Molecular genetics and microarray gene expression data analysis with applications to livestock

Instructor:  Dr. Romdhane Rekaya
348 Rhodes Center For Animal & Dairy Science
(706) 542 0949
rrekaya@uga.edu

Topics:

  1. Introduction
    1. Mendelian genetics
    2. Molecular genetics
  2. Genetic and physical mapping
    1. Polymorphism and information
    2. Genetic map construction
    3. Physical map
  3. Single-locus models
    1. Segregation ratios
    2. Marker screening
  4. Two locus model
    1. Controlled crosses
    2. Natural population
    3. Linkage disequilibruim
  5. Locus ordering and linkage grouping
    1. Three locus
    2. Multiple locus
    3. Estimation of the probability of locus order
  6. Multiple locus models
    1. Map distance
    2. Mapping function
    3. Marker coverage and map density
  7. QTL mapping
    1. Single marker analysis
    2. Interval mapping
    3. Composite interval mapping
  8. Marker assisted selection
    1. Theory and models
    2. Computation
    3. Examples and application
  9. Design and analysis of microarray gene expression experiments
    1. Introduction to microarray technology
      - cDNA microarrays
      - Affymetrix microarrays
    2. Design of microarray experiments
      - Replication
      - Blocking
      - Design and related issues (power, false positive and negative rates
    3. Low level analysis
      - Date preprocessing
      - Diagnostic and outliers detection
      - Data transformation
    4. Statistical analysis
      - Two sample tests
      - Data adjustments
      - Microarray mixed effects models for Affymetrix data and cDNA data
      - Implementation and computational requirements
      - Multiple testing considerations