genetic research designs in the real world vishwajit l nimgaonkar md, phd university of pittsburgh...
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Genetic research designs in the real world
Vishwajit L Nimgaonkar MD, PhD
University of Pittsburgh
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?
t
Discrete(disease)
Continuous(liability)
0 1
What is the phenotype?
(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
Marker A2Marker A1
Marker B1 Marker B2
*Mutation* Haplotype 1
Gene mapping concepts
control case
Recombination based gene mapping
Generations:
Transmission Of Disease Gene
Ill Individual
1
2
3
n
Transmission Of Normal Gene
Healthy Individual
Linkage / Association
Linkage
Association
gen
erat
ion
s
founder
What is the study design?
POSITIONAL CLONINGStep 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 A,C A,BA,BA,B C,D
Alleles shared IBD: 0 1
Prevalence:
2
0.25 0.50 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
100
1,000
10,000
100,000
0 0.1 0.2 0.3 0.4 0.5Heritability due to QTL
Num
ber
of In
divi
dual
s
PedigreeSibship (2)Sibship (4)
Sample size required for 80% power to detect linkage to a QTL at a LOD of 3
(Almasy et al.)
Associations at the population-level
Generations:
Transmission Of Disease Gene
Ill Individual
1
2
3
n
Transmission Of Normal Gene
Healthy Individual
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, C B, D
A, B C, D
Hypothetical control
Transmission Disequilibrium Test (TDT)
A1, A1
A1, A3
A1, A2 A3, A4
A1, A4
A2, A1 A4, A3A2, A2
A1, A2
AcceptReject 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