Bioinformatics definitions, challenges and impact on health care systems

Bioinformatics: Definitions, Challenges and Impact on Health Care Systems Joyce Mitchell, PhD Professor and Chair Department of Biomedical Informatics University of Utah School of Medicine http://uuhsc.utah.edu/medinfo Topics 1. What is Bioinformatics? 2. Scope of Bioinformatics a) Genomics b) Proteomics c) Functional genomics 3. Genomics data and patient care 4. Impact of Bioinformatics on Health Information Systems 5. What is coming? Central Dogma of Molecular Biology DNA RNA Protein Phenotype Phenotype Transcription Translation Replication Post Translational Modification What is Bioinformatics? Definitions… NIH Definition  Bioinformatics applies principles of information sciences and technologies to make the vast, diverse, and complex life sciences data more understandable and useful. NIH Definition cont… Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data. http://www.bisti.nih.gov/CompuBioDef.pdf Another… NCBI (National Center for Biotechnology Information) Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights and to create a global perspective from which unifying principles in biology can be discerned. http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html Bioinformatics & Health Informatics  Bioinformatics is the study of the flow of information in biological sciences.  Health Informatics is the study of the flow of information in patient care.  These two field are on a collision course as genomics data becomes used in patient care.  Russ Altman,MD, PhD, Stanford Univ. [...]... Variants among individuals Genomics – study of the sequence, structure and function of the genome Study relationships among sets of genes rather than single genes Comparative genomics – study of the differences among species Usually covers evolutionary studies of differences & conservation over time Genome Databases (e.g., GenBank)  Consists of    long strings of DNA bases – ATCG… Annotations of this... International research effort Determine sequence of human genome and other model organisms Began 1990, completed 2003 We are now in the “Post-Genomic” era Next steps for ~20,000 genes    Function and regulation of all genes Significance of variations between people Cures, therapies, “genomic healthcare” Genome and Genomics  Genome – entire complement of DNA in a species     Both nuclear and mitochondrial/chloroplast... transcriptome and proteome is complex, due to longevity of mRNA signal, subsequent control of translation to protein, and post translational modifications Functional Genomics Technologies: Gene Chips, Microarrays, etc Functional Genomics – Microarrays     Transcriptome and transcriptomics High throughput technique designed to measure the relative abundance of mRNA in a cell or tissue in response to... Transcriptomics Functional Genetics Proteomics Proteome and Proteomics   Proteome – the entire set of proteins (and other gene products) made by the genome Proteomics – study of the interactions among proteins in the proteome, including networks of interacting proteins and metabolic considerations Also includes differences in developmental stages, tissues and organs Protein Functions      Catalysis... underdetermined systems Kohane IS, Kho AT, Butte AJ Microarrays for an Integrative Genomics (The MIT Press; Cambridge, MA; 2003), p 11 GWAS Studies      Genome Wide Association Studies Use SNP chips data to look for associations between SNP profiles and diseases Beyond single gene studies into multiple gene studies Usually common diseases Beyond family studies into population studies Some analyses on combining... sequences (DNA and RNA) Databanks and search algorithms Supports studies of molecular evolution (“Tree wars”) Linkage studies GWAS studies (genome wide association studies) Systems Biology (metabolomics)   Metabolites and interacting systems (interactomics) Graphs, visualization, modeling, networks of entities Central Dogma of Molecular Biology DNA Structural Genomics RNA Functional Genomics (Transcriptomics)...Omes and Omics  Genomics     Proteomics      Microarray data (and SNP Chips) Databanks, analysis tools, controlled terminologies Genetic Epidemiology – finding gene-disease associations    Sequences (Protein) and structures Mass spectrometry, X-ray crystallography Databanks, knowledge bases, visualization Functional Genomics (transcriptomics)   Primarily sequences (DNA and RNA) Databanks... Also includes differences in developmental stages, tissues and organs Protein Functions      Catalysis Transport Nutrition and storage Contraction and mobility Structural elements     Defense mechanisms Regulation  Cytoskeleton Basement membranes   Genetic Hormonal Buffering capacity ... each of 1 million spots DNA microarray synthesis: http://www.hhmi.org/biointeractive/media/gene_chips-lg.mov Characteristics of Array Data    Voluminous – tens of thousands of variables with relatively few observations of each (upside down vs classical biostatistics) Noisy – error rates up to 8% Methods designed to detect patterns and associations always find patterns and associations Experimental... algorithms and similarity measures  BLAST and its many forms Central Dogma of Molecular Biology DNA Genomics RNA Protein Transcriptomics Functional Genetics Phenotype Phenotype Proteomics Proteome vs Transcriptome    Functional genomics (transcriptomics) looks at the timing and regulation of gene products (mRNA, primarily) Proteome is final end-product (set of many or all proteins) Relationship between . Bioinformatics: Definitions, Challenges and Impact on Health Care Systems Joyce Mitchell, PhD Professor and Chair Department of Biomedical Informatics University. What is Bioinformatics? 2. Scope of Bioinformatics a) Genomics b) Proteomics c) Functional genomics 3. Genomics data and patient care 4. Impact of Bioinformatics on Health Information Systems 5 RNA Protein Phenotype Phenotype Transcription Translation Replication Post Translational Modification What is Bioinformatics? Definitions… NIH Definition  Bioinformatics applies principles of information sciences and technologies