Supporting high throughput high-biotechnologies in today’s research environment trends in...

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SJCRH

Supporting HighSupporting High--throughput throughput BiotechnologiesBiotechnologies in Today’s in Today’s

Research EnvironmentResearch Environment

Clayton W. Naeve, Clayton W. Naeve, PhPh.D..D.

SJCRH

OverviewOverview• Trends in Biomedical Science.• Options.• Organization.

– St. Jude Children’s Research Hospital– Hartwell Center and Molecular Biotechnology

• Integrated Services– High-throughput DNA Sequencing & Genotyping

– Macromolecular Synthesis– Functional Genomics (cDNA microarray laboratory)

– Clinical Applications Core Technology (Affymetrix laboratory)– Proteomics/Mass Spectrometry

– Bioinformatics• Impact• Oversight• Space• Budget• Staff• Summary - Keys to Success

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Trends in Biomedical ScienceTrends in Biomedical Science

• Multidisciplinary– genetics, molecular biology, computer sciences, mathematics, biostatistics, bioinformatics……

– departmental distinctions are blurring.

– multidisciplinary programs emerging to address specific problems.

• High-throughput– High-throughput biotechnologies becoming critical to competitiveness.

• DNA microarrays.

• Proteomics/Mass spectrometry.• HTS.

• High-throughput DNA sequencing.

• High-throughput SNP detection.

• High-throughput structure analysis.

• Bioinformatics dependent– High-throughput methods.

– HGP etc.

How does an institution provide these “resources” to remain

competitive?

SJCRH

OptionsOptions

• Outsourcing.

• Individual faculty supported biotechnologies.

• Distributed shared resources.

• Consolidated or integrated shared resource(s).

Less Desirable

More Desirable

Hartwell Center for Bioinformatics & Biotechnology@

St. Jude Children’s Research Hospital

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Hartwell Center Hartwell Center -- OrganizationOrganization

St. Jude Children’s Research HospitalSt. Jude Children’s Research Hospital

– 180 Faculty (~100 basic and ~80 clinical).– 200 postdoctoral fellows.

– 16 laboratory-based research departments.– $250M annual budget, ~$50M derived from research grants.

– Major expansion plan announced in 1999.

SJCRH

Hartwell Center Hartwell Center -- OrganizationOrganization

Hartwell Center (Service) Molecular Biotechnology (Research)

CACT

HT Sequencing.

MacromolecularSynthesis

FunctionalGenomics

Proteomics/MS

Bioinformatics 6 faculty6 postdoctoral fellows

Director, SJCRH

Deputy Director, SJCRH

Director, Hartwell Center

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• Services:– DNA sequence analysis using high-throughput

methods (robotics, automated sequencers, bioinformatics).

– Genotyping/SNP analysis (FY01).• Resources:

– Instrumentation:• Biomek 2000 robot.• four MJR thermalcyclers .• two ABI 3700 DNA sequencers.• one ABI 3100 Genetic Analyzer.

– Bioinformatics resources:• On-line ordering/tracking.• hcWebFetch (sequence retrieval).• Sequence archives, etc.• Data analysis.

• Staff: 3 staff members.

• Production:– ~1,000,000 bases per month.– >50,000 templates/year.

Hartwell Center Hartwell Center -- ServicesServicesHighHigh--throughput DNA Sequencing & Genotypingthroughput DNA Sequencing & Genotyping

SJCRH

Hartwell Center Hartwell Center -- ServicesServicesMacromolecular SynthesisMacromolecular Synthesis

• Services– Organic synthesis of DNA and protein molecules (using

automated instruments).

• Resources– Instrumentation:

• one PE/ABI 394 DNA synthesizers.• two PE/ABI 3900 (48 col.) DNA synthesizer.• two PE/ABI 431 peptide synthesizers• one Advanced ChemTech 396 MPS.• one Rainin Symphony Multiplex (12 col.)• analytical and preparative HPLCs.

• Staff: 3 staff members.

• Production:– 10,000 oligonucleotides/year (66,000 oligo’s to date).– 1,500 peptides/year (5,346 to date).

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Hartwell Center Hartwell Center -- Services Services Functional GenomicsFunctional Genomics

• Services– The measurement of gene expression using DNA

microarray technology.• cDNA library management

– 75,000 cDNA clones (mouse and human)• Dye-labeling (direct or indirect)• cDNA microarray production• hybridization• scanning, gridding, data upload to ArrayDB

• Resources– Instrumentation:

• Flexys (library management)• HiGro (clone growth)• RevPrep (plasmid preps)• MWG RoboAmp (PCR reaction setup)• Qiagen Biorobot 3000 (PCR reaction cleanup)• OmniGrid (arrayer)• GeneTAC• ScanArray 5000 & ScanArray Lite

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Hartwell Center Hartwell Center -- ServicesServicesFunctional GenomicsFunctional Genomics

– Bioinformatics:• ScanArray• ScanAlyze (image analysis)• ArrayDB (array database, Oracle version)• GenExplore (cluster analysis software)• GenoMax• Spotfire

• Staff: 3 staff members.

• Production:– 75 hybridizations in first month.

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Hartwell Center Hartwell Center -- ServicesServicesClinical Applications Core TechnologyClinical Applications Core Technology

• Services– Measure gene expression levels using oligonucleotide

microarrays and develop clinical applications for the technology (GeneChips, Affymetrix, Inc.).

• RNA QC using Agilent “Lab-on-a-Chip”.• Biotin-labeling target RNA.• Hybridization to GeneChips.• Image analysis.• Bioinformatics support.

• Resources– Affymetrix GeneChips (human, mouse, cancer gene,

yeast, etc.)– Instrumentation

• Hybridization oven (2).• Fluidics workstations (3).• scanning laser confocal reader (2).• computer workstation (4).

– Bioinformatics Resources• Affymetrix LIMS. , GenExplore, Spotfire, GenoMax.

• Staff: 2 staff members.• Production:

– 900 GeneChips in first 9 months.– 40-50 arrays/week. SJCRH

Hartwell Center Hartwell Center -- ServicesServicesProteomicsProteomics/Mass Spectrometry/Mass Spectrometry

• Services– High-throughput protein identification.

• 2-D gel analysis• Mass spectrometry

• Resources– Instrumentation:

• ABI 494 cLC Procise Protein Sequencer.• ABI 177AMicroblotter.• Biacore 3000.• PerSeptive Biosystems, Inc. Voyager DE RP MALDI -TOF mass spectrometer.• Finnigan LCQdecca ion-trap mass spectrometer.• Micromass LCT.• Michrom Magic capillary LC system.• Waters Masslynx capillary LC system.• Fuji LAS1000 image analysis system.

– Bioinformatics resources:• Xcaliber, SEQUEST, Protein Prospector, etc.

• Staff: 5 staff members.• Production:

– Microsequence analysis (200 samples/year, 1,300 to date).– Molecular Interaction analysis (Biacore, 1600 samples to date)– Mass Spectrometry (2,700 samples/year, 8,556 total).

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Hartwell Center Hartwell Center -- Services Services BioinformaticsBioinformatics

• Services– Bioinformatics Support [~1000 user accounts].

– High-Performance Computing Environment.– Hartwell Center laboratory support.

• Resources– Computer Hardware:

• Compaq GS140 (10 cpus, 12 Gb RAM); Oracle DB server.• SGI InfiniteReality OnyxII (16 cpus, 9 Gb RAM);

Applications/Graphics server.• SANs system (6 Tb disk storage, 7 Tb tape backup system)• many other small systems supporting various applications.

– Software/Databases:• DNA/Protein Sequence Analysis Software (Vector NTI,

GenoMax, GCG, Spotfire, etc.)• DNA/Protein Sequence Databases (all public, Celera , etc.• ArrayDB and Affymetrix LIMS system for array data• Hartwell Center Database (invoicing, on -line

ordering/tracking, etc.)– -Internet Resources:

• Firewall• Internet Connectivity (T3 lines)

• Staff: 10 staff members.High-Performance Computing Facility

SJCRH

• Scientific Impact– DNA Sequence Analysis: 191,074 templates; 69,500,000 base pairs.

– DNA Synthesis: 65,911 oligonucleotides; 1,690,000 base pairs.– Peptide Synthesis: 5,346 peptides; 67,246 couplings.

– Protein Sequence Analysis: 1,321 samples; 13,030 residues.

– Mass Spectrometry: 8,556 samples.

– Affymetrix GeneChip Analysis: >900 samples in first 9 months.– cDNA Microarray Hybridizations: 75 samples in first month.

– Bioinformatics support for ~1000 users

– Contributions to hundreds of publications, grant applications, etc.

– Key role in numerous discoveries.

• Organizational Impact– Promotes collaborative studies.

– Promotes the application of state -of-the-art technology in research efforts

– Financial savings realized by consolidation• common database for invoicing.

• single on-line ordering/tracking system.

• single administrative staff.

• Recruiting Impact– Key role in recruiting new faculty, department chairs, postdoctoral fellows, staff.

– Impacts fund-raising.

Hartwell Center Hartwell Center -- ImpactImpact

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Hartwell Center Hartwell Center -- OversightOversight

• Hartwell Center Scientific Advisory Board– External scientific advisory group; meets yearly.

– Boguski , Meltzer, Burlingame, States, Curran, Downing• Hartwell Center Advisory Board

– Internal advisory group; meets quarterly.– benefactor, 4 members of ALSAC Board of Governors, Deputy Director, 2 Dept.

Chairs.

• Hartwell Center Liaison Group– Internal departmental representatives; meets bi-monthly.

– 21 representatives from all laboratory-based departments at SJCRH.

SJCRH

Hartwell Center Hartwell Center -- SpaceSpaceHigh-throughput DNA Sequencing & Genotyping 440 sq. ft.Macromolecular Synthesis 440 sq. ft.Functional Genomics 660 sq. ft.Proteomics 660 sq. ft.Mass Spectrometry 500 sq. ft.Clinical Applications Core Technology 800 sq. ft.Bioinformatics 3000 sq. ftAdministrative/office space 1000 sq. ft

Total 7,500 sq. ft.

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Hartwell Center Hartwell Center -- BudgetBudget

Budget FY 2000 FY 2001 FY 2002

Opera t i ng $ 3 , 4 2 7 , 0 2 6 $ 4 , 5 8 8 , 9 2 0 $ 5 , 2 3 6 , 6 6 4

C a p i t a l & R e n o v a t i o n s 4 ,433 ,689 2 ,622 ,000 2 ,312 ,000

Ind i rec t Cos ts 1 ,960 ,729 2 ,339 ,214 2 ,578 ,699

S u b t o t a l 9 ,821 ,444 9 ,550 ,134 1 0 , 1 2 7 , 3 6 3

Less : Mo lecu la r Pa tho logy (1 ,495,300) (1 ,063,496) (1 ,132,436)

Tota l Hartwel l Center $ 8 , 3 2 6 , 1 4 4 $ 8 , 4 8 6 , 6 3 8 $ 8 , 9 9 4 , 9 2 7

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Hartwell Center Hartwell Center -- StaffStaff

• C l a y t o n W . N a e v e , P h. D .

• C l i v e S laugh te r , P h. D .

• B r e n d a A l n e m y

• K r i s h n a S a n k h a v a r a m

• A n d r e w P a p p a s

• S c o t t M a l o n e

• P e r d e e p M e h t a , P h. D .

• Bill P a p p a s

• M a t t S t i n e

• Karen R a k e s t r a w

• M a r g a r e t C i r t a i n

• S t e v e n T u r n e r

• S c o t t O l s o n

• A n u S a n k h a v a r a m

• P h i l i p P o s t o n, P h. D .

• C h r i s t p h e r P e t u c c i , P h. D .

• C h r i s t i n e S h a m b l i n

• B o b C a s s e l l

• S t e p h a n i e T a t e

• D e a n n a N a e v e

• L i l i M a l e k i

• B i l l Lewi s , P h. D .

• D i v y e n Patel , P h. D .

• D a w n W i l k i n s , P h.D . ,V i s i t i ng Sc i en t i s t

• Er i c D u n c a v a g e, In te rn

• J e n n i f e r C a m p b e l l

• J o h n M o r r i s

• A s h u t o s h M i s h r a

• V i c k i B e a l

• Pa t r i c i a Fo rd

3 0 s t a f f t o t a l , 7 Ph .D.s

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Summary Summary -- Key Elements to SuccessKey Elements to Success

• S t r a t e g i c P l a n n i n g– Applied sciences/services must be integral to institution’s research plan.

– Scientific direction must guide the deployment of biotechnologies.

• L e a d e r s h i p– Multidisciplinary expertise.

– Vision.

• A t t r a c t i v e C a r e e r P a t h– “Service” is not a pejorative word.

– Appropriate career ladder to attract and retain skilled staff.

• I n t e g r a t i o n o f K e y T e c h n o l o g i e s– Depends on research environment.

– High -throughput biotechnologies likely required.

– Bioinformatics essential.

• S c i e n t i f i c O v e r s i g h t– Critical to help guide development, establish strategic plan, ov ersee progress.

• B u d g e t S u p p o r t– Appropriate and consistent to meet institutional needs.

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Hartwell Center Web SiteHartwell Center Web Site

http://www.hartwellcenter.org

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Thank You!