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遺傳統計導論

遺傳統計導論 . 2006.2.24—2006.6.16 高振宏 、 程毅豪 、 杜憶萍 教授. 課程綱要 I. Week 1: Course Overview, Basic Knowledge of Genome Biology, Basic Principles of Population Genetics Week 2: Linkage Analysis for Family Data – I Week 3: Linkage Analysis for Family Data – II

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遺傳統計導論

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  1. 遺傳統計導論 2006.2.24—2006.6.16 高振宏、程毅豪、杜憶萍教授

  2. 課程綱要 I • Week 1: Course Overview, Basic Knowledge of Genome Biology, Basic Principles of Population Genetics • Week 2: Linkage Analysis for Family Data – I • Week 3: Linkage Analysis for Family Data – II • Week 4: Introduction to Microarray Data Analysis • Week 5: Nature of Discrete Genetic data & Estimating Frequencies • Week 6: Disequilibrium & Diversity • Week 7: Population Structure, Individual Identification & Outcrossing And Selection • Week 8: Linkage • Week 9: Midterm

  3. 課程綱要 II • Week 10. Phylogeny Reconstruction & Quantitative Genetics I • Week 11: Quantitative Genetics II • Week 12: QTL mapping I • Week 13: QTL mapping II • Week 14: Population-based Association Analysis • Week 15: Family-based Association Analysis • Week 16: Multipoint Association Analysis • Week 17: Genomewide Association Analysis

  4. Thomas Andrew Knight (1759-1838) Thomas Andrew Knight, the first man to practice large-scale, systematic strawberry breeding, which produced two famous varieties: the Downton and the Elton. As a founder and long-time president of England's Royal Horticultural Society, he encouraged others to breed better varieties of fruits and vegetables.

  5. Thomas Andrew Knight • Knight's father was a Herefordshire clergyman who died when his son was five years old. The boy's education was neglected, and until he was nine he remained almost illiterate. Since he was unable to read as a child, he concentrated his curiosity on the plant and animal life on the family estate. One day, says a story, hesaw a gardener planting beans. The boy asked why the man was planting sticks of wood and was told they would grow up to be beans. The gardener's prediction came true. Knight immediately planted his pocket knife and waited in anticipation for the miraculous growth of new knives. When the experiment failed he sat down to consider the difference in the two cases. Already he was engrossed with the mysteries of the vital processes in plants, a preoccupation which would lead later to his reputation as a brilliant plant physiologist.

  6. Downton (1817) Elton (1828)

  7. Knight didn’t count, Mendel did count.

  8. By the 1890's, the invention of better microscopes allowed biologists to discover the basic facts of cell division and sexual reproduction.  The focus of genetics research then shifted to understanding what really happens in the transmission of hereditary traits from parents to children.  A number of hypotheses were suggested to explain heredity, but Gregor Mendel, a little known Central European monk, was the only one who got it more or less right.  His ideas had been published in 1866 but largely went unrecognized until 1900, which was long after his death.  His early adult life was spent in relative obscurity doing basic genetics research and teaching high school mathematics, physics, and Greek in Brno (now in the Czech Republic).  In his later years, he became the abbot of his monastery and put aside his scientific work. Gregor Mendel    1822-1884 

  9. 因為簡單, 所以偉大

  10. James Watson 1928-- Francis Crick 1916--2004

  11. Slides 15—36 are edited from

  12. and Bonnie Berger MIT

  13. The human genome • The cell is the fundamental working unit of every living organism. • Humans: trillions of cells (metazoa); other organisms like yeast: one cell (protozoa). • Cells are of many different types (e.g. blood, skin, nerve cells), but all can be traced back to a single cell, the fertilized egg.

  14. Nucleus

  15. Eukaryota: More on Morphology

  16. The human genome in numbers • 23 pairs of chromosomes; • 2 meters of DNA; • 3,000,000,000 bp; • 35 M (males 27M, females 44M); • 30,000-40,000 genes.

  17. The human genome • The genome, or blueprint for all cellular structures and activities in our body, is encoded in DNA molecules. • Each cell contains a complete copy of the organism’s genome.

  18. The human genome • The human genome is distributed along 23 pairs of chromosomes 22 autosomal pairs; the sex chromosome pair, XX for females and XY for males. • In each pair, one chromosome is paternally inherited, the other maternally inherited (cf. meiosis).

  19. The human genome • Chromosomes are made of compressed and entwined DNA. • A (protein-coding) gene is a segment of chromosomal DNA that directs the synthesis of a protein.

  20. DNA • A deoxyribonucleic acid or DNA molecule is a double-stranded polymer composed of four basic molecular units called nucleotides. • Each nucleotide comprises a phosphate group, a deoxyribose sugar, and one of four nitrogen bases: adenine (A), guanine (G),Cytosine (C), and thymine (T) • The two chains are held together by hydrogen bonds between nitrogen bases. • Base-pairing occurs according to the following rule: G pairs with C, and A pairs with T.

  21. Genes control the making of cell parts • The gene is a fundamental unit of inheritance • DNA molecule contains tens of thousands of genes • Each gene governs the making of one functional element, one “part” of the cell machine • Every time a “part” must be made, a piece of the genome is copied, transported, and used as a blueprint • RNA is a temporary copy • The medium for transporting genetic information from the DNA information repository to the protein-making machinery is and RNA molecule • The more parts are needed, the more copies are made • Each mRNA only lasts a limited time before degradation

  22. The genetic code • DNA: sequence of four different nucleotides. • Protein: sequence of twenty different amino acids. • The correspondence between DNA’s four-letter alphabet and a protein’s twenty-letter alphabet is specified by the genetic code, which relates nucleotide triplets or codons to amino acids.

  23. Big Picture

  24. Basic human genetics • 46 chromosomes • 22 pairs of autosomal chromosomes and • 2 sex chromosomes • Double stranded DNA • 4 bases: A = Adenine p-arm T = Thymine q-arm G = Guanine Centromere C = Cytosine Approximately 3 000 000 000 basepairs in the human genome

  25. The Central Dogma of Molecular Biology

  26. Basic Principles of Population Genetics Reference: Kenneth Lange Mathematical and Statistical Methods for Genetic Analysis

  27. Mendel’s experiment data Trait           Characteristics          Dominant      Recessive

  28. Mendel’s First Law • First Generation RR x rr • Second Generation Rr x Rr (self cross) • Third generation RR+Rr (3/4) rr (1/4)

  29. Mendel’s Second LawIndependent two traits

  30. What if the traits are not independent?

  31. Genetic and physical maps • Physical distance: number of base pairs (bp). • Genetic distance: expected number of crossovers between two loci, per chromatid, per meiosis. Measured in Morgans (M) or centiMorgans (cM). • 1cM ~ 1 million bp (1Mb).

  32. Definition • The genetic map distance (in units of Morgans) between two loci is defined as the expected (average) number of crossovers occuring on a single chromosome (in a gamete) between two loci. Ex: Chromosome 1: Physical length: 263 Mb Female map length: 3.76 M = 376 cM Male map length: 2.21 M = 221 cM Note: 1 Mb . 1 cM

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