BIOS 743 Genomics, Proteomics and Bioinformatics
Instructors: Professor Lance Liotta MD PhD (Room 323 Bull Run Hall) and
Professor Emanuel Petricoin PhD (Room 324 Bull Run Hall)
Thursdays 4:30-7:10 p.m. at the Prince William campus, Bull Run Hall
Room 248
Office Hours: Thursdays 230-430 Room 323 and 324 Bull Run Hall and by
appointment (contact Ms. Peggy Hackett, phackett@gmu.edu)
Description of the course:
The new era of personalized therapy and molecular medicine is a perfect
example where the functional aspects of genomics, proteomics and
bioinformatics comes to together at the bedside. This course will focus on
the practical use of these three areas for the diagnosis, prevention and
treatment of disease. Real world case studies will be used to illustrate and
educate students, as well as touch on the downstream issues in regard to
the regulation of such new platforms and assays.
- Week 1 Jan 24 Instructor: Liotta
Introduction to the course. Cancer Molecular Biology and introduction to
cellular proteomics and genomics. Discussion of basic principles of molecular
medicine, including the definition and the need for individualized diagnostics and
therapeutics. Review of cancer medicine and the basics of cancer molecular
biology. Functional principles of protein synthesis, protein folding, receptors,
protein functions, and protein signal transduction. Review of the major advances
in these fields which have relevance to molecular medicine of the future
- Week 2 Jan 31 Instructor Petricoin
Introduction to genetics and genomics. Sequencing the human genome,
Cancer genomics, cancer transcriptomics. Review of the major advances in
these fields which have relevance to molecular medicine of the future.
Application of genetics and genomics to the prediction of disease.
- Week 3 Feb 7 Instructor Luchini
Nanotechnology Guest Professor: Alessandra Luchini
Introduction to the definitions and principles of nanotechnology. Microfabrication
nanomachines, nanofluidics, application of nanotechnology to personalized
therapy and the future of molecular medicine.
- Week 4 Feb 14 Instructor: Vaisman
Introduction to Bioinformatics: Guest Professor: Iosif Vaisman
Definition bioinformatics. Review of bioinformatics tools. Data categories and
reliability of data. Sources of bias and variability.
- Week 5 Feb 21: Instructor: Espina
Clinical chemistry and clinical pathology: applications to proteomics,
genomics and bioinformatics. Guest Professor: Virginia Espina
Review of tissue and blood clinical chemistry principles. Specimen collection,
fixation, histologic examination and scoring, sources of bias in clinical research
trials, definition of sensitivity, Tissue microdissection, precision, and accuracy.
- Week 6 Feb 28: Instructor: Russo
Mass Spectrometry techniques applied to proteomic-based biomarker
discovery. Guest Professor: Paul Russo
Principles of mass spectrometry. Differences between MALDI and ES.
Introduction to ETD. and MRM. Software and bioinformatics tools for scoring and
identification of candidate protein sequences. Post translational modifications in
proteins. Application of Mass Spectrometry to the discovery of biomarkers for
human disease. Blood biomarkers. Bottom up versus Top down approach.
Discovery versus validation. Correct design of a discovery and validation trial.
Examples of recent findings related to cancer diagnosis.
- Week 7 March 7: MIDTERM EXAM
- Week 8 March 14: Spring Break No Class
- Week 9 March 21: Liotta
Next generation multiplex Assay Technology for Proteins. Immunoassay
principles. Antibody validation, Protein arrays, Particle and bead assays,
Biosensors, Plasmon Resonance, Flow Cytometry. Examples of applications to
cancer diagnostics.
- Week 10 March 28: Petricoin
Next generation Multiplex Assay Technology for genomics. Hybridization
principles. Array platforms, Transcript arrays, RNA versus DNA, DNA
methylation, Examples of applications to cancer diagnostics. Regulatory
considerations for high complexity testing and multi-analytes.
- Week 11 April 4 Instructor: Sharrer
Medical Ethics in the Era of Genomics and Proteomics: Guest Professor:
Terry Sharrer
Ethics of Clinical research trials and incorporation of Omic technologies into
clinical trials.
- Week 12 April 11 Instructor: Mueller
Focused Proteomic Analysis: Kinases, Phosphatases, and Nitric Oxide:
Role in health and disease. Basic enzymatic principles, role in cell biology and
diseases, therapeutic strategies, and relevance to individualized therapy
-Week 13 April 18
Project Class Presentations
- Week 14 April 25
Project Class Presentations
- Week 15 May 2
Project Class Presentations
- Week 16 May 9 Final Exam
Additional references and project topic ideas will be provided during the
course discussions.
Grades will be based on:
Mid Term Exam: 33%
Final Exam: 33%
Project Presentation: 34%
Fundamental questions of Molecular Diagnostics, Proteomics, Genomics
and Bioinformatics that one should address during this course.
1. What is the current and future role of molecular diagnostics in medicine?
2. What is the definition of individualized therapy and what are the implications
for medical care and the biotechnology community?
3. How is cancer diagnosed and treated today? How is this envisioned to change
in the future?
4. How do nucleic acids and proteins differ in their functional role in disease
pathogenesis?
5. What are the current tools for measuring nucleic acids and proteins? What are
the challenges and limitations of conventional measurement technologies?
6. Explain the requirements for biomarker clinical validation.
7. What are some of the emerging technologies and bioinformatics tools to
measure genetic and proteomic molecules in tissue and body fluids?
8. Provide real world case studies for the application of individualized therapy to
human disease.