PHARMACOGENOMICS ANALYSIS LABORATORY

Cooperative Studies Program (CSP)Office of Research & Development,

Department of Veterans Affairs

Central Arkansas Veterans Healthcare System (CAVHS)

Little Rock, AR

CSP ORGANIZATION

VETERANS HEALTH ADMINVETERANS HEALTH ADMINOffice of Research &Office of Research &

DevelopmentDevelopment

VETERANS HEALTH ADMINVETERANS HEALTH ADMINOffice of Research &Office of Research &

DevelopmentDevelopment

BiomedicalLaboratory

R&D

RehabilitationR&D

Clinical Science

R&D

Health Services

R&D

Cooperative Studies Program

Pharmacogenomics Analysis Laboratory (PAL)

CSP MISSION

To advance the health and care of Veterans through collaborative research studies that produce innovative and effective solutions to national healthcare problems.

CSP OVERVIEW

• CSP is a national infrastructure for sponsoring, developing & executing: Multi-site clinical trials Epidemiological & population research Genomics research

• First Cooperative Study conducted in 1940s on streptomycin for treating tuberculosis in WWII veterans Program formally established in 1972

• Over 175 clinical trials and observational studies completed including landmark studies in cardiovascular disease / cardiovascular surgery, infectious diseases, surgery, gastroenterology, mental health, oncology, and endocrinology.

CSP CENTER LOCATIONS

West Haven, CT

Seattle, WA

Palo Alto, CA

Albuquerque, NM

Durham, NC

Hines, IL

Washington, DC

Perry Point, MD

Boston, MA

Little Rock, AR

VA Genomic Medicine Program

• In 2006, the Department of Veterans Affairs launched the Genomic Medicine Program:

to examine the potential of emerging genomic technologies

to optimize medical care for veterans to enhance the development of tests and

treatments for relevant diseases

• Genomic Medicine Program Advisory Committee

• Veterans’ Consultation Project 83% supported; 71% willing to participate

• Scientific Projects Investigator-initiated Large scale cohorts (SMI, PTSD, ALS)

Million Veteran Program (non-disease based)

Genomic Medicine Program Con’t

Infrastructure Development

Expansion of Biorepository CSP DNA Bank (~30,000 samples) Expansion to ~4M; robotic store; automation

IT and Informatics Genomic Information System for Integrated

Sciences(GenISIS) Pharmacogenomics Laboratory (PAL)

Established in 2007

Pharmacogenomics Analysis

Laboratory (PAL)

•CLIA88 approved laboratory with capacity to conduct medium to high throughput genotyping and gene expression assays.

•Support ongoing and future pharmacogenomics observational studies and clinical trials.

•Improving treatment of most illnesses by reducing toxicity and increasing efficacy of drugs by facilitating optimal treatment selection, appropriate dose individualization, and drug discovery.

PAL Organizational FlowChart

Dr. Steven A. Schichman

PAL Director

Weleetka Carter, Maria Winters, Angie Stone

DIRECTOR Steven A. Schichman, M.D., Ph.D.

DNA Purification & Quantification

RNA Purification & Quantification

Gene Expression

miRNA

SNP Genotyping

Copy Number, EpiGenetic Events

Data Analysis & Final Reports

Protein Analysis

Protein Quantification

PAL

ABI Taqman, Illumina iScan & BeadXpress

ABI Taqman, Illumina iScan & BeadXpress

ABI Taqman, Illumina iScan & BeadXpress

ABI Taqman

Illumina BeadXpressNanoDrop UV/Vis, Agilent Bioanalyzer

NanoDrop UV/Vis, Agilent Bioanalyzer, Biotek Plate Reader (PicoGreen Fluorescence)TaqMan RNAse P

NanoDrop UV/Vis, Agilent Bioanalyzer, Biotek Plate Reader (RiboGreen Fluorescence)TaqMan RNAse P

CAVHS

miRNA

ABI 7900HT TaqMan System

The ABI 7900HT (Applied Biosystems, Inc., Foster City, CA) is a PCR-based, real-time thermal cycling instrument with fluorescence detection for low-to-moderate throughput genotyping and gene expression

Applications Supported by ABI7900HT TaqMan

Genotyping by Allelic Discrimination Real-Time Quantification

Gene Expression Copy Number Variation

Illumina iScan System

•iScan microarray scanner (Illumina, Inc., San Diego, CA) is a confocal laser scanner with dual fluorescent channels for imaging Illumina’s array-based genetic analysis products. •Automation with the AutoLoader2 provides high-throughput scanning.

Copy Number Variation: Discovery and AnalysisBeadChip Genotyping Array: Whole-Genome SNP Analyses, Cytogenetic Analysis, Linkage Profiling

0 10000 20000 30000Control_AVG_Signal

Gene Expression

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20000

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Whole-Genome Expression Profiling, Differ-ential Gene Expression, microRNA profiling

Whole-Genome Methylation Analyses, Differential Methylation, Dendrograms (Cluster Analysis)

iScan Applications

Illumina iScan Array Products

Illumina BeadXpress System

Illumina’s BeadXpress Reader is a dual-color laser detection system for custom low- to mid-plex genotyping, methylation analysis, SNP detection and protein screening.

ADME Core Panel for Pharmacogenetic Genotyping

► Investigate genetic associations to drug

• Response• Dosing• Safety

► Personalized Medicine

*Absorption, Distribution, Metabolism, and Excretion

VeraCode ADME Core Panel

ADME Core (34 genes, 184 markers)

ABCB1 CYP2C9 NAT1 SULT1A1

ABCC2 CYP2D6 NAT2 TPMT

ABCG2 CYP2E1 SLC15A2 UGT1A1

CYP1A1 CYP3A4 SLC22A1 UGT2B15

CYP1A2 CYP3A5 SLC22A2 UGT2B17

CYP2A6 DPYD SLC22A6 UGT2B7

CYP2B6 GSTM1 SLCO1B1 VKORC1

CYP2C19 GSTP1 SLCO1B3

CYP2C8 GSTT1 SLCO2B1

>95% Pharma ADME Core List: www.pharmaadme.org

IT Requirements

• Large capacity Terabyte Servers

• 64-Bit Computers

• GenomeStudio Software Suite

• Statistical Discovery Software

CSP 500b: Genetic Epidemiology of Amyotrophic

Lateral Sclerosis (ALS)• GWAS analysis by Affymetrix & Illumina platforms

completed• 1200 ALS patients ; 400 Controls

• Analysis of data ongoing at the Durham VA and Duke University

CSP Study Update

Durham VA Medical Center

North Carolina

Principal Investigators in CSP500b:Durham VAMC and Duke University Medical Center, NC

Eugene Z. Oddone, M.D., M.H.S.Silke Schmidt, Ph.D.Dawn Provenzale, M.D., M.S.Michael A. Hauser, Ph.D.

Boston MAVERIC and Tissue Core Biorepository, MAMary Brophy, M.D.Donald E. Humphries, Ph.D.

Summary

• PAL serves as a national VA resource for various molecular, genetic and genomic analyses (low to high throughput)

• Isolation to data analysis

• CLIA certified