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Study Design for Linkage, Association and TDT Studies

Study Design for Linkage, Association and TDT Studies. 林明薇 Ming-Wei Lin, PhD 陽明大學醫學系家庭醫學科 台北榮民總醫院教學研究部. Collins FS. (1992) Nature genetics 1:3-6. Collins FS. (1992) Nature genetics 1:3-6. Linkage Mapping for Disease Genes. Linkage analysis (Lod score method) Allele-sharing methods.

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Study Design for Linkage, Association and TDT Studies

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  1. Study Design for Linkage, Association and TDT Studies 林明薇Ming-Wei Lin, PhD 陽明大學醫學系家庭醫學科 台北榮民總醫院教學研究部 YMGC Genotyping Core

  2. Collins FS. (1992) Nature genetics 1:3-6 YMGC Genotyping Core

  3. Collins FS. (1992) Nature genetics 1:3-6 YMGC Genotyping Core

  4. Linkage Mapping for Disease Genes • Linkage analysis (Lod score method) • Allele-sharing methods YMGC Genotyping Core

  5. Gregor Mendel • The principle of segregation of alleles. • The principle of independent assortment. YMGC Genotyping Core

  6. Linkage Linkage describes the phenomenon whereby allele at neighbouring loci are close to one another on the same chromosome, they will be transmitted together more frequently than chance. YMGC Genotyping Core

  7. Linkage Family YMGC Genotyping Core

  8. Recombinant Gametes Crossing over between two neighbouring loci will produce recombinant gametes. YMGC Genotyping Core

  9. Recombination Fraction Recombination fraction (θ) = number of recombinant gametes ---------------------------------------total gametes YMGC Genotyping Core

  10. Recombination Fraction • Recombination fraction is a measure of genetic distance. • 1cM= 1% chance of recombination between two loci. YMGC Genotyping Core

  11. YMGC Genotyping Core

  12. YMGC Genotyping Core

  13. Estimation of Recombination Fraction • Direct Method: count recombinants. • Maximum Likelihood Method: Unknown phases Incomplete penetrance Heterogeneity YMGC Genotyping Core

  14. Likelihood Odds Likelihood of data if loci linked at θ Likelihood odds = Likelihood of data if loci unlinked L(θ< 0.5) = L(θ= 0.5) YMGC Genotyping Core

  15. Lod Score L(θ< 0.5) Lod score (θ) = log10 L(θ = 0.5) YMGC Genotyping Core

  16. Phase Known Family D d A F D d A B R N N N N N YMGC Genotyping Core

  17. Phase Known L(θ) = (θ)r (1-θ) n-r r: No. of recombinants n: All meiosis YMGC Genotyping Core

  18. Lod ScorePhase Known L(θ) LOD = log L(θ= 0.5) (θ) r (1-θ) n-r = log [ ] (0.5) n = log 2nθr(1-θ)n-r YMGC Genotyping Core

  19. Phase Unknown Family D D or A B D D d d or B A B A N R A: N N N N R R N R R R B: YMGC Genotyping Core

  20. Phase Unknown L(θ) = 1/2 (θ)r (1-θ)n-r +1/2 (θ)n-r(1-θ)r r: No. of recombinants n: All meiosis YMGC Genotyping Core

  21. Lod ScorePhase Unknown L(θ) LOD = log L(θ= 0.5) 1/2[(θ) r(1-θ) n-r+(θ)n-r(1-θ)r ] =log { } (0.5) n = log {2n-1[θr(1-θ)n-r +θn-r(1-θ)r ]} YMGC Genotyping Core

  22. Lod Score - Maximum Likelihood Estimate (Z) • Can be calculated at any values of  between 0 and 0.5, but are conventionally reported at  =0, 0.01, 0.05, 0.1, 0.2, 0.3, and 0.4. • Zmax is the maximum likelihood estimate (MLE) of . YMGC Genotyping Core

  23. Total Lod Score Lod score obtained from individual families can be added together to calculate the total lod score. YMGC Genotyping Core

  24. Statistical Significance of the Lod Score lod score > 3: evidence of linkage 2 < lod score < 3: suggestive evidence of linkage -2 < lod score < 2: uninformative of linkage lod score < -2: exclusion of linkage YMGC Genotyping Core

  25. Lod Score • Two-point lod score analysis • Multipoint lod score analysis YMGC Genotyping Core

  26. YMGC Genotyping Core

  27. YMGC Genotyping Core

  28. Is a Pedigree Useful for linkage Analysis? • Are critical individuals in the pedigrees doubly heterozygous at the loci? (Informative) • Can the offsprings be scored as recombinants or nonrecombinants? (Phase) YMGC Genotyping Core

  29. Parameters Assumed in Lod Score Analysis • Transmission mode of disease • Recombination fraction • Trait allele frequencies • Penetrance values for each possible disease phenotypes • Marker allele frequencies. YMGC Genotyping Core

  30. Advantages of Lod Score Analysis • Statistically, it is more powerful approach than any nonparametric method. • Utilizes every family member’s phenotypic and genotypic information. • Provides an estimate of the recombination fraction. • Provides a statistical test for linkage and for genetic (locus) heterogeneity. YMGC Genotyping Core

  31. Limitations of Lod Score Method • assumes single locus inheritance • requires specification of disease gene frequency and penetrance • has reduced power when disease model is grossly misspecified YMGC Genotyping Core

  32. Successful Examples Using Lod Score Method • Cystic fibrosis • CFTR gene • Huntington disease • HD gene • Alzheimer disease • APP • Hereditary breast cancer • BRCA1 • BRCA2 YMGC Genotyping Core

  33. Complex Diseases • No clear pattern of Mendelian inheritance • A mix of genetic and environmental factors • Incomplete penetrance • Phenocopies • Oligogenic or polygenic • Heterogeneity • High frequency of disease-causing allele YMGC Genotyping Core

  34. Recurrence Risk Ratio (λ) Frequency in relatives of affected person λr = ------------------------------------------------------- Population frequency r denotes the degree of relationship YMGC Genotyping Core

  35. Recurrence Risk Ratio Genetic mapping is much easier for traits with high λs (λs > 10) than for those with low λs (λs < 2). YMGC Genotyping Core

  36. Recurrence Risk Ratio of Different Diseases YMGC Genotyping Core

  37. Allele-sharing Methods • Identical by state (I.B.S.) Two alleles of the same form. • Identical by descent (I.B.D.) Two alleles are descended from the same ancestral allele. YMGC Genotyping Core

  38. Allele-sharing Methods Testing whether affected relatives inherited a region IBD (or IBS) more often than expected under random Mendelian segregation. YMGC Genotyping Core

  39. AC AB AC BC AB CD BC BC AC AB AD BC IBD = 0 IBD = 2 IBD = 1 YMGC Genotyping Core

  40. BC BC AB AD BC AC IBS = 0 IBS = 2 IBS = 1 YMGC Genotyping Core

  41. Affected Sib-pair Methods An affected sib-pair may share 0,1, 2 alleles identical by descent (IBD) with probabilities of 0.25, 0.5, 0.25, respectively, at any marker locus. YMGC Genotyping Core

  42. AB AC IBD = 2 BC BC 25% BC AB IBD = 1 50% AC IBD = 0 25% BC AA YMGC Genotyping Core

  43. Affected Sib-pair Methods If the marker locus is independent of the trait locus, the probabilities of the affected sib-pairs share 0,1, 2 alleles ibd will remain as 0.25, 0.50, 0.25. YMGC Genotyping Core

  44. Affected Sib-pair Methods If the marker locus is linked to the trait locus, an excess of affected sib-pair sharing two alleles ibd will be expected. YMGC Genotyping Core

  45. Allele-sharing Methods • Affected Sib-pairs • Affected Pedigree Member YMGC Genotyping Core

  46. Pearson 2 statistics Comparing observed numbers of sib-pairs sharing 0, 1, 2 alleles IBD with their expectations under the null hypothesis. YMGC Genotyping Core

  47. Pearson 2 statistics • Alternative hypothesis: IBD sharing 0 1 2 observed n0 n1 n2N = n0 + n1 + n2 • Null hypothesis:IBD sharing: 0 1 2 expected N/4 N/2 N/4 YMGC Genotyping Core

  48. Comments on Allele-Sharing Method • There is no need to specify any genetic parameters of the transmission model. • Less powerful to detect linkage compared with the lod score method if the genetic transmission model can be specified correctly. • It is poor at providing a precise location of the disease gene. YMGC Genotyping Core

  49. Successful Examples Using Sib Pair Method • Insulin-dependent diabetes • Non-insulin-dependent diabetes • Multiple sclerosis • Alzheimer disease YMGC Genotyping Core

  50. Thresholds for Mapping Complex Traits YMGC Genotyping Core

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