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Quality mapping in model living beings

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  1. Gene mapping in model organisms

  2. Goal • Identify genes that contribute to common human diseases.

  3. Inbred mice

  4. Advantages of the mouse • Small and cheap • Inbred lines • Large, controlled crosses • Experimental interventions • Knock-outs and knock-ins

  5. The mouse as a model • Same genes? • The genes involved in a phenotype in the mouse may also be involved in similar phenotypes in the human. • Similar complexity? • The complexity of the etiology underlying a mouse phenotype provides some indication of the complexity of similar human phenotypes. • Transfer of statistical methods. • The statistical methods developed for gene mapping in the mouse serve as a basis for similar methods applicable in direct human studies.

  6. The intercross

  7. The data • Phenotypes,yi • Genotypes, xij = AA/AB/BB, at genetic markers • A genetic map, giving the locations of the markers.

  8. Phenotypes 133 females (NOD B6)  (NOD B6)

  9. NOD

  10. C57BL/6

  11. Agouti coat

  12. Genetic map

  13. Genotype data

  14. Goals • Identify genomic regions (QTLs) that contribute to variation in the trait. • Obtain interval estimates of the QTL locations. • Estimate the effects of the QTLs.

  15. Statistical structure • Missing data: markers  QTL • Model selection: genotypes  phenotype

  16. Models: recombination • No crossover interference • Locations of breakpoints according to a Poisson process. • Genotypes along chromosome follow a Markov chain. • Clearly wrong, but super convenient.

  17. Models: gen  phe Phenotype = y, whole-genome genotype = g Imagine thatpsites are all that matter. E(y | g) = (g1,…,gp) SD(y | g) = (g1,…,gp) Simplifying assumptions: • SD(y | g) = , independent of g • y | g ~ normal( (g1,…,gp),  ) • (g1,…,gp) =  + ∑ j 1{gj = AB} + j 1{gj = BB}

  18. Before you do anything… Check data quality • Genetic markers on the correct chromosomes • Markers in the correct order • Identify and resolve likely errors in the genotype data

  19. The simplest method “Marker regression” • Consider a single marker • Split mice into groups according to their genotype at a marker • Do an ANOVA (or t-test) • Repeat for each marker

  20. Marker regression Advantages • Simple • Easily incorporates covariates • Easily extended to more complex models Disadvantages • Must exclude individuals with missing genotypes data • Imperfect information about QTL location • Suffers in low density scans • Only considers one QTL at a time

  21. Interval mapping Lander and Botstein 1989 • Imagine that there is a single QTL, at position z. • Let qi = genotype of mouse i at the QTL, and assume yi | qi ~ normal( (qi),  ) • We won’t know qi, but we can calculate (by an HMM) pig = Pr(qi = g | marker data) • yi, given the marker data, follows a mixture of normal distributions with known mixing proportions (the pig). • Use an EM algorithm to get MLEs of  = (AA, AB, BB, ). • Measure the evidence for a QTL via the LODscore, which is the log10 likelihood ratio comparing the hypothesis of a single QTL at position z to the hypothesis of no QTL anywhere.

  22. Interval mapping Advantages • Takes proper account of missing data • Allows examination of positions between markers • Gives improved estimates of QTL effects • Provides pretty graphs Disadvantages • Increased computation time • Requires specialized software • Difficult to generalize • Only considers one QTL at a time

  23. LOD curves

  24. LOD thresholds • To account for the genome-wide search, compare the observed LOD scores to the distribution of the maximum LOD score, genome-wide, that would be obtained if there were no QTL anywhere. • The 95th percentile of this distribution is used as a significance threshold. • Such a threshold may be estimated via permutations (Churchill and Doerge 1994).

  25. Permutation test • Shuffle the phenotypes relative to the genotypes. • Calculate M* = max LOD*, with the shuffled data. • Repeat many times. • LOD threshold = 95th percentile of M* • P-value = Pr(M* ≥ M)

  26. Permutation distribution

  27. Chr 9 and 11

  28. Epistasis

  29. Going after multiple QTLs • Greater ability to detect QTLs. • Separate linked QTLs. • Learn about interactions between QTLs (epistasis).

  30. Multiple QTL mapping Simplistic but illustrative situation: • No missing genotype data • Dense markers (so ignore positions between markers) • No gene-gene interactions Which j  0?  Model selection in regression

  31. Model selection • Choose a class of models • Additive; pairwise interactions; regression trees • Fit a model (allow for missing genotype data) • Linear regression; ML via EM; Bayes via MCMC • Search model space • Forward/backward/stepwise selection; MCMC • Compare models • BIC() = log L() + (/2) || log n Miss important loci  include extraneous loci.

  32. Special features • Relationship among the covariates • Missing covariate information • Identify the key players vs. minimize prediction error

  33. Opportunities for improvements • Each individual is unique. • Must genotype each mouse. • Unable to obtain multiple invasive phenotypes (e.g., in multiple environmental conditions) on the same genotype. • Relatively low mapping precision. • Design a set of inbred mouse strains. • Genotype once. • Study multiple phenotypes on the same genotype.

  34. Recombinant inbred lines

  35. AXB/BXA panel

  36. AXB/BXA panel

  37. LOD curves

  38. Chr 7 and 19

  39. Pairwiserecombination fractions Upper-tri: rec. fracs. Lower-tri: lik. ratios Red = association Blue = no association

  40. RI lines Advantages • Each strain is a eternal resource. • Only need to genotype once. • Reduce individual variation by phenotyping multiple individuals from each strain. • Study multiple phenotypes on the same genotype. • Greater mapping precision. Disadvantages • Time and expense. • Available panels are generally too small (10-30 lines). • Can learn only about 2 particular alleles. • All individuals homozygous.

  41. The RIX design

  42. The “Collaborative Cross”

  43. Genome of an 8-way RI

  44. The “Collaborative Cross” Advantages • Great mapping precision. • Eternal resource. • Genotype only once. • Study multiple invasive phenotypes on the same genotype. Barriers • Advantages not widely appreciated. • Ask one question at a time, or Ask many questions at once? • Time. • Expense. • Requires large-scale collaboration.

  45. To be worked out • Breakpoint process along an 8-way RI chromosome. • Reconstruction of genotypes given multipoint marker data. • QTL analyses. • Mixed models, with random effects for strains and genotypes/alleles. • Power and precision (relative to an intercross).

  46. Haldane & Waddington 1931 r = recombination fraction per meiosis between two loci Autosomes Pr(G1=AA) = Pr(G1=BB) = 1/2 Pr(G2=BB | G1=AA) = Pr(G2=AA | G1=BB) = 4r / (1+6r) X chromosome Pr(G1=AA) = 2/3 Pr(G1=BB) = 1/3 Pr(G2=BB | G1=AA) = 2r / (1+4r) Pr(G2=AA | G1=BB) = 4r / (1+4r) Pr(G2  G1) = (8/3) r / (1+4r)

  47. 8-way RILs Autosomes Pr(G1 = i) = 1/8 Pr(G2 = j | G1 = i) = r / (1+6r)for i  j Pr(G2  G1) = 7r / (1+6r) X chromosome Pr(G1=AA) = Pr(G1=BB) = Pr(G1=EE) = Pr(G1=FF) =1/6 Pr(G1=CC) = 1/3 Pr(G2=AA | G1=CC) = r / (1+4r) Pr(G2=CC | G1=AA) = 2r / (1+4r) Pr(G2=BB | G1=AA) = r / (1+4r) Pr(G2  G1) = (14/3) r / (1+4r)

  48. Areas for research • Model selection procedures for QTL mapping • Gene expression microarrays + QTL mapping • Combining multiple crosses • Association analysis: mapping across mouse strains • Analysis of multi-way recombinant inbred lines

  49. References • Broman KW (2001) Review of statistical methods for QTL mapping in experimental crosses. Lab Animal 30:44–52 • Jansen RC (2001) Quantitative trait loci in inbred lines. In Balding DJ et al., Handbook of statistical genetics, Wiley, New York, pp 567–597 • Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185 – 199 • Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971 • Kruglyak L, Lander ES (1995) A nonparametric approach for mapping quantitative trait loci. Genetics 139:1421-1428 • Broman KW (2003) Mapping quantitative trait loci in the case of a spike in the phenotype distribution. Genetics 163:1169–1175 • Miller AJ (2002) Subset selection in regression, 2nd edition. Chapman & Hall, New York

  50. More references • Broman KW, Speed TP (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses (with discussion). J R Statist Soc B 64:641-656, 737-775 • Zeng Z-B, Kao C-H, Basten CJ (1999) Estimating the genetic architecture of quantitative traits. Genet Res 74:279-289 • Mott R, Talbot CJ, Turri MG, Collins AC, Flint J (2000) A method for fine mapping quantitative trait loci in outbred animal stocks. Proc Natl Acad Sci U S A 97:12649-12654 • Mott R, Flint J (2002) Simultaneous detection and fine mapping of quantitative trait loci in mice using heterogeneous stocks. Genetics 160:1609-1618 • The Complex Trait Consortium (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nature Genetics 36:1133-1137 • Broman KW. The genomes of recombinant inbred lines. Genetics, in press