MW 3:30 – 4:45
Professor: Dr. José R. Fernández
435 Webb Building – (205) 934-2029
After the remarkable achievements of the human genome project, the field of genetics has dramatically increased its importance in clinical areas and biomedical research. The course is aimed to graduate students interested in developing an expertise in statistical genetics or to research-oriented individuals who would like to understand the biological basis underlying statistical approaches for gene mapping. Students will receive an overview of the field of genetics as an initial exposure to those interested in understanding the process of identifying genes influencing complex traits. Individuals who register for the course must have a basic understanding of statistics and regression models. Although no prerequisites are established for this course, the sequence BST 601 and BST 602 (or its equivalent) is highly recommended.
During their experience in the course, students will be exposed to principles of Mendelian and molecular genetics, statistics, the use of animal and human models for genetic investigations, and the use of association and linkage techniques to identify genetic influences in population traits. Also, students will participate in computer lab exercises that will facilitate the understanding of the techniques discussed in class and will demonstrate their application to the identification of genetic influences in complex traits.
Lynch, M. & Walsh, B. (1998) Genetics Analysis of Quantitative Traits. Sunderland, MA: Sinauers
Klug, W.S. & Cummings M.R. (2001) Essentials of Genetics, Fourth Edition. Upper Sadle River, New Jersey: Prentice Hall.
Optional Recommended Books:
Gonic, L. & Smith, W. (1993) The cartoon guide to statistics. Harper-Collings Publishers, Inc.
Gonic, L. & Wheelis, M. (1991) The cartoon guide to genetics. Harper-Collings Publishers, Inc.
Grading:
Students’ final grade for this course will be based on a total of 100 points, distributed in the following manner:
a) Attendance (7 points): A signing sheet will be passed around during each class to record students’ attendance. Students will receive .25 point of the final grade for every class they attend except for 1/22 and 2/25.
b) Data Analysis Project (3 points): This project will account for 3 points of your final grade. Further details about this project will be provided after the midterm. This project will be due on 4/3.
c) Midterm (30 points): The midterm exam will consist of 8 questions representing the topics discussed in the course by the time of this exam. Students will choose 6 questions to be answered. Each question will have a value of 5 points. No extra credit will be offered.
d) Final paper (30 points): A written final paper will be due on May 1st, 2002. This paper could be done individually or in groups and should follow the style of a manuscript submitted for publication.
e) Oral presentation (30 points): A 10-20 minute oral presentation is expected for every final paper. This oral presentation should simulate a talk at a professional meeting.
Final Grade will be based on: A = 100 - 90; B = 89.9 – 80; C = 79.9 – 65; D=64.9 – 50; F = less than 49.9
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DATE |
TOPIC
|
READINGS |
||
Essentials
of Genetics
|
Genetics and Analysis of QT |
Notes |
||
|
Wed 1/2 |
Review of Statistics |
|
Chapter 2 |
Guest Lecturer: UAB -
Biostatistics |
|
Mon 1/7 |
Introduction / History of Genetics / Basic Concepts |
Chapter 1 |
|
|
|
Wed 1/9 |
Mendelian Genetics and Hardy-Weinberg Equilibrium |
Sections 3.1 -
3.7, 22.1 - 22.5 |
Pages 51-54; 60 |
|
|
Mon 1/14 |
Mitosis, Meiosis and Chromosomal Segregation |
Chapter 2 |
|
|
|
Wed 1/16 |
DNA Structure and Central Dogma |
Chapter 10 |
|
|
|
Mon 1/21 |
NO CLASS- Martin Luther King Holiday |
|
|
|
|
Wed 1/23 |
Genetic Markers and Recombinant DNA |
Chapter 16 |
Pages 390-398 |
Sunnucks (2000) |
|
Mon 1/28 |
Molecular techniques |
Chapter 16 |
|
Guest Lecturer: Dr. Mark Shriver Penn State Univ. |
|
Wed 1/30 |
Microarrays |
Pages 398-399 |
|
Xiang and Chen
(2000) |
|
Mon 2/4 |
Breeding Crosses in Animal Models (P1, P2, F1,
F2, RIs) |
Page 37; Section 22.11 |
|
|
|
Wed 2/6 |
Transgenics, Congenics, Knockouts, tissue-specific knockouts, inducible
knock-outs |
Section 14.10 |
Pages 405 - 413 |
|
|
Mon 2/11 |
Multifactorial Inheritance: Genetic Variance |
Section 6.1 |
Pages 61 - 79 |
|
|
Wed 2/13 |
Heritability Estimation |
Section 6.3 |
Pages 170 – 175 |
|
|
Mon 2/18 |
Human Models: Family Structure and Pedigrees |
Section 3.9 |
|
|
|
Wed 2/20 |
Twin and Adoption Studies / Review |
|
Chapter 19 |
MacGregor et al.
(2000) |
|
Mon 2/25 |
MID TERM EXAM |
|
|
|
|
Wed 2/27 |
Linkage, Association, Linkage Disequilibrium, and Haplotype Analysis |
Sections 8.1 –
8.2 |
|
Goldstein and
Weale (2001) |
|
Mon 3/4 |
QTL Mapping |
Section 6.4 |
Pages 321 – 328;
398 – 402; 431 – 436; 442 - 453 |
Broman (2001) |
|
Wed 3/6 |
Complexities: Oligogenes, Dominance, Epistasis, Imprinting,
Overdominance, etc. |
Chapter 4 |
Pages 82 – 85; 457 - 463 |
Fernández et al.
(2000) |
|
Mon 3/11 |
LAB Exercise |
|
|
|
|
Wed 3/13 |
Resemblance Among Relatives |
|
Pages 131 – 145 |
|
|
Mon 3/18 |
Linkage: Sib-Pair Analysis |
|
Pages 513 – 521 |
Amos &
de Andrade (2001) |
|
Wed 3/20 |
LAB Exercise |
|
|
|
|
Mon 3/25 |
NO CLASS – SPRING BREAK |
|
|
|
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Wed 3/27 |
NO CLASS – SPRING BREAK |
|
|
|
|
Mon 4/1 |
Discussion of Lab Exercises |
|
|
|
|
Wed 4/3 |
Data Analysis Project Due Variance Component Methods |
|
Pages 510 - 512 |
Guest
Lecturer: Dr. Carol Etzel MD Anderson
Cancer Center |
|
Mon 4/8 |
TDT: Quantitative Traits |
Guest
Lecturer: Dr. David Allison |
Pages 419 – 422 |
Guest
Lecturer: UAB –
Biostatistics; Allison (1997) |
|
Wed 4/10 |
MALD |
|
|
|
|
Mon 4/15 |
Environmental Variation, Gene x Environment interaction, Gene by Environment correlation |
|
Chapter 6; Chapter 22 |
Guest
Lecturer: UAB –
Biostatistics |
|
Wed 4/17 |
Analysis of Microarray Data |
|
|
Guest
Lecturer: UAB –
Biostatistics Allison et al.
(2001) |
|
Mon 4/22 |
Oral Presentations |
|
|
|
|
Wed 4/24 |
Oral Presentations |
|
|
|
|
May 1 |
FINAL PAPER DUE |
|
|
|
REFERENCES:
Allison D. (1997) Transmission-disequilibrium
tests for quantitative traits.
American Journal of Human Genetics, 60 (3): 676-690.
Allison,
D. B., Gadbury, G., Heo, M, Fernandez, J, Lee, C-K, Prolla, T. A., &
Weindruch, R. (in press). A mixture model approach for the analysis of
microarray gene expression data. Computational Statistics & Data
Analysis.
Amos CI & de Andrade M. (2001) Genetic linkage methods for
quantitative traits. Statistical
Methods for Medical Research, 10(1): 3-25.
Browman KW (2001) Review of statistical methods for QTL mapping in experimental
crosses. Laboratory Animal (NY), 30
(7): 44-52
Fernández JR, Tarantino LM, Hofer SM, Vogler GP
& McClearn GE (2000) Epistatic
quantitative trait loci for alcohol preference in mice. Behavior Genetics, 30(6): 431-437.
McGregor AJ, Snieder H, Schork NJ & Spector
TD (2000) Twins. Novel uses to study
complex traits and genetic diseases.
Trends of Genetics, 16(3): 131-134.
Sunnucks P (2000)
Efficient genetic markers for population biology Trends in Ecology &
Evolution, 15(5): 199-203
Xiang CC & Chen Y
(2000) cDNA microaary technology and its applications. Biotechnology
Advances 18: 35-46.
Goldstein DB & Weale ME (2001) Population
genomics: Linage disequilibrium holds
the key. Current Biology, 11: 14
R576-R579.