Transcript Genetics of Schizophrenia - University of Pittsburgh

Genetic research designs
in the real world
Vishwajit L Nimgaonkar MD, PhD
University of Pittsburgh
[email protected]
Complex disorders: models of
causation
Genetic factors: Several genes induce
cumulative, small but discrete effects
+
Environmental factors: etiological role /
increased variability
-No Etiological Factor Necessary or Sufficient
-Formal proof dependent on statistical analyses
Factors influencing
mapping efforts
• What is the phenotype?
• What polymorphisms are being
used?
• What is the study design?
Key phenotype issues
• Is the phenotype heritable?
– Proportion of risk due to genetic
factors?
– Proportion of risk due to an individual
gene (# genes?)
• Familial aggregation does not necessarily
prove genetic etiology
• Can the phenotype be evaluated reliably?
What is the phenotype?
Discrete
Continuous
(disease)
(liability)
0
1
t
(L Almasy, PhD)
Phenotypes
• Qualitative (diagnostic status)
– Clinically relevant
– Difficulties in delineating ‘genetic’ phenotype
• Quantitative (‘endophenotype’)
– Heritable
– Differences between cases and controls
– Differences between unaffected relatives &
controls
– Plausible role in pathogenesis,
proximate to Dx
What polymorphisms?
• Single nucleotide polymorphisms:
SNPs
• Repeat polymorphisms
• Insertions / deletions
What is the study design?
Gene mapping studies: concepts
• Examine correlation between
genetic variation and trait of
interest
• Significant correlation
establishes genetic etiology
Human genome: 3 billion base pairs
(estimated variations = 8,000,000 – 10,000,000)
Problems
1. All genetic variations unknown
2. All variants can not be evaluated
Recombination
Gene mapping concepts
control
Marker A1
Marker B1
case
Marker A2
*Mutation*
Marker B2
Haplotype 1
Recombination based gene mapping
Ill Individual
Transmission Of
Disease Gene
Generations:
1
2
3
n
Healthy Individual
Transmission Of
Normal Gene
Linkage / Association
generations
founder
Linkage
Association
What is the study design?
POSITIONAL CLONING
Step 1: Identify large shared
chromosomal segments
among cases within families
(LINKAGE)
Step 2: Narrow the shared region
using cases and controls
(ASSOCIATION).
Linkage: haplotype sharing
Related issues
• Ascertainment and recruitment!
• Power: more is better! ‘much, much
more’ preferred
• Design modification
– Two stage design (accept lower lod
cutoffs)
– Covariate based analyses
Linkage: affected sib-pairs
(identity by descent)
A,B
C,D
Alleles shared
0
IBD:
Prevalence: 0.25
A,B
A,C
1
0.50
A,B
A,B
2
0.25
ASP analysis
• Convenient design
• Concerns
– Truncation of family size due to
morbidity
– ‘True’ sibling recurrence risk
– Uncertain paternity
– Twinning
• Power: n = 400 ASPs; power >
80% for λs = 3.0 (LOD = 3)
Quantitative trait mapping
• Quantitative trait analyses
– Standard variance component analyses
– Multipoint analyses
– Sequential search strategies
– Epistasis
– Multivariate analyses
– Bivariate analyses with diagnosis + trait
Sample size required for 80% power to
detect linkage to a QTL at a LOD of 3
(Almasy et al.)
Number of Individuals
100,000
Pedigree
Sibship (2)
Sibship (4)
10,000
1,000
100
0
0.1
0.2
0.3
Heritability due to QTL
0.4
0.5
Associations at the population-level
Ill Individual
Transmission Of
Disease Gene
Generations:
1
2
3
n
Healthy Individual
Transmission Of
Normal Gene
Factors influencing associations
•
•
•
•
•
•
Sample selection & size
Population history (fitness, drift, migration)
Features of mutations (no, age, frequency)
Features of markers (informativeness, LD)
Number of comparisons
Ethnic admixture
Family based associations
(haplotype relative risk)
A, B
C, D
A, C
B, D
Hypothetical
control
Transmission Disequilibrium
Test (TDT)
A1, A1
A2, A2
A1, A2
A3, A4
A2, A1
A4, A3
A1, A2
A1, A3
A1, A4
Reject
Accept
Accept
Family based associations
•
•
•
•
Recruitment expensive
Ascertainment may be biased
Easier than multiplex pedigrees
Power: Issues
– Uncertain paternity
– Genotyping errors
– Power diminishes for case-parent
duos
‘Novel’ designs
• Cytogenetic abnormalities
• Pooled DNA analyses
Thank you!!
• Collaborators:
– Laura Almasy, PhD
– Bernie Devlin, PhD
– Rodeny Go, PhD
– Ruben Gur, PhD
– Raquel Gur, MD, PhD