Genboree Discovery Process Integration

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Genboree Discovery Process Integration

• Aleksandar Milosavljevic, PhD
• Baylor College of Medicine
• January 10th, 2008 modified April 1st 2008.

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Genboree design has evolved to support diverse
discovery processes
Authors Gonzalez-Garay, M.L.1,2, Morgan, M.B
2, Miller, CA1,3, Jackson, A.R. 1,2, Tong,
M.1,2 , Gibbs, R.A.2,3, Milosavljevic,
A.1,2,3 1Bioinformatics Research Laboratory
2Human Genome Sequencing Center, Department of
Molecular and Human Genetics 3Program in
Structural and Computational Biology and
Molecular Biophysics, Baylor College of
Medicine, Houston, Texas, USA
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Genboree design has evolved to support diverse
discovery processes

• Genome sequencing and annotation
• human Ch 3, 12 sea urchin tribolium, nasonia
  bacterial
• Genome comparison
• rat, mammals, rhesus macaque, primates
• High-throughput microchip analysis
• array CGH, BCM cytogenetics laboratory
• DNA sequencing
• PCR-based resequencing mapping rearrangements
  in cancer genomes using next generation
  sequencing technologies

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Genboree software development

• Understanding of users needs and opportunities
• Focus on complete process
• Identify recurrent use patterns
• Generalize, minimize assumptions for widest use
• Design generic components for reuse across
  projects
• Fast prototyping
• Frequent feedback
• Extensive optimization of key components

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Usage of Genboree.org as of Dec 31 2007

• 923 registered users
• 100 users each working day
• 10,000 clicks per day
• 112 collaborating groups with 2 researchers,
  with a median of 7 and average of 23.5 members
  per group
• many collaborating groups still maintain private
  access to their pre-publication data and
• 23 databases have been made widely accessible via
  internet by the collaborating groups

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Genborees current focusTranslational studies
of genome variation

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Example 1 research at the clinical cytogentics
laboratory at BCM

• Agilent array design for array CGH (version 7)
  identifying hypermutable Low Copy Repeat regions
  for deeper probing
• Analysis of a single case
• Upload Agilent array data
• Perform segmentation (invoke Bioconductor tool)
• Subtract polymorphisms (databases, current
  literature)
• Establish preliminary diagnosis/ hypothesis
• Integrate downstream data ( paternal testing,
  FISH, etc.)
• Share diagnosis and data view with reporting
  physician
• Identify recurrent events (based on BCM database)
• Identify new syndromes

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Translational studies of genome variation

High volume anchoring (by Pash 2.0) integrated
with Genboree
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Genboree overview


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Integration of Genboree into caBIG
infrastructure and caGRID


Current state
Integrated state
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Example 3 Pilot TCGA pilot project

• Target selection ( Target Selection Group, Mr.
  Chris Miller, Dr. Anna Lapuk)
• Data integration (Level 3,4 data)
• Collaborative target selection
• Target allocation across centers (Manuel)
• PCR assay design integration with the HGSC LIMS
  system for probe design hole filling,
  polymorphisms, repeats, tiling (Dr. Manuel
  Gonzalez-Garay)
• Quarterly Report for PCR resequencing (Dr. Manuel
  Gonzalez-Garay)
• ( Mutation annotation, sharing of PCR assays,
  prioritization of mutations for collaborative
  downstream studies )

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TCGA Project Quarterly Resequencing Report
Annotation object - viewer - editor - PCR primer
designer - other tools

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TCGA Project Quarterly Resequencing Report
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Key challenge lowering threshold to adoption of
genomic technologies by clinical researchers

• Key challenge Integration of discovery
  processes.
• -gt Integration of data and tools required but
  not sufficient.
• Genboree follows internet-based hosting
  model
• (Software as a Service).
• -gt No installation, maintenance, needed.
• -gt Open source release in Q2 2008.
• -gt Commercial launch of the Genboree Early
  Access Hosting program ( www.genboree.com ) on
  March 1st 2008.