Genomic, mRNA and Array Probes and Tools

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Genomic, mRNA and Array Probes and Tools
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Human Genome Project and Competitors

• Human genome project --NIH, etc
• Full sequence by 2003-2005
• Including genes and other Genomics regions
• Incyte
• 140,000 genes, in process, IP problems
• Celera
• Interesting approach-- overlapping clones
• IP problems
• July, 00?

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Expressed Sequence Tag
AAAAAAA
3 UT
5 UT
TTTTTTTT
EST
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Hybridization
A C A T T G C G
T G T A A C G C
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Selecting Genes to Pursue

• Consistent Responsiveness of the Gene to the
  Illness across Subjects.
• Pattern of Responsiveness of the Gene across
  Brain Regions.
• Type of Protein which is Encoded by the Gene.
• Presence of an Understandable Profile of Altered
  Regulation as Part of an Ensemble.
• Additional Considerations
• Existence of Allelic Variants
• Modulation by Antidepressants in Animals
• Selective Effects in Specific Types of Depression
  

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Gene Array Analysis form Hypothalamus of
Antidepressant Treated Rats
Gene A
Gene B
Gene C
Gene D
Gene E
Gene F
Gene G
Saline
Saline
Bupropion
Fluoxetine
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GAPIII mRNA In Situ Hybridization
Gene Array GAP III
saline
165

fluoxetine
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Overview of µMArray System

• Research Genetics Sequenced Verified Clones- Rat,
  Mouse and Human-Funded by the U of Michigan
• One EST per Unigene Cluster-- an interesting and
  moving target--Number of Genes, Cost, Variable
  Arrays...
• Mother Node is MHRI and Psychiatry
• STS Human Probes from Stanford Human Genome
  Center
• Co-Directed by Thompson and Meng

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Overview of µMArray System
Research Investigators
cDNA clones from RG
Data entry, retrieval and analysis via Web
interface
Clone Management
Clone Replication
MARRAY Database (Oracle 8i)
Image Processing Software
Data Uploading
PCR products
Retrieve Raw Images
ARRAY
Glass Slides
Array Hybridization
Raw image files
Cye3/Cye5-labeled cDNA Probes
mRNA from candidate tissues
Note Process FlowData Flow
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Bioinformatics and Special Chips

• Need ANY Help We Can Get
• U of M is Looking into Deals with Affymetrix,
  Celera and Incyte. Huda and I are the Hosts/Lead.
• Use all Public Data Sources
• Plan Studies of Circuits and Systems to See How
  They Actually Function
• Stanford Guidance
• Debbie Yu and Bay City Capital-Technical Advise

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Aim II Genetic Studies

• Studies of Candidate Genes in Families and
  Population Isolates.

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David Cox is Head of the Stanford Genome Center.
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Affymetrix Chips

• mRNA Expression
• Sequencing By Hybridization
• Drug Metabolism Data

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Aim III Neurobiological Studies

• Rodent Studies
• Anatomical Mapping and Relation to Other Relevant
  Molecules
• Structure/Function Analysis of Protein Products.
• Regulatory Studies in Vivo
• Genetic Studies Using Transgenics, Knockouts and
  Induceable Systems.
• Primate Studies

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Basic Neuroscience Models

• Richest dataset we havemany decades of
  cumulative experience
• Rodent behavioral, anatomical-circuit, molecular
  and pharmacological studies
• Primate- excellent tool for studying human
  fundamentals
• Stanford colony- superb behavioral and genetic
  colony-for all classes of studies
• Michigan/NIH Alcohol Institute- postmortem study
  of selected primate brain

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Technical Update and Changes

• Invader Assay (Stanford, Cox) very sensitive
  and specific. Added this year to the tools we
  plan to use following Arrays
• Shifted Arrays to the U of M Array Lab.
• Internally readjusted work load and finances No
  change in global budget
• This process of technology evaluation will be an
  annual feature of our scientific and budget
  process

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Consortium Agreement and IP Issues

• Nothing is signed, awaiting a common document.
• Scope of Work for all 5 years and 4 sites and a
  firm Year 1 budget for each site has been
  prepared.
• U of M has completed its edits and has verbally
  agreed.
• Stanford seems to be in process.
• UC system has many issues. Tom Barton and the U
  of M office are working with the UC staff to
  explain it.

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Relationships Between the Consortium and the
Network

• Overlap between the two sets of scientists, with
  additional scientific skills available from each
  system.
• Report of the Consortiums progress to the
  Network at the spring meeting.
• Sees the two systems as part of the same
  Foundation structure.
• Natural and preferred collaborators.