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The Center for Computational Genomics and Data Science (CGDS)

Team Purpose

The Center for Computational Genomics and Data Science (CGDS) seeks to develop and apply tools and methods to uncover new and novel information that provide benefits for patients suffering from rare, undiagnosed, or misdiagnosed diseases, their families, and the people that care for them. CGDS focuses on interpreting molecular variation with regards to its correlation with patient phenotypes. We seek to identify and interpret causal molecular variation as well as variations that alter patients’ clinical severity and progression through modification of phenotype or through alteration of response to therapeutics (pharmacogenomics). Although we aim to generate knowledge that can be utilized for the study of human disease in general, we strive to produce and apply knowledge for individuals (patients, their families, and the clinicians who take care of them) in need of information to assist with clinical decision making in the present. CGDS diligently works to create and maintain a productive and friendly team environment where we continuously educate one another, contributeto scientific education, and disseminate new information locally and globally.

The Center for Computational Genomics and Data Science (CGDS) seeks to advance delivery of precision medicine to patients and to advance research discoveries through the application multi-omics data science and innovations in alignment with the UAB School of Medicine (SOM) goals. Transfer of advancements is accomplished through education, patient care, basic research, translational research, and clinical research.

Duration and Time Commitment

The CGDS work week consists of core hours that each member is expected to include in their workday; remaining hours in the work day are flexible. We ask that you do your best to be in your office during core hours and schedule non-work appointments outside those core hours. Flexibility for team members is absolutely supported and does not reflect a lack of their commitment, but rather an acknowledgment of how life really happens.

In return for this flexibility, team members are asked to be flexible in return, by working in the evenings or on weekends in exchange for taking time off during the week. Absences that can be planned outside of core hours (like doctor/dentist checkups) should be planned for early or late in the day. Minimizing absences within core hours whenever possible will help to dispel misunderstandings and reduce project impact.

If you have an emergency or sickness, notify Liz and communicate with the team as soon as you can. Your commitment to communicating planned and unplanned events will reduce the possibility of tension and/or conflicts.

Scope

At this point, the science in our areas of interest is just beginning to unravel the complexities of a multitude of questions. It’s important for us to keep focus on our goals and keep project scope in manageable tasks.

We also acknowledge that every project we take on, contributes towards improving patient outcomes and patient’s quality of life even when negative results are achieved. This approach demands perseverance to stay on track, pursuing wherever the data may lead in planned increments.

  1. Development of expanded capabilities in the area of molecular diagnostics for oncology and rare disease and other mis- or undiagnosed diseases.
  2. Organization of data science innovations across the UAB SOM as a whole.
  3. Driving or enabling differentiation and growth for key UAB clinical service lines using omics-based data science.
  4. Supporting the empowerment of physicians by providing the information they need to enable data science driven precision care.
  5. Development of grant revenue streams for Data Science related to; precision medicine, phenotype-to-genotype studies, polygenic risk score analyses, pharmacogenomics, molecular diagnostics, etc.
  6. Development of materials for education of students, residents, and healthcare providers.
  7. Evaluation, prioritization, and development of partnership and other opportunities both within and external to UAB.
  8. Development of philanthropic opportunities in the area of -omics data science in support of UAB SOM missions.

Keys to Success

Team success is achieved by building on existing talent, relationships, investments, and accomplishments. Success also relies on strengthening intra- and inter- institution communications and collaborations. It is important to initiate, support, and reinforce interdisciplinary collaborations among our CGDS teams and with UAB researchers, clinicians, pathologists, laboratory administrators, and other specialists and other teams who bring important knowledge to these efforts. Although there may be a gap between research goals and the application of new discoveries in clinically-useful manner, our team will work towards development of tests and procedures that useful for patients and can be reimbursed through health insurance providers.

Members (Nov 2019)

In order to meet the needs of our distinctive units, the Department of Pathology, the Department of Pediatrics, the UAB School of Medicine Omics-based Data Science Program, and the clinical- and research-focused Worthey Lab Research Program, teams of software developers, data scientists, statisticians and researchers peopled by junior and senior research scientists, and students will focus their efforts into Software Development, Data Science, and Molecular Variation Interpretation. Many CGDS members will work across many of these foci including an administrative associate, the lab manager, a system administrator, and research IT. This structure allows CGDS to define teams and reporting structures, and ensures cohesion among the teams given that success will require significant amounts of cross team interaction.

Dr. Liz Worthey

Director for the Center for Computational Genomics and Data Science within the departments of Pediatrics and Pathology in UAB School of Medicine
Director of the Bioinformatics Section in Division of Genomics Diagnostics and Bioinformatics within the department of Pathology in UAB School of Medicine
Associate Director in Hugh Kaul Precision Medicine Institute
Associate Professor Pediatrics and Pathology
Scientist the O’Neal Comprehensive Cancer Center

Arthur Weborg

Software Architect - Genomics

Angelina Uno-Antonison

Software Developer III - Genomics

Donna Brown

Molecular Variant Analyst

Brandon Wilk

Software Developer III - Genomics

Dr. Manavalan Gajapathy

Data Scientist - Genomics

Alex Moss

Software Developer I - Genomics

Team Sponsor Dr. Selwyn Vickers

Senior Vice President of Medicine Dean of the University of Alabama at Birmingham School of Medicine

Dr. Vickers has held these posts since October 2013. He is a world-renowned surgeon, pancreatic cancer researcher, and pioneer in health disparities research. Dr. Vickers is a member of the National Academy of Medicine (Institute of Medicine) and of the Johns Hopkins Society of Scholars. Dr. Vickers personally recruited this team to UAB.

Other sponsors or key stakeholders

  • Dr. Matt Might
  • Dr. George Netto
  • Dr. Bruce Korf
  • Dr. Mitch Cohen

Desired End Result

We will focus on development and application of tools and methods to identify and interpret causal molecular variation i.e. ending of diagnostic odysseys, as well as identification of variation that otherwise alters a patient's clinical picture through modification of their phenotype or through alteration of response to therapeutics (pharmacogenomics). Critically our goals are clinical; although we aim to generate generalizable knowledge for future studies, we strive to produce and apply knowledge for these individuals today; not ten years down the road in their journey.

Supporting Resources

The supporting resources include other people not assigned as team members but who aid our overall purpose. Other resources may be called upon to supply needed resources (blue prints, meeting rooms, travel budgets, corporate authority, software, etc.)

Management of Projects

Due to the vast variety of project types within the CGDS, each project shall have a project charter using the CGDS project charter template. The Project Charter will be shared among all project members to communicate scope and work required. In regards to reports, the charter informs report format, method of delivery, frequency of delivery, and to whom it must be delivered to.

Deliverable

Project charters characterize the summation of work within the CGDS. This document defines the project intentions, resources, activities, and goals. Each project charter uses the CGDS project charter template as a guide to ensure all members understand the scope and purpose of the work. Goals within the project charter must map directly to the goals of the CGDS which correspond directly from the UAB School of Medicine. The individual goals for members of the CGDS must fall within the scope of the project’s goals. Project charters also define project status reports and final project deliverables.