Overview of Health Informatics. ITI BMI-Dept

Transcription

1 Overview of Health Informatics ITI BMI-Dept

2 Fellowship Week 5 Overview of Health Informatics ITI, BMI-Dept Day 10 7/5/2010 2

3 Agenda 1-Bioinformatics Definitions 2-System Biology 3-Bioinformatics vs Computational biology 4-Bioinformatics vs Clinical informatics 5-Bioinformatics Elements 6-For whom is Bioinformatics 7-Bioinformatics challenges 8-Bioinformatics today and future 9-Genomics, Proteomics and Pharmacogenomics 10-Gene Databases 11-Human Genome Project 12-Private sectors corporation

4 Bioinformatics Definitions the computational branch of molecular biology. 1 the study of how information is represented and analyzed in biological systems, starting at the molecular level 2 field of science in which biology, computer science and information technology merge to form a single discipline 3

5 Bioinformatics Definitions Cont. The systematic development and application of computing systems and computational solution techniques to the analysis of biological data obtained by experiments, modeling, database search, and instrumentation. 4 In Vivo In Vitro In Silico

6 System Biology 11 the study of an organism, viewed as an integrated and interacting network of genes, proteins and biochemical reactions which give rise to life. tries to understand how proteins and genes interact at a cellular level 2 Build upon results of HGP Moving from understanding single component understanding All components and interactions among them, as a System, which is true!! Please visit: Source:

7 Bioinformatics vs Computational biology Computational biology focuses on applying the Computer science techniques to develop models and simulations of biological systems. Bioinformatics focuses of analysis and generation of new knowledge from available data using the information and communication technologies. Bioinformatics Biology Computer Science Information Technology

8 Bioinformatics Vs Clinical informatics 2 Whereas clinical informatics deals with the management of information related to the delivery of health care, bioinformatics focuses on the management of information related to the underlying basic biological sciences Both are complex and related to living systems. Clinical Informatics deals with: Social systems of medicine Cognitive processes of medicine Technologies required to understand human physiology

9 Bioinformatics Elements I. Biological data II. Algorithm III. Software IV. Hardware V. Bioinformatician

10 Bioinformatics Elements cont. I. Biological data: DNA è Genome RNA è Transcriptome Protein è Proteome Biological Pathways Mutations..etc.

11 Bioinformatics Elements cont. II. Algorithm: An algorithm is an effective method for solving a problem using a finite sequence of instructions. Algorithms are used for calculation, data processing, and many other fields. 5 E.g. Gotoh's algorithm and Myers-Miller's algorithm, for Glopal Alignment, based on Dynamic Programming

12 Bioinformatics Elements cont. III. Software: A program or computational tool used to solve a problem depending on a specific Algorithm. E.g. Binding Affinity Prediction of Protein- Ligand (BAPPL). Please visit: ppl.jsp

13 Bioinformatics Elements cont. IV. Hardware: PCs, Servers, Super computers, Networks, etc. E.g. NCBI and EBI Networks

14 Bioinformatics Elements cont. V. Bioinformatician: Skills Required: A basic knowledge of molecular biology Experience with one more of Molecular Biology software packages Operating system's Computer Programming Language Database Management Systems or

15 For whom is Bioinformatics People from 1 : Biology Medical field Computer science Pharmaceutical fields Legalization authorities Investing companies etc.

16 Bioinformatics challenges 6 Lots of data what does it mean? Collecting data using data predicting data Genome annotation (functional genomics) What does this piece of DNA do? Protein structure is related to function (protein folding) Can we predict structure from sequence and basic physics? [Source:

17 Bioinformatics today and future cont. 1. Molecular medicine More drug targets Personalised medicine Preventative medicine Gene therapy 2. Microbial genome applications Waste cleanup Climate change Alternative energy sources Biotechnology Antibiotic resistance Forensic analysis of microbes The reality of bio-weapon creation Evolutionary studies - At this point Bioinformatics seems like - New a field Diagnostic remote from and medicine, Prognostic but that - Proteomics Build models will change with of: more Molecules, receptor Cells, Mutual Pharmacogenomics techniques Tissues, benefits Organisms, between Systems. bio For 2 pharmacogenomics and more and specific personal drug application genetic profiles and - Diagnosing Personalized clinical about 7 simulation informatics. Medicine s of 3000 drug hereditary targeting. 6 interactions. diseases -...bioinformatics to align with the 6 practice of medicine Agriculture Crops Insect resistance Improve nutritional quality Grow crops in poorer soils and that are drought resistant 4. Animals 5. Comparative studies Please visit: Source:

18 Important Opservations 6 Different people respond to drugs differently Many drugs Many genetic differences between people In addition, genetics influence Risk factors are you going to get the disease? (e.g. smoking emphysema, heart disease) Operative risk How to collect and use these data? Memory is not enough, need some tools [Source:

19 Genomics, Proteomics and Pharmacogenomics 7 Genomics: the field that analyzes genetic material from a species Proteomics: the study of gene expression at the level of proteins Pharmacogenomics: the study of genetic material to look for drug targets Patient genetic Profile Patient genetic Profile EHR

20 Pharmacogenomics Knowledge base Mission: collect, encode, and disseminate knowledge about the impact of human genetic variations on drug response Process: Curate primary genotype and phenotype data Annotate gene variants and gene-drug-disease relationships via literature review Summarize important PGx genes and drug pathways Provide Tutorials, for searching and using PharmGKB Please visit:

21 Gene Databases 8 Sequence Databases There are three major co-operating DBs (EMBL-EU, GenBank-USA, DNA Data Bank-Japan) containing millions of sequences with billions of nucleotides from several organisms with exponential growth. Secondary Sequence Databases Suitable for Microarray experiments. Contain better annotation and meta-information. Example: UniGene, TIGR, RefSeq Genomic Databases Examine sequences for microarrays from a genomic perspective Contain gene names and annotations (rather than gene sequences) organized per organism. Example: Ensembl, CMR (Microbial Genomes). Gene Expression Databases For more databases that are related to Bioinformatics, please visit: [Source:

22 Data Growth Growth of Protein Structures in Protein Data Bank ( ) Yearly Total Year Base Pairs Sequences , ,116,431,942 98,868,465 Year Yearly Totally Source:

23 EMBL, GenBank, DDBJ SWISS-PROT, TrEMBL, PIR- PSD PDB, EBI- MSD, NDB dbest, TGI, Mendel ESTs, Bodymap 3DInSight MolMovDB Source:

24 National center for Biotechnology Information (NCBI) 7 Created 1988 Part of NIH NLM Host 10 different genetic databases The Largest Biomedical Research Center Provide access to about 1, 000 organisms genome Please visit:

25 Human Genome Project (HGP) International Collaborative research Project. Goal was the complete mapping and understanding of all the genes of human beings 9 Sequencing, Identifying location and Mapping of about 25, 000 genes , 000 SNPs have been identified by mid Please check: map_search.cgi?taxid=9606 (courtesy National Library of Medicine)

26 What is after HGP?!! 10 National Institute of Health initiated the Human Microbiome Project (HMP). Sequencing 600 Health related microbes. 5 year project. Aims to: Developing a reference set of microbial genome sequences and preliminary characterization of the human microbiome Relationship between disease and changes in the human microbiome Development of new technologies Development of new tools for computational analysis Establishing a Data Analysis and Coordinating Center (DACC) Establishing a resource repository Ethical, legal and social implications (ELSI) of HMP research Please visit :

27 Private sectors corporation 10 Celera Genomics Genetic Mapping and Pharmacogenomics. DNA Direct Genetic Testing and Counseling Decode Genetics Corporation, Iceland initiative, decodeme Genome Analysis for diagnosing about 29 common diseases. Oracle Corporation and Thailand Initiative. Others!!!

28 Thanks By: ITI-BMI Dept. 7/5/

29 References 1. Jean-Michel Claverie. Cedric Notredame. Bioinformatics for Dummies 2 nd Edition. Wiley Edward H. Shortliffe. James J. Cimino. Biomedical Informatics: Computer Applications in Health Care and Biomedicine 3 rd Edition. Springer NCBI. A Science Primer. (Accessed December ). 4. Helge Weissig. Introduction to Bioinformatics Wikipedia. Algorithm. (Accessed December ). 6. Elmer V. Bernstam, School of Health Information Sciences and Internal Medicine, UT Houston. Health Informatics Presentation: (Accessed December ). 7. Robert E. Hoyt. Melanie Sutton. Ann Yoshihashi. Medical Informatics: Practical Guide for the Healthcare Professional 2 nd Edition. Lulu.com Alexandros Kanterakis. Heraklion, Crete. MineGene Presentation: (Accessed December ) 9. National Human Genome Research institute, National Institute of Health. Human Genome Project: (Accessed December ) 10. National Institute of Health. Human Microbiome Project: (Accessed December ). 11. Institute for System Biology. _the_21st_century_science (Accessed Decemeber )