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

November 17, 2007 Georgia Tech / ORNL Bioinformatics Conference 1

Opportunities at the NIH

Peter Good, Ph.D. NHGRI

November 17, 2007

6th Georgia Tech / ORNL International Conference on Bioinformatics


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


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


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


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


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.


April, 2003April, 1953


Notes From the Front Lines of the Genomic Revolution

• Comparative genomics is providing a wealth of information about the human genome

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




• DNA sequencing is undergoing revolutionary technical advances


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


http://cancergenome.nih.gov



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


NIH Roadmap for Medical Research

ACCELERATING MEDICAL DISCOVERY TO IMPROVE HEALTH

www.nihroadmap.nih.gov

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


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


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





• Experimental approaches to determining genome function are moving forward rapidly

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


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





• Experimental approaches to determining genome function are moving forward rapidly

• Genetic factors in many common diseases are being rapidly revealed

Progress in Genotyping Technology

1 10 102 103 104 105 106

Nb of SNPs

Cost

per

gen

oty

pe

(Cen

ts,

US

D)10

1

102

ABITaqMan

ABISNPlex

IlluminaGolden

Gate

IlluminaInfinium/

Sentrix Affymetrix

100K/500K

Perlegen

Affymetrix

MegAllele

2001 2005

Affymetrix

10K

Courtesy S. Chanock, NCI

26 Georgia Tech / ORNL Bioinformatics Conference November 17, 2007

CholesterolObesityCoronary DiseaseQT intervalAtrial FibrillationType 2 Diabetes Prostate cancerBreast cancerColon cancer

KCNJ11

2003

2000

PPAR

2001

IBD5NOD2

2005

2006

2002

CTLA4

2004

PTPN22

Age Related Macular DegenerationCrohn’s DiseaseType 1 DiabetesSystemic Lupus ErythematosusAsthmaRestless leg syndromeGallstone disease

CD25IRF5

PCSK9CFH

NOS1APIFIH1

PCSK9CFB/C2

LOC3877158q24IL23R

TCF7L2

2007

CDKN2A8q24 #28q24 #38q24 #48q24 #58q24 #6

ATG16L15p13

10q21IRGM

NKX2-3IL12B3p211q24

PTPN2TCF2

CDKN2AIGF2BP2CDKAL1

HHEXSLC30A8

MEIS1LBXCOR1

BTBD9C3

8q24ORMDL3

4q25TCF2GCKRFTO

C12orf30ERBB3

KIAA0350CD22616p13PTPN2SH2B3FGFR2TNRC9

MAP3K1LSP18q24

Confirmed genetic contributors to common human diseases (August 2007)


A partnership to advance the genetic analysis ofADHD

Diabetic nephropathySchizophreniaSchizophreniaBipolar illnessBipolar illness

PsoriasisPsoriasisMajor depressionMajor depression


Genes and Environment Initiative

EXPOSURE BIOLOGY PROGRAM

Identify genetic

variants

GENETICS PROGRAM

GXEDevelop technology and biomarkers

• GWA Studies

• Data Analysis

• Replication

• Sequencing

• Database

• Function

• Translation

• Diet• Physical Activity• Environmental Exposures• Psychosocial Stress and

Addictive Substances



Peter Good

National Human Genome Research Institute

[email protected]

Documents

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