ACCEL Video Series

Big Data to Knowledge: Integrated Bioinformatics towards Systems Biology and Precision Medicine

With the advent of next-generation sequencing (NGS) and other high-throughput omics technologies, systems integration is becoming the driving force for 21st century biology and medicine. To fully realize the value of such genome-scale data for knowledge discovery and disease understanding requires advanced bioinformatics for integration, mining, comparative analysis, and functional interpretation. We have developed a bioinformatics research infrastructure that integrates disparate databases and text mining tools in an ontological framework for automatic construction of knowledge networks and visual analysis of omics data. Our natural language processing (NLP) framework supports full-scale literature mining and generalizable relation extraction to connect gene/protein, mutation, miRNA to drug, disease and phenotype in personalized medicine context. This talk will highlight our collaborative projects with large-scale national initiatives, including the NIH LINCS-BD2K (Big Data to Knowledge) and TCGA/CPTAC cancer consortium projects to understand the impact of kinase inhibitor drugs on signaling pathways in cancer therapy.

Dr. Cathy Wu is the Edward G. Jefferson Chair and Director of the Center for Bioinformatics & Computational Biology (CBCB) at University of Delaware. She has conducted bioinformatics research for 25 years and has led/co-led several large multi-institutional Consortium grants, including the Delaware INBRE. She directs the Protein Information Resource (PIR), a member of the UniProt Consortium with 5 million pageviews per month from 500,000 sites worldwide. She has published 250 peer-reviewed papers and is recognized as a “Highly Cited Researcher” (top 1%). The CBCB provides cutting-edge bioinformatics infrastructure, including Big Data and clinical genomics analytics capabilities for precision medicine.

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Identifying Optimal Cut-Points for Continuous Predictors to Discriminate Disease Outcomes

Variables are often dichotomized for decision making in clinical practice and appropriate management of patients requires optimizing a cut-point to discriminate disease risk. If true cut-points for one or more variables exist, the challenge is identifying them. We examine dichotomization methods to identify which methods recover a true cut-point and present evidence that maximizing odds ratio, Youden's statistic, Gini Index, chi-square statistic, relative risk and kappa statistic theoretically recover a cut-point. Simulations evaluating these statistics for recovery of a cut-point indicate that the chi-square statistic and Gini Index have the smallest bias and variability. There are limited methods for simultaneously optimizing cut-points for more than 1 variable. We propose a method for jointly dichotomizing two or more variables and conduct simulations to compare joint and marginal dichotomization for the ability to recover the cut-points. Our results show that cut-points selected jointly exhibit smaller error and similar bias relative to marginal selection.

Dr. Wolf is an Assistant Professor of Biostatistics in the Department of Public Health Sciences at the Medical University of South Carolina (MUSC). She has a PhD in biostatistics from MUSC, a Master’s degree in environmental chemistry from UNC Wilmington, and a Bachelor’s degree in chemistry and anthropology from Rice University. Her statistics research interests focus on developing statistical methods for biomarker discovery and disease prediction modeling. Her translational interest focus on development of prediction models and diagnostic tools for rheumatic diseases and on examining the impact of environmental contaminants in the food chain of human populations.

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2017 Community Research Exchange Conference

Below please find the video recordings from the ACCEL Community Research Exchange Conference held on Monday, May 15, 2017 at the University of Delaware Clayton Hall Conference Center.

Part 3: Includes Afternoon Panel Discussion on Behavioral and Mental Health:

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2017 Community Research Exchange Conference

Below please find the video recordings from the ACCEL Community Research Exchange Conference held on Monday, May 15, 2017 at the University of Delaware Clayton Hall Conference Center.

Part 2: Includes Second Session of Oral Presentations, Secretary Kara Odom Walker comments:

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2017 Community Research Exchange Conference

Below please find the video recordings from the ACCEL Community Research Exchange Conference held on Monday, May 15, 2017 at the University of Delaware Clayton Hall Conference Center.

Part 1: Includes Welcome/Intro remarks, Keynote Presentation, First Session of Oral Presentations of Community Engaged Research:  

 

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Single Molecule DNA and RNA Sequencing to Detect Residual Cancer and Clonal Hematopoiesis

May 19, 2017: Dr. Druley will discuss novel strategies for single molecule DNA and RNA sequencing as a modality for characterization of clonal hematopoiesis and minimal residual disease (MRD) detection in cancer. Despite "deep sequencing," next-generation platforms have an error rate of 0.5-1.0%, precluding straightforward sequencing for MRD, which requires sensitivity of <1:1,000. However, using a single molecule labeling strategy to correct sequencing errors, the Druley lab has published multiple studies identifying rare clonal mutations at levels as low as 1:10,000 from heterogenous DNA samples. His group is now moving this strategy into RNA sequencing to identify aberrant slice isoforms, allele-specific expression and cryptic fusions in addition to point mutations. The ultimate goal is to combine a toolbox of technologies for precise genomic characterization of individual cancers with machine learning to improve molecular diagnostics, risk stratification, therapeutic selection and outcomes for children with cancer.

Dr. Druley is a board-certified pediatric hematologist/oncologist and Assistant Professor of Pediatrics, Developmental Biology and Genetics at Washington University School of Medicine. Research in the Druley Lab is based on characterizing the link between abnormal human development and early childhood cancer, particularly infant leukemia. The lab has a track record for genomic methodology development and is currently applying that technology to improve molecular diagnostics in pediatric AML. Clinically, Dr. Druley is focused on pediatric cancer predisposition and serves as the co-director of the Pediatric Cancer Predisposition Program at St. Louis Children’s Hospital.

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Mixed-Methods with Teens: A Research Imperative

May 12, 2017: Mixed-methods research and adolescent males aren't often paired in the same sentence. However, they could - and should - be! Join Dr. Judith Herrman and Katie Haigh from the University of Delaware and Christopher Moore from the Department of Family and Community Medicine as they present their research evaluating the impact of the Wise Guys Male Responsibility program. This interactive, grand rounds-style session will present data collection methods, quantitative and qualitative research findings, and a variety of lessons learned.

Dr. Judy Herrman is an advocate for youth locally and nationally. As a nurse, educator, and researcher, Judy has worked with and for teens and young adults to address teen pregnancy prevention, sexuality education, prevention of teen dating violence, and access to reproductive health services. Judy served on the Delaware Teen Pregnancy Prevention Advisory Board, Delaware Senate Task for the Prevention of Teen Dating Violence, Delaware Girls Initiative, and various roles with the Delaware Adolescent Program (DAPI). Judy currently serves as secretary of the Delaware School Based Health Alliance, on the Wilmington Teen Pregnancy Coalition, and on the Board of Directors. She also chairs the Public Policy Committee for the Healthy Teen Network, a national organization charged with promoting better outcomes for adolescents and young adults. Judy will retire in August 2017 from the School of Nursing at the University of Delaware (UD) after 24 years of teaching and research.

Christopher Moore is the Senior Program Manager, Community Health, for Christiana Care Health System’s Department of Family and Community Medicine. Mr. Moore has oversight of staff, programming and evaluation for the department’s grant-funded initiatives which aim to improve the public health across the lifespan. These programs include the Alliance for Adolescent Pregnancy Prevention, one the largest statewide providers of evidence-based reproductive health education; Camp FRESH, a nationally recognized program for urban youth; and Christiana Care’s Health Ambassador Program, which provides access to education and resources for new and expectant mothers. Mr. Moore also co-leads two of the health system’s integrated practice teams; one of which is focused on LGBT patient health equity, the other on increased access to long-acting, reversible contraceptives. He has been collaborating with colleagues from the University of Delaware since 2014 on a robust, mixed-methods evaluation of the Wise Guys Male Responsibility curriculum, the results of which have been presented nationally.

Katie Haigh has been certified through the American Association of Nurse Practitioners and has worked as a Nurse Practitioner since 2007. Most of her clinical work has been in the field of reproductive endocrinology, although she has worked with both adults and children throughout her 16-year career as a nurse. She received her Bachelor of Science degree in Nursing from the University of Delaware in 2001, her Master of Science degree in Nursing specializing in family healthcare from the University of Delaware in 2007, and is currently pursuing her Doctor of Philosophy (PhD) in Applied Physiology at the University of Delaware. Katherine has a passion for educating young adults on wellness and how to prepare for family building in the future. She has also been able to participate in research focusing on adolescent sexual decision making and teen intimate partner violence. In the future, Katherine would like to continue her research looking at clinical differences in young adults who may have an impaired fertility potential, and how this will impact their overall health and decision making in the future regarding family building and fertility preservation.

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Differences in Patient and Physician Perceptions of Care for Patients with Myeloproliferative Neoplasms

April 21, 2017: This talk will focus on data collected from the Landmark Survey, a large survey of patients with myeloproliferative neoplasms (MPNs, namely essential thrombocytosis, primary myelofibrosis, and polycythemia vera) and the providers who take care of patients with MPNs.  The Landmark Survey focused on quality of life issues surrounding the diagnosis of MPNs and differences in patient and physician perceptions of the impact of those symptoms on patient quality of life. Differences in patient and physician perceptions of goals of treatment and important objectives in treating these disorders were also examined. Landmark Survey data can be used to improve communication between patients with MPNs and their physicians and this approach can be generalizable to other disease states as well.

Dr. Mangan is an assistant professor of clinical medicine in the division of hematology/oncology at the Perelman School of Medicine at the University of Pennsylvania. Dr. Mangan specializes in treatment of hematologic malignancies and bone marrow transplant.  He has both clinical and research interests in acute and chronic leukemias, myelodysplastic syndromes, and myeloproliferative disorders and the use of allogeneic stem cell transplantation to treat these disorders. Dr. Mangan is a member of the American Society of Hematology.

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