Statistics 790G:  Statistics in Genetic Epidemiology (Spring 2008)

Note the classroom has been changed to 102 Clark (David Clark Lab) starting 1/17/2008!!!

Instructor: Jung-Ying Tzeng

Office: 1505 Partners II Building (Centennial Campus)

Phone: 919-513-2723

Email: jytzeng@stat.ncsu.edu

Office Hour: Tuesdays and Thursdays after class, and by appointment at my office on Centennial campus

Course website: http://www.stat.ncsu.edu/people/tzeng/courses/st790g/syllabus.htm

                             (Can get access through WolfWare locker at http://www.courses.ncsu.edu/st790g)

Class: Tuesday and Thursday 3pm-4:15pm in 102 Clark (i.e., David Clark Lab)

Textbook: none

Reference book:

Thomas DC (2004) Statistical Methods in Genetic Epidemiology. Oxford University Press, New York

Khoury MJ, Beaty TH, Cohen B (1993) Fundamentals of Genetic Epidemiology. Oxford University Press, Oxford.

Sham P (1998) Statistics in human genetics. Arnold, London.

Lange K (1997) Mathematical and statistical methods for genetic analysis. Springer-Verlag, New York.

Ott J (1999) Analysis of human genetic linkage, 3rd edition. Johns Hopkins University Press, Baltimore.

Weir BS (1996) Genetic data analysis II. Sinauer Associates, Sunderland, MA.

Course Description: The course aims at providing the statistical tools for understanding the genetic effects of human traits. The focus will be on both research and statistical methodologies required to investigate questions in genetic epidemiology, such as how to evaluate evidence for a genetic component in disease (familial aggregation and segregation analysis), and how to identify genes responsible for them (linkage analysis and association analysis). Other analytical topics such as population stratification, multiple testing adjustment, haplotype analysis, gene-environment/gene-gene interaction, and copy number variation analysis will also be covered in the course.

Grading: Course grade will be calculated based on homework (50%), midterm (20%), and final project (30%). The final project will be announced in the middle of the semester.

• Homework: There will be homework assignments at the end of each topic that is covered in this class. You are encouraged to discuss homework problems with classmates, but you should always work through them yourself and complete all assignments independently.
• Midterm: There will be a midterm on 2/21. The exam will be open notes.
• Final Project: There will be a small final project instead of a final exam. The details of the final project will be announced in the middle of the semester.

Class evaluation:

• Schedule: Online class evaluations will be available for students to complete during the last two weeks of class. Students will receive an email message directing them to a website where they can login using their Unity ID and complete evaluations.  All evaluations are confidential; instructors will never know how any one student responded to any question, and students will never know the ratings for any particular instructors.
• Evaluation website: https://classeval.ncsu.edu (4.12.08 ~ 4.28.08)
• Student help desk: classeval@ncsu.edu
• More information about ClassEval: http://www2.acs.ncsu.edu/UPA/classeval/index.htm

Academic Integrity: Students should refer to the University policy on academic integrity found in the University code of student conduct. Sections 7 through 13 are particularly relevant. By putting their name on any test, homework assignment or examination script, the student gives their agreement that they neither received nor gave unauthorized aid on that piece of work. Typically this means that that the item in question represents the student's own work. The previous statement does not mean that students cannot ask each other for help or work together to a reasonable extent on homework assignments. What it means is that you cannot simply copy or paraphrase someone else's work.

Access for Students with Disabilities: Reasonable accommodations will be made for students with verifiable disabilities. In order to take advantage of available accommodations, students must register with Disability Services for Students at 1900 Student Health Center, Campus Box 7509, 515-7653 (website: http://www.ncsu.edu/provost/offices/affirm_action/dss/). For more information on NC State's policy on working with students with disabilities please see website: http://www.ncsu.edu/provost/hat/current/appendix/appen_k.html.

Tentative Class Schedule: (subject to change)

week1	1/10	Overview of genetic epidemiology
week2	1/15	Principles of Mendelian Inheritance Pedigree data and Genetic identity coefficients I
	1/17	Genetic identity coefficients I
week3	1/22	Genetic identity coefficients II
	1/24	Hardy-Weinberg Equilibrium	HW1
week4	1/29	Familial aggregation
	1/31	Segregation analysis I
week5	2/5	Segregation analysis II	HW1 Due
	2/7	Meiotic recombination	HW2
week6	2/12	Genetic map function
	2/14	Parametric linkage analysis
week7	2/19	Parametric linkage analysis	HW2 Due
	2/21	Quantitative trait loci (QTL) mapping in human	Distribute Take-Home Exam
week8	2/26	Association analysis	Take Home Exam Due
	2/28	X-linked association analysis (Dr. Ren-Hua Chuang, Center for Human Genetics, Duke University)
week9	3/4	Spring Break; no class
	3/6	Spring Break; no class
week10	3/11	Measure of LD Non-parametric linkage analysis I
	3/13	Non-parametric linkage analysis II
week11	3/18	ENAR; no class
	3/20	Gene-gene/gene-environmental interaction (Dr. Alison Motsinger-Reif; NCSU)
week12	3/25	Genome-wide association studies I Multiple testing
	3/27	Genome-wide association studies II Genotyping; QC
week13	4/1	Genome-wide association studies II Genotyping; QC
	4/3	Adjusting Population substructures I
week14	4/8	Adjusting Population substructures II
	4/10	Haplotype Analysis I—HapMap Project	* Reading Project I (Silliven et al. 08) * Reading Project II (Marchini et al. 05)
week15	4/15	Haplotype Analysis II—Haplotype reconstruction;
	4/17	Family-based association analysis (Dr. Yi-Ju Li, Center for Human Genetics, Duke University)
week16	4/22	Haplotype Analysis III—Haploytpe-based association analysis
	4/24	Haplotype Analysis IV—Haplotype length determination; SNP Imputation

**: The date is only tentatively scheduled.