A LargeScale, Systematic approach to GenotypePhenotype correlations using workflows

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A Large-Scale, Systematic approach to
Genotype-Phenotype correlations using workflows
Paul Fisher Dr. Robert Stevens Prof. Andrew Brass
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Genotype

• The entire genetic identity of an individual that
  does not show any outward characteristics, e.g.
  Genes, mutations

Genes
DNA
Mutations
ACTGCACTGACTGTACGTATATCT ACTGCACTGTGTGTACGTATATCT
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Phenotype

• (harder to characterise)
• The observable expression of genes producing
  notable characteristics in an individual, e.g.
  Hair or eye colour, body mass, resistance to
  disease

vs.
Brown
White and Brown
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Genotype to Phenotype
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Current Methods
Genotype
Phenotype
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What processes to investigate?
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Microarrays
Expression Data values
Scanned (laser)
Transcribed
Hybridised (bound)
Glass slide
DNA
RNA

• Measure RNA levels in cell under specific
  condition
• Provide detailed information on a genome wide
  scale
• Provides a link between genes and the observed
  characteristic, e.g. Diabetes, Colitis or
  Trypanosomiasis

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Phenotype
Genotype
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Metabolic pathways
Phenotypic response investigated using microarray
in form of expressed genes or evidence provided
through QTL mapping
Genes captured in microarray experiment and
present in QTL (Quantitative Trait Loci ) region
Microarray QTL
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Phenotype
Pathway A
CHR
literature
Pathway linked to phenotype high priority
QTL
Gene A
Pathway B
Gene B
literature
Pathway not linked to phenotype medium priority
Gene C
Pathway C
literature
Genotype
Pathway not linked to QTL low priority
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Issues with current approaches

• Scale of analysis task
• User bias and premature filtering
• Hypothesis-Driven approach to data analysis
• Constant flux of data - problems with
  re-analysis of data
• Implicit methodologies (hyper-linking through web
  pages)
• Error proliferation from any of the listed issues
• Solution Automate through workflows

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The Two Ws

• Web Services
• Technology and standard for exposing code /
  database with an means that can be consumed by a
  third party remotely
• Describes how to interact with it
• Workflows
• General technique for describing and executing a
  process
• Describes what you want to do

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Taverna Workflow Workbench
http//taverna.sf.net
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QTL mapping study
Microarray gene expression study
Statistical analysis
Identify genes in QTL regions
Identify differentially expressed genes
Genomic Resource
Annotate genes with biological pathways
Annotate genes with biological pathways
Pathway Resource
Select common biological pathways
Hypothesis generation and verification
Wet Lab
Literature
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Evaluation through Test cases

• Trypanosomiasis infection (Sleeping sickness)
• Cost billions of US dollars each year for
  trypanocidal agents
• Affects Humans
• native African cattle species resistant, mice
  strains show some resistance
• Mouse model used for study and research purposes
• 3 QTL regions mapped in lab experiments
• Strongest QTL region was analysed using
  workflows, relating to trypanotolerance
• High quality microarray data obtained from mice
  and cattle

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Preliminary Results

• A strong candidate gene was found for
  Trypanosomiasis resistance DAXX
• Daxx not found using manual investigation methods
• The gene was identified from analysis of
  biological pathway information
• Sequencing of the Daxx gene in Wet Lab showed
  mutations that changed the structure of the
  protein
• Mutation was published in scientific literature,
  noting its effect on the binding of Daxx protein
  to another protein other protein controls one
  of the phenotypes of Trypanosomiasis resistance
• FOUND NEW BIOLOGY !!!!

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To Sum Up .

• Shown that by using workflows and a pathway
  approach, we are able to
• Reduced the premature filtering of data sets
• Process all data systematically through the
  workflows
• Support a data-driven analysis approach
• Support hypothesis generation to be inferred
  from the workflow results
• Workflows explicitly captured the data analysis
  methodologies
• Re-use of the workflows in subsequent
  investigations
• The total number of errors reduced

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Questions ?