1. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference1 Opportunities at the NIH Peter Good, Ph.D. NHGRI November 17, 2007 6th Georgia Tech / ORNL International Conference on Bioinformatics

2. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference2 How is NIH funding? I don’t know. NIH is only funded one year at a time through congressional appropriations Current bill requesting a 3% increase over last year (inflation) was vetoed by the president

3. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference3 How to get an NIH grant in computational biology/bioinformatics Pick an important problem in biomedicine Know the field Develop a plan to improve on the state of the art Include a plan to validate computational approach with experimental data Spend time to write a good application

4. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference4 Biomedical Information Science and Technology Initiative (BISTI) BISTI is aimed at making optimal use of computer science and technology BISTI Consortium (BISTIC) program representatives from many NIH Institutes and Centers Develop programs to encourage bioinformatics and computational biology www.bisti.nih.gov

5. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference5 Funding opportunities through BISTI Innovations in Biomedical Computational Science and Technology PAR-07-344 Mechanism: R01 Exploratory Innovations in Biomed. Comp. Science and Technology PAR-06-411 Mechanism: R21 Continued Development and Maintenance of SoftwarePAR-08-010 Mechanism: R01 Predictive Multiscale Models of the Physiome in Health and Disease PAR-08-023 Mechanism: R01

6. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference6 Title: Data Ontologies for Biomedical Research (R01) Program Announcement (PA) Number: PAR-07-425 ….develop an ontology that will make it possible for software to understand how two or more existing data sets relate to each other. Title: Sharing Data and Tools: Federation using the BIRN and caBIG Infrastructures (R01) Program Announcement (PA) Number: PAR-07-426 …make either data or tools more broadly available to the research community by making use of the BIRN and/or the caBIG™ infrastructure.

7. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference7 April, 2003April, 1953

8. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference8 Notes From the Front Lines of the Genomic Revolution Comparative genomics is providing a wealth of information about the human genome

9. Elliott H. Margulies et al. Genome Res. 2007; 17: 760-774

10. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference10 Notes From the Front Lines of the Genomic Revolution Comparative genomics is providing a wealth of information about the human genome DNA sequencing is undergoing revolutionary technical advances

11. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference11 1000 Genomes Project (meeting in Cambridge, UK, Sept. 17-18, 2007) Goal is to sequence 1000 genomes at sufficient depth to identify nearly all variants with frequency of minor allele greater than 1% (down to 0.2% in exons) Will be an excellent test of new sequencing technologies Pilot projects getting underway

12. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference12 http://cancergenome.nih.gov

13. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference13

14. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference14 Title: Advanced Genomic Data Analysis and Visualization Methods for the Cancer Genome Atlas (TCGA) Data (R21) Request For Applications (RFA) Number: RFA-CA-08-005

15. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference15 NIH Roadmap for Medical Research ACCELERATING MEDICAL DISCOVERY TO IMPROVE HEALTH www.nihroadmap.nih.gov

16. The goal of the Human Microbiome Project, funded by the NIH Roadmap, is to characterize the microbial content of sites in the human body and examine whether changes in the microbiome can be related to disease. http://nihroadmap.nih.gov/hmp

17. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference17 HMP Roadmap Initiatives 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 (Computational and Experimental) Establishing a Data Analysis and Coordinating Center (DACC) NCBI Short Read Archive Data Repository Establishing a resource repository Ethical, legal and social implications (ELSI) of HMP research

18. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference18 NIH Roadmap for Epigenomics REFERENCE EPIGENOME MAPPING CENTERS EPIGENOMICS DATA ANALYSIS AND COORDINATION CENTER (EDACC) NCBI REPOSITORY AND PORTAL FOR EPIGENOMIC DATA TECHNOLOGY DEVELOPMENT IN EPIGENOMICS DISCOVERY OF NOVEL EPIGENETIC MARKS IN MAMMALIAN CELLS EPIGENOMICS OF HUMAN HEALTH AND DISEASE http://nihroadmap.nih.gov/epigenomics/grants.asp

19. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference19 Notes From the Front Lines of the Genomic Revolution Comparative genomics is providing a wealth of information about the human genome DNA sequencing is undergoing revolutionary technical advances Experimental approaches to determining genome function are moving forward rapidly

22. ENCODE Scale to ENCODE Project to identify functional elements in the whole genome –Transcripts, protein coding genes, chromatin modications, transcription factor binding sites, promoter elements Continue some pilot projects –Promoter elements, RNA binding protein sites Data Coordinating Center and Data Analysis Center

23. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference23 modENCODE ENCODE project on model organisms –Learn how to identify functional elements in a model system –Support projects in Drosophila and C. elegans www.modencode.org

24. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference24 Notes From the Front Lines of the Genomic Revolution Comparative genomics is providing a wealth of information about the human genome DNA sequencing is undergoing revolutionary technical advances Experimental approaches to determining genome function are moving forward rapidly Genetic factors in many common diseases are being rapidly revealed

25. Progress in Genotyping Technology 11010 2 10 3 10 4 10 5 10 6 Nb of SNPs Cost per genotype (Cents, USD) 10 1 10 2 ABI TaqMan ABI SNPlex Illumina Golden Gate Illumina Infinium/Sentrix Affymetrix 100K/500K Perlegen Affymetrix MegAllele 20012005 Affymetrix 10K Courtesy S. Chanock, NCI

26. Cholesterol Obesity Coronary Disease QT interval Atrial Fibrillation Type 2 Diabetes Prostate cancer Breast cancer Colon cancer KCNJ11 20032000 PPAR  2001 IBD5 NOD2 20052006 2002 CTLA4 2004 PTPN22 Age Related Macular Degeneration Crohn’s Disease Type 1 Diabetes Systemic Lupus Erythematosus Asthma Restless leg syndrome Gallstone disease CD25 IRF5 PCSK9 CFH NOS1AP IFIH1 PCSK9 CFB/C2 LOC387715 8q24 IL23R TCF7L2 2007 CDKN2A 8q24 #2 8q24 #3 8q24 #4 8q24 #5 8q24 #6 ATG16L1 5p13 10q21 IRGM NKX2-3 IL12B 3p21 1q24 PTPN2 TCF2 CDKN2A IGF2BP2 CDKAL1 HHEX SLC30A8 MEIS1 LBXCOR1 BTBD9 C3 8q24 ORMDL3 4q25 TCF2 GCKR FTO C12orf30 ERBB3 KIAA0350 CD226 16p13 PTPN2 SH2B3 FGFR2 TNRC9 MAP3K1 LSP1 8q24 Confirmed genetic contributors to common human diseases (August 2007)

27. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference27 A partnership to advance the genetic analysis of ADHD Diabetic nephropathySchizophrenia Bipolar illness Psoriasis Major depression

28. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference28 Genes and Environment Initiative EXPOSURE BIOLOGY PROGRAM Identify genetic variants GENETICS PROGRAM GXE Develop technology and biomarkers GWA Studies Data Analysis Replication Sequencing Database Function Translation Diet Physical Activity Environmental Exposures Psychosocial Stress and Addictive Substances

29. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference29

30. November 17, 2007Georgia Tech / ORNL Bioinformatics Conference30 Peter Good National Human Genome Research Institute Goodp@mail.nih.gov