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Genetic research designs in the real world. Vishwajit L Nimgaonkar MD, PhD University of Pittsburgh nimga@pitt.edu. Complex disorders: models of causation. Genetic factors : Several genes induce cumulative, small but discrete effects +
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Genetic research designs in the real world Vishwajit L Nimgaonkar MD, PhD University of Pittsburgh nimga@pitt.edu
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?
Discrete Continuous (disease) (liability) 0 1 t 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
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
*Mutation* Haplotype 1 Marker A1 Marker A2 Marker B1 Marker B2 Gene mapping concepts case control
Transmission Of Normal Gene Generations: 1 2 Ill Individual Healthy Individual 3 Transmission Of Disease Gene n Recombination based gene mapping
founder generations Linkage Association 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).
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
A,B A,C A,B A,B A,B C,D Linkage: affected sib-pairs (identity by descent) Alleles shared IBD: 2 0 1 0.25 Prevalence: 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
Sample size required for 80% power to detect linkage to a QTL at a LOD of 3 (Almasy et al.)
Transmission Of Normal Gene Generations: 1 2 Ill Individual Healthy Individual 3 Transmission Of Disease Gene n Associations at the population-level
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
A, B C, D A, C B, D Family based associations (haplotype relative risk) Hypothetical control
Transmission Disequilibrium Test (TDT) A1, A2 A3, A4 A4, A3 A1, A1 A2, A2 A2, A1 A1, A2 A1, A4 A1, A3 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