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 ADMIN Office of Research & Development Biomedical Laboratory R&D Clinical Science R&D

Cooperative Studies Program

Health Services R&D Rehabilitation R&D 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 Seattle, WA Palo Alto, CA Albuquerque, NM Hines, IL Little Rock, AR Boston, MA West Haven, CT Perry Point, MD Washington, DC Durham, NC

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 Con’t

• 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)

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

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

LABORATORY MANAGER Angie Stone, B.S.

Weleetka Carter, Maria Winters, Angie Stone Dr. Steven A. Schichman PAL Director PROJECT MANAGER Maria Winters, M.P.H. PROJECT COORDINATOR Weleetka Carter, B.S.

Gene Expression RNA Purification & Quantification NanoDrop UV/Vis, Agilent Bioanalyzer, Biotek Plate Reader (RiboGreen Fluorescence) TaqMan RNAse P DNA Purification & Quantification NanoDrop UV/Vis, Agilent Bioanalyzer, Biotek Plate Reader (PicoGreen Fluorescence) TaqMan RNAse P ABI Taqman, Illumina iScan & BeadXpress

PAL

ABI Taqman SNP Genotyping Data Analysis & Final Reports ABI Taqman, Illumina iScan & BeadXpress Copy Number, EpiGenetic Events ABI Taqman, Illumina iScan & BeadXpress

CAVHS

Protein Quantification Protein Analysis NanoDrop UV/Vis, Agilent Bioanalyzer Illumina BeadXpress

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 AutoLoader 2 provides high-throughput scanning.

iScan Applications

Copy Number Variation: Discovery and Analysis

Gene Expression 30000

BeadChip Genotyping Array: Whole-Genome SNP Analyses, Cytogenetic Analysis, Linkage Profiling

20000 10000 0 0 10000 30000 20000 Cont rol_AVG_Signal

Whole-Genome Expression Profiling, Differ ential Gene Expression, microRNA profiling Whole-Genome Methylation Analyses, Differential Methylation, Dendrograms (Cluster Analysis)

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 ABCC2 ABCG2 CYP1A1 CYP1A2 CYP2A6 CYP2B6 CYP2C19 CYP2C8 CYP2C9 CYP2D6 CYP2E1 CYP3A4 CYP3A5 DPYD GSTM1 GSTP1 GSTT1 NAT1 NAT2 SLC15A2 SLC22A1 SLC22A2 SLC22A6 SLCO1B1 SLCO1B3 SLCO2B1 SULT1A1 TPMT UGT1A1 UGT2B15 UGT2B17 UGT2B7 VKORC1 >95% Pharma ADME Core List: www.pharmaadme.org

IT Requirements

• Large capacity Terabyte Servers • 64-Bit Computers • GenomeStudio Software Suite • Statistical Discovery Software

CSP Study Update

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

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, MA

Mary Brophy, M.D.

Donald E. Humphries, Ph.D.

Durham VA Medical Center North Carolina

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