Outline: Statistical Genetics I: Discrete Mendelian traits.

Ch 1: Simple Mendelian traits

Mon 9/27: 1.1 Mendel's first law -- Mendelian segregation.
  • General background and course logistics.
  • An SNP is a discrete Mendelian trait!
  • Introduction to DNA, chromosomes, locus, alleles, genotypes
  • Phenotypes: dominant, recessive and codominant alleles
  • What is a gene? -- a word to be used only when necessary--
    the segment of coding DNA, or the more abstract entity transmitted from parents to offspring
  • Mendel's laws. Written in terms of binary meiosis indicators.
    Wed 9/29: 1.2.1 Population allele frequencies.
    (This part of the course will use Weir Chapter 2, as basis)
  • Some basics about maximum likelihood estimation.
  • Hardy Weinberg equilibrium-- estimation of allele frequencies.
  • Estimation of recessive allele frequencies
    Fri 10/1: Homework discussion
  • Hardy Weinberg equilibrium, and simple prob computations

    Mon 10/4: 1.2.2 Testing from allele frequency estimates.

  • Estimation of allele frequencies from relatives (simple example)
  • Testing Hardy-Weinberg equilibrium
    Wed 10/6: 1.2.3 Gene counting and the EM algorithm
  • Bernstein's population frequency test for ABO determination
  • Expected complete-data log-likelihood -- the EM algorithm
    Fri 10/8: Homework 2 discussion

    Mon 10/11:

  • More EM algorithm examples -- ABO allele frequencies
    1.3 Inheritance patterns and trait frequencies
    1.3.1 Dominant, recessive and X-linked traits
    1.3.2 Mutation selection balance
    Wed 10/13:
    1.3.3 Subdivided populations
    1.3.4 Random genetic drift

    Fri 10/15: Warwick Daw
    Effects of errors and uncertainty in allele frequencies, in real studies.

    Mon 10/18:
    1.3.5 Probability and rates of fixation; mutation-drift balance;
    Gene identity by descent at the population level.

    Wed 10/20: Eric Anderson
    Monte Carlo estimation of expectations; importance sampling

    Chapter 2: Data on related individuals
    Fri 10/22: Homework3, and computing set-up; pedigrees.

    Mon 10/25:
    2.1 Gene identity by descent, inbreeding and recessive traits
    Wed 10/27:
    2.2 Kinship coefficients; Simple relationships; the general formula;
    Fri 10/29:
    Homework 4: project outline due
    Examples of kinship coefficients and gene ibd on JV pedigree.

    Mon 11/1:
    Probability of data on pairs of relatives More about patterns of gene ibd for two non-inbred individuals
    Kinship, the relationship triangle, a constraint on ibd probabilities

    Wed 11/3: Quadruple half-first-cousins
    Chapter 3: Genetic linkage
    3.1 Genetic linkage; crossovers and recombination;
    Fri 11/5: Discussion of homework 5.

    Mon 11/8: 3.2 Meiosis, haplotype frequencies, and linkage disequilibrium.
    Wed 11/10: 3.3 Likelihoods and testing for two-locus linkage
    Fri 11/12: Brief presentations of project ideas.

    Mon 11/15: 3.4 Power, sample-size, elods, and K-L information.
    Wed 11/17: 3.5 Two-locus ibd, and homozygosity mapping;
    Fri 11/19: Discussion of homework 6

    Mon 11/22: 3.5 contd. Homozygosity mapping; linkage and association
    Wed 11/24: Chapter 4: Multiple marker loci
    4.1 Multiple marker loci, meiosis indicators, and data probabilities.

    Fri 11/26: Thanksgiving holiday
    Mon 11/29: Class cancelled

    Wed 12/1: Projects due!.
    4.2 The hidden Markov structure and the Lander-Green algorithm
    Fri 12/3: 4.3 The Baum algorithm for probabilities conditional on data

    Mon 12/6: Homework 7 discussion; lods and elods
    Multilocus IBD probabilities by Monte Carlo.
    Wed 12/8: 4.4 Monte Carlo likelihoods and importance sampling.