SECOND ANNUAL NSF-FUNDED SHORT COURSE ON STATISTICAL GENETICS & STATISTICAL GENOMICS

Focusing on the analysis of complex traits characterized by quantitative variation, this five-day course will offer an interactive program to enhance researchers' ability to understand & use statistical genetic methods, as well as implement & interpret sophisticated genetic analyses. Including hands-on computer demonstrations and practice, the course will be useful to a wide range of investigators studying the genetics of plants, model organisms, livestock, wildlife, and humans, helping investigators to better understand, use, and, in some cases even undertake research on, statistical genetic methods. Statistical genetic methodology is critical to advancing basic biology which is, in turn, critical to fields like genetic epidemiology, evolutionary biology, ecology, pest management, marine biology, medicine, forestry, and agriculture.

Schedule of Events: [PDF file]

Mon 7/13/2009

Time	Topic	Speaker	Resource(s)
08:00 – 08:45 AM	Registration
08:45 - 09:00 AM	Introductory Remarks	Hemant K. Tiwari, Ph.D.
09:00 - 10:30 AM	Introduction to Biostatistics	Warren Ewens, Ph.D.
	Introduction to Genetic Analysis	Bruce Walsh, Ph.D.	no slides available
10:30 – 10:45 AM	BREAK
10:45 – 12:00 PM	Association Analysis: Genome-Wide Association and Haplotype Analysis	Carl Langefeld, Ph.D.
12:00 – 1:00 PM	Lunch
01:00 – 02:15 PM	The qualitative and the quantitative TDT	Warren Ewens, Ph.D.
02:15 – 2:45 PM	Open Discussion	All Faculty
02:45 – 03:00 PM	BREAK
03:00 – 04:15 PM	Intro to software demo lab & ssglabvm	Jelai Wang
04:15 – 05:45 PM	Imputation Methods in GWAS	Carl Langefeld, Ph.D.

Tue 7/14/2009

Time	Topic	Speaker	Resource(s)
08:00 – 09:15 AM	Background ancestry and other covariate modeling in genomic-wide association studies: state of the art and ongoing challenges	David B. Allison, Ph.D.
09:15 – 10:30 AM	Microarray Data Analysis	Rebecka Jörnsten, Ph.D.
10:30 – 10:45 AM	BREAK
10:45– 12:00 PM	Design of Microarray Experiments	Guilherme Rosa, Ph.D
12:00 – 01:00 PM	Lunch
1:00 – 1:30 PM	Open Discussion	All Faculty
01:30 – 03:00 PM	Haplotype Software Demo & Hands-on	Hemant K. Tiwari, Ph.D.
03:00 – 03:15 PM	BREAK
03:15 – 05:45 PM	Microarray Software Demo & Hands-on	Jelai Wang

Wed 7/15/2009

Time	Topic	Speaker	Resource(s)
08:00 – 09:15 AM	Basic QTL Analysis	Soledad Fernandez, Ph.D.
09:15 – 10:30 AM	Bayesian Interval Mapping	Brian Yandell, Ph.D.
10:30 – 10:45 AM	BREAK
10:45 – 12:00 PM	Multivariate trait selection and estimation of multivariate fitness functions	Bruce Walsh, Ph.D.	no slides available
12:00 – 01:00 PM	Lunch
01:00 - 02:30 PM	Whole Genome Enable Marker Assisted Selection	Guilherme Rosa, Ph.D.
02:30 – 03:00 PM	Open Discussion	All Faculty
03:00 – 03:15 PM	BREAK
03:15 – 05:45 PM	R/qtlbim Demo & Hands-on	Brian Yandell, Ph.D.

Thu 7/16/2009

Time	Topic	Speaker	Resource(s)
08:00 – 09:15 AM	Design & Analysis of Copy number polymorphisms	Hemant Tiwari, Ph.D.
09:15 – 10:30 AM	Pathway Analysis: Functional Statistical Genetics & Bioinformatics	L. Kelly Vaughan, Ph.D./ David B. Allison, Ph.D.
10:30 – 10:45 AM	BREAK
10:45– 12:00 PM	Low-level Analysis of Proteomics Data	Kimberly Sellers, Ph.D.
12:00– 01:00 PM	Lunch
01:00 - 02:15 PM	Exploring Systems Medicine Using Translational Bioinformatics	Atul Butte, Ph.D.
02:15 – 02:30 PM	BREAK
02:30 – 05:30 PM	CNV & Pathway Demo & Hands-on	Faculty (led by Hemant K. Tiwari, Ph.D.)

Fri 7/17/2009

Software Hands-On: Participants Pre-read
To insure the depth and practicality of the training program, we will provide 10 laptops to students or student pairs in the classroom. Each computer will be loaded with statistical software including but not limited to SAGE, Mx, Genehunter, Genomic Control programs, STRUCTURE, Ancestry Map, SIMWALK, MERLIN, QTL Express, R/QTL, BQTL, Dandelion, HDBSTAT!, Bioconductor Suite, Phase and Arlequin (all freely available) as well as S-Plus, SPSS and SAS. Many of the faculty have substantial expertise with the use of software for statistical genetics and have even authored some. Please feel invited to bring your own laptop.

In response to feedback from last year’s short course, we have also re-scheduled the relevant software demonstration and hands-on computer lab immediately after the lectures on each day. For example, the microarray software demo and hands-on lab will immediately follow the lectures on microarray analysis that day. In addition, the instructors will provide well-annotated slides and structure the software demonstration in such a way that students may follow each hands-on example on their own computers. Also, we have reserved four hours on the last day of the course for additional guided practice and to address remaining software questions.

UAB Faculty:

• David Allison, Ph.D.
• Hemant Tiwari, Ph.D.
• L. Kelly Vaughan, Ph.D.
• Jelai Wang

External Faculty:

• Atul Butte, M.D., Ph.D.: Stanford University
• Warren J Ewens, Ph.D.: The University of Pennsylvania
• Soledad Fernandez, Ph.D.: Ohio State University
• Rebecka Jenny Jornsten, Ph.D.: Rutgers University - Busch Campus
• Carl Langefeld, Ph.D: Wake Forest University
• Kimberly F. Sellers, Ph.D.: Georgetown University
• Guilherme J. M. Rosa, Ph.D.: University of Wisconsin - Madison
• Bruce Walsh, Ph.D.: University of Arizona - Tucson
• Brian Yandell, Ph.D.: University of Wisconsin - Madison

Full List of External Rotating Faculty can be found by Click here.

Contact Information:

Logistics: Richard Sarver
Department of Biostatistics
1665 University Blvd, RPHB 414
University of Alabama at Birmingham
Birmingham, AL 35294-0022
Phone: (205) 975-9169
Email: rsarver@uab.edu

Scientific: Hemant K Tiwari, PhD
Department of Biostatistics
1665 University Blvd, 420B
University of Alabama at Birmingham
Birmingham, AL 35294-0022
Phone: (205) 934-4907
Email: HTiwari@ms.soph.uab.edu