Data Analysis and Management Core
A huge amount of high-throughput sequencing data is expected to be generated from TCC, ChIP-ePENS, BirA-BLRP-seq, ChIP-seq, MBDCap-seq, CLIP-seq, GRO-seq, and population-cell or single-cell RNA-seq assays and proteomic analysis in the three projects of the proposed SA-Duke Research Center for Cancer Systems Biology (SA-Duke RCCSB). Thus, it is critical to establishing a central data process hub in order to meet the scientific missions and goals of our center. The Data Analysis and Management Core (DAMC) will ensure a unified approach to data analysis and management for all three projects, including the following tasks: 1) implementing and maintaining new software tools for computational models developed in the three projects and intra-center pilot projects; 2) designing and supporting the data analysis flow using existing public or our own software tools; 3) managing data submission to public archives, maintaining data repository and exploring data visualization; and 4) coordinating with the Data Coordination Center (DCC) within the Research Centers for Cancer Systems Biology (RCCSB) Consortium. To accomplish these tasks, the DAMC will leverage existing infrastructure and computational expertise at the University of Texas at San Antonio of both Health Science Center (UTHSCSA) and Academics (UTSA), Duke University, and Baylor College of Medicine. We will establish a leadership team to develop and coordinate ongoing support of cancer omics research and to communicate monthly with the Executive Committee in the Administrative Core. Members of the DAMC leadership team include the leader of the DAMC and senior investigators of the three projects – Drs. Jin (Chair), Ruan, Weintraub, and Li who have extensive experience in large-scale data management, computational, statistical, genomic and proteomic analyses, and coordination of data analytic efforts within multi-project centers. Members of the DAMC will also be involved in all phases of project planning, from design to execution, to ensure that the flow of data from projects to the relevant cores and is well-coordinated.
The goals of the Core are to enhance the awareness and knowledge of cancer systems biology, recruit next-generation trainees interested in epigenomics, and expand the scope of early-stage and established investigators to engage in omics analysis as part of their research portfolio. Two experienced Core leaders, Dr. Nameer Kirma (UT Health San Antonio) and Dr. Pearlly Yan (OSU), will coordinate outreach/training activities within the two central sites. In Aim 1, knowledge of advances in cancer systems biology will be disseminated through seminar series and the annual symposium. Workshops will provide practical training of novel omics technologies. To maximize exposure and capitalize on our existing expertise, these symposia and workshops will be held every year alternating between the two center sites. In Aim 2, we plan to train new scientists and retool established investigators in systems epigenomics. Postdoctoral fellows and early-stage investigators will have the opportunity to participate in cross-pollination training beyond their current expertise, facilitating a more rounded understanding of systems biology. Early-stage and established investigators will have the opportunity to re-sharpen their research skills in omics analyses through the three proposed projects in our center and the release of annual RFA for supporting two Intra-center Pilot Projects (IPPs). In addition, the Core will organize summer programs for at least six undergraduate students and visiting scientists who will have the opportunity to engage in short-term research projects using omics approaches. Given that both sites have access to a great pool of minority and underserved students in South Texas and Appalachia, we will encourage them to apply for these programs. In Aim 3, we plan to interact with investigators in the RCCSB Consortium and other genomics communities. Working with the leaders of our Administrative Core, we will send a delegation consisting of 10 senior and early-stage investigators and IPP awardees to participate in the annual RCCSB Consortium Steering Committee meeting. Through platform and poster presentations and face-to-face meetings, our investigators will find opportunities and niches for collaboration and data sharing with scientists in the Consortium. Furthermore, we will make contact with members of the NIH-funded 4D nucleosome programs and other genomics forums, such as the Cold Spring Harbor Nuclear Organization and Function Symposium, to share our epigenomic findings. To disseminate knowledge on epigenomic advances, we will work with the staff in the Data Analysis and Management Core to set up searchable databases. Ongoing and to-be-developed toolkits will be made available to researchers through our website portal. Collectively, these integrative efforts are expected to nurture next-generation trainees in the area of systems biology and to foster a collaborative spirit with investigators in the RCCSB Consortium and other genomics communities.
The goals of the Administrative Core are to provide streamline governance of our center and to promote collaboration and integration among experimental and computational researchers. Oversight and effective management by the Core will enhance intra- and inter-center communication and to facilitate data dissemination through the NCI’s Research Center for Cancer Systems Biology (RCCSB) Consortium. The Executive Committee of the Core will monitor monthly progress of omics studies and outreach/training activities, conduct scientific reviews of Intra-center Pilot Project (IPP) applications, and prioritize access to high-performance computing servers and biospecimens including primary tumors, patient-derived xenograft (PDX) lines, and circulating tumor cells. To foster innovative ideas of cancer omics research, the Administrative Core will encourage IPP applications from mathematicians, computer scientists, engineers, and biophysicists who are interested in interfacing with biomedical researchers in participating institutions. Prior evidence of omics research is not necessary for submission of a proposal although an eventual avenue for integrative and translational applications should be apparent. Funding of IPPs is supported in part by the proposed RCCSB budget and matching funds from the Alice P. McDermott Endowment at the University of Texas Health Science Center at San Antonio. A robust and transparent peer review process will be established to evaluate submitted proposals and to regularly review the progress of funded proposals. In addition, two mentors – one experimentalist and one computational modeler will be assigned to each junior awardee to instill the concept of team-oriented research and to monitor career development of the awardee in systems biology. External Advisory Board (EAB) members, with expertise in 4D nucleosome, omics data integration or anti-hormone therapy, will independently conduct annual reviews of all aspects of our intra- and inter-center research activities, including experimental designs, statistical and mathematical approaches, translational applications, mentoring and outreach training, and administrative effectiveness. The EAB will provide recommendations regarding continuation and alterations of specific sub-aims or objectives of each project and core. Other recommendations by EAB are expected to expand the horizon of our cancer omics research. Through these administrative mechanisms, the Core will promote high-quality, team-oriented, and niche-focused research in our proposed U54 center.