Discovering Disease Genes- The Example of Schizophrenia

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Discovering Disease Genes- The Example of
Schizophrenia
Pippa Thomson, Medical Genetics Section, Dept of
Medical Sciences, MMC, University of Edinburgh.
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Importance of the illness

• Severe psychiatric
• Affects 1 of the population
• One of the top 10 causes of disability worldwide
• Economic cost (23 Drug, 14 Hospital)
• Pharmacological rationale for treatment weak or
  absent
• 1/3rd patients unresponsive or experience
  unacceptable side effects
• Strong genetic component
• concordance rate between identical twins of 60

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Altered brain structure function
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High Heels Cause Schizophrenia and 6 Other
Outlandish Medical Theories
2. High-heeled shoes cause schizophrenia. You
have to wonder where some medical theories
originate. Why did Swedish scientist Jarl
Flensmark decide to study a connection between
heeled shoes and the incidence of schizophrenia?
The world may never know. But his initial
research seems sound, and he has connected
certain brain activity with stimulation of
certain points on the feet. The spread of
schizophrenia around the globe has closely
followed the spread of availability of heeled
shoes. Is it an eerie coincidence or a real cause
for concern? Look out, men - this theory applies
not only to stilettos, but to any shoe with a
heel.
remedicated.com
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Relative risk of developing Schizophrenia
Environment !
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Benefits of gene identification

• Understand aetiology
• Improved drug development testing
• Development of definitive diagnostic tests
• Understanding of interaction with non-genetic
  risk factors
• Insight into normal brain development function

Kraepelin, 1896 As we do not know what causes
the illness there cannot be a rational treatment
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Allelic architecture and mapping strategy
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Locus Identification-problems

• Uncertainty in diagnostic boundaries
• Non-Mendelian inheritance
• Variable age of onset
• Genetic heterogeneity
• Many different genes can cause the illness
• 1 risk world wide
• phenotypic variation
• Oligogenic/polygenic causation
• More than one mutant gene required to produce
  phenotype

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Locus identification- reducing the problems

• Single large families
• Avoid bilineal descent
• rigorous interviews
• family history
• Reduce genetic heterogeneity
• Significant LOD score gene of major effect
• Reduce uncertainty of diagnosis
• classify minor diagnoses as unaffected
• gt1 category of affected phenotype

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Linkage Analysis

• Marker analysis in multiply affected family or
  families
• Look for co-segregation of a particular allele
  with phenotype
• Results expressed as a LOD score (Significant at
  gt 3)
• log (likelihood of data, if locus disease
  are linked)
• ---------------------------------------------
  -------------------
• (likelihood of data, if locus disease are
  not linked)
• Generally a large region is identified

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A balanced t(111)(q42q14) translocation
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t(111) co-segregates with major mental illness
translocation increases risk by 50-fold
?
schizophrenia
(111)(q42q14) translocation
recurrent major depression
unaffected
bipolar affective disorder
minor diagnosis
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Controls
Schizophrenics

• Genetic association studies seek to relate
  variation in human DNA sequence with a disease or
  trait
• Association method provides greater power to
  detect common genetic variants conferring
  susceptibility to complex phenotypes
• Estimates population attributable risk (effect
  size)
• Controls should match cases and be a
  representative sample of the population.

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Case-control association studies

• Comparison of frequencies of polymorphisms
  between populations of cases and controls
  (usually a simple chi-square test or logistic
  regression)
• Polymorphism studied can be directly responsible
  for the defect ? frequency of cases gtgtgt
  controls
• Polymorphism studied can be in linkage
  disequilibrium with the mutation responsible for
  the disease ? T cases gtgt controls
• Association studies can be conducted for
  candidate genes, or through a whole region or
  across the whole genome (WTCCC)

p
Mb
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International HapMap project
SNPs are genotyped in parent-offspring trios,
initially in CEPH trios. This can be used to
identify SNPs that co-segregate (i.e. are in
linkage disequilibrium) versus those that
segregate independently. A subset of SNPs can
therefore be chosen that best represent the
genetic diversity in a region/gene, reducing the
costs of genotyping. Summary of genotyped SNPs
Populations CEU CHBJPT YRI Total
Non-Redundant 3,204,709 3,244,897
3,150,433
http//www.hapmap.org/
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Region of interest
HapMap genotyped SNPs
Known SNPs
Known genes in the regions
Linkage Disequilibrium (LD)
http//www.ncbi.nlm.nih.gov/SNP/
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Tagging SNP selection
Proportion of haplotype diversity explained
SNPs 1-23 - 97 SNPs 24-46 - 98
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Genetic evidence implicating DISC1 in psychiatric
illness
LOD7.1, SCOTLAND
SCZ BPAD MDD
TRANSLOCATION
p0.0044, p0.0016
SCOTLAND
SCZ, BPAD
HAPLOTYPE
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DISC2
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Genes for Schizophrenia ?
gt130 genes implicated
Table 1. Summary of current evidence supporting
several of the more promising genes implicated in
schizophrenia, bipolar disorder, and mixed
bipolar-psychosis phenotypes
Craddock et al., SCZ Bulletin, 2006
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DISC1 interactome protein-protein interactions
Chris Carter, http//www.polygenicpathways.co.uk/d
isc11_vml.htm
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Effects of altered DISC1 on gene expression

• ENU generated mouse mutants
• Two independent lines with missense mutations in
  DISC1 exon 2
• Q31L (Glutamine-Leucine)
• Q- hydrophillic L hydrophobic
• L100P (Leucine-Proline)
• Predicted to cause transition in polypeptide
  chain direction
• Normal levels of DISC1 protein in brain
• L100P line models schizophrenia Q31L, depression

Clapcote et al., Neuron. 2007 May
354(3)387-402.
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Effects of Altered DISC1 on Behaviour (How do you
know if a mouse is schizophrenic?)
Schizophrenia
Depression
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Effects of altered DISC1 on gene expression

• Samples collected and microarray study ongoing
• Mutated lines vs background strain (C57/BL6)
• 47,000 transcripts
• Hippocampus
• Adult and embryonic stage- Microarray
• Confirmation/Investigation of changes
• Series of embryonic postnatal and adult stages
• Drug treated adult mice

Detect disrupted pathways
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Whole genome sequencing

• Resequencing, SNP detection, genome comparisons,
  gene expression, transcription factor studies,
  small RNA analysis
• Individual genomes All SNPs in each individual
• Currently
• Using the Illumina 1G to sequence genes in the
  DISC1 pathway.
• Total sequence read 3.5megabases in 1200
  individuals
• Identify coding and non-coding polymorphisms
• Mutation detection
• Detection of variants in conserved regions
• Detection of variants affecting binding of
  transcription factors

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Psychiatric Genetics-Unanswered Questions

• How many susceptibility genes are there? What is
  their function? Is function conserved across
  species? Can we relate gene (dys)function to
  mental (dis)order? Do gene variants predict risk,
  course, outcome and response to treatment? Will
  gene discovery lead to drug discovery? How do
  genes and environment interact? How and when will
  the patient benefit?

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Acknowledgements
DISC1 Kirsty Millar Shaun Mackie Fumiaki
Ogawa Jennifer Chubb Becky Carlyle Nick
Bradshaw Sheila Christie Steve Clapcote Kathy
Evans Sarah Brown William Hennah
Medical Genetics Prof David Porteous Prof
Douglas Blackwood Walter Muir Ben Pickard Other
collaborators DISC1 Consortium Wellcome Trust
CRF Illumina, San Diego Cold Spring Harbor
laboratories