV. Immunohistochemical staining of radixin and moesin in prostatic adenocarcinoma. BMC Clin Pathol. 2011 Jan 14;11(1):1. PMC 3029218
Bartholow TL, Becich MJ, Chandran UR, Parwani AV. Immunohistochemical staining of slit2 in primary and metastatic prostatic adenocarcinoma. Transl Oncol. 2011 Oct;4(5):314-20. Epub 2011 Oct 1. PMC 3162306
Batholow TL, Becich MJ, Chandran UR, Parwani AV. Immunohistochemical Analysis of ezrin-radixin-moesin-binding phosphoprotein 50 in prostatic adenocarcinoma. BMC Urol. 2011 Jun 14;11(1):12. [Epub ahead of print] PMID: 21672215. PMC 3132203
Maxwell GL, Hood BL, Day R, Chandran U, Kirchner D, Kolli VS, Bateman NW, Allard J, Miller C, Sun M, Flint MS, Zahn C, Oliver J, Banerjee S, Litzi T, Parwani A, Sandburg G, Rose S, Becich MJ, Berchuck A, Kohn E, Risinger JI, Conrads TP.Proteomic analysis of stage I endometrial cancer tissue: Identification of proteins associated with oxidative processes and inflammation.Gynecol Oncol. 2011 Jun 1;121(3):586-94. Epub 2011 Apr 1. PMID: 21458040 PubMed Journal - in process