Summer Institute in Statistical Genetics

North Carolina State University - Raleigh, NC

May 26-June 11, 1999

Welcome

Welcome to the 4^th annual Summer Institute in Statistical Genetics offered by the Department of Statistics at North Carolina State University from May 26 through June 11, 1999.

General Information

A series of three-day workshops designed to introduce geneticists to modern methods of statistical analysis and to introduce statisticians to quantitative problems arising in modern genetics. The workshops will be held on the campus of NC State University. Continuing education units (CEUs) will be awarded to all participants. Prerequisites are minimal, and the modular nature of the Institute will enable participants to devise a program to suit their background and interests.

Course Credits

Continuing Education Units (CEUs) are offered for the modules attended. CEUs are awarded as 1.8 continuing education units per module.

Fees

There is a one-time, non-refundable application fee of $25 per person regardless of how many modules are requested. Each module has a tuition fee of $300. Graduate students and postdoctoral students may apply for scholarships to offset some of the tuition costs and provide some travel assistance (see Application Procedure below). Fees cover tuition, course notes, textbooks, breaks and lunches.

Scholarships

A small number of tuition and/or travel scholarships are available for students (undergraduate, graduate and postdoctoral). Applications should be received by March 31, 1999 and should consist of a letter to explain the reason for interest in the Institute, a one-page CV, and a letter from the student's major advisor.

Housing

On and off-campus housing is available. Hotel rates are listed below; reservations should be made directly with the hotel.

Off-Campus - Hotels

Brownestone Hotel, 1707 Hillsborough Street, Raleigh NC 27607 (half-mile from campus)

Rates: Single Room: $69 per night Double: $79 per night

(includes full breakfast buffet)

For reservations, call:

1-800-331-7919 (in NC) 1-800-237-0772 (outside NC)

Velvet Cloak Inn, 1505 Hillsborough Street, Raleigh NC 27605 (3/4 mile from campus)

Rates: Single Room: $69 per night Double $79 per night

For reservations, call:

1-800-662-8829 (inside NC) 1-800-334-4372 (outside NC)

Reference the Summer Institute when making reservations. Both hotels are within walking distance to the University and the Summer Institute.

On-Campus - University Towers

Room rate: $36 per night

University Towers is a private dormitory, within 5 minutes walking distance to the Summer Institute. It is located on Friendly Drive, which is directly off of Hillsborough Street. Parking is available free-of-charge and there is someone at the front desk 24-hours a day. Each room is air-conditioned and accommodates two people; every two rooms share a bath. The facility has a lounge on each floor, and a coin-operated laundry, exercise room, and outdoor pool. University Towers also has a cafeteria, which provides breakfasts and dinners Monday through Friday for a minimal fee; meal tickets can be purchased at the front desk (lunches are already included in the module fee and will be provided during your participation in the Summer Institute). Linens will be provided and are changed weekly. For on-campus room reservations, please check the box on the application form or contact Debra Hibbard at the address below.

Administrative Staff

Program Director

Dr. Bruce S. Weir

William Neal Reynolds Professor of Statistics and Genetics

Program in Statistical Genetics, Department of Statistics

NC State University

Computing Coordinator

Dr. Christopher Basten

Research Associate Statistician

Program in Statistical Genetics, Department of Statistics

NC State University

Program Coordinator

Debra Hibbard

Program in Statistical Genetics

Department of Statistics

NC State University

Faculty

Faculty involved in the instructional program include:

Dr. Christopher J. Basten, Research Associate Statistician

Program in Statistical Genetics, Department of Statistics, NC State University

Dr. Roger L. Berger, Professor

Department of Statistics, NC State University

Dr. Dennis D. Boos, Professor of Statistics

Department of Statistics, N.C. State University

Dr. John C. Brocklebank, Manager

Analytic Solutions

SAS Institute Inc.

Cary, NC

Dr. John Buckleton, Science Leader

ESR:Forensic, New Zealand

Dr. Edward S. Buckler III, Assistant Professor

Department of Genetics, NC State University

Dr. James M. Curran, Postdoctoral Fellow

Program in Statistical Genetics, Department of Statistics, NC State University

Dr. Marie Davidian, Professor of Statistics

Department of Statistics, NC State University

Dr. Rebecca Doerge, Assistant Professor

Department of Statistics

Purdue University

West Lafayette, IN

Dr. Ted H. Emigh, Associate Professor

Department of Genetics, NC State University

Dr. James Fry, Assistant Professor

Department of Biology

Utah State University

Dr. Brandon S. Gaut, Assistant Professor

Department of Ecology and Evolutionary Biology

University of California

Irvine, CA

Dr. Sujit K. Ghosh, Assistant Professor

Department of Statistics, NC State University

Dr. Jotun J. Hein, Associate Professor

University of Aarhus

Aarhus, Denmark

Dr. Ina Hoeschele, Professor of Genetics

Virginia Polytechnic Institute and State University

Blacksburg, VA

Dr. Jacqueline Hughes-Oliver, Assistant Professor

Department of Statistics, NC State University

Dr. Lynn B. Jorde, Professor and Associate Chairman

Department of Human Genetics

University of Utah

Dr. Peter Keightley, Royal Society University Research Fellow

Institute for Cell, Animal and Population Biology

University of Edinburgh

Edinburgh, Scotland, UK

Dr. Thomas B. Kepler, Associate Professor

Department of Statistics, NC State University

Charles E. Lawrence, Chief, Biometrics Laboratory

Wadsworth Center

New York State Department of Health

Paul O. Lewis, Assistant Professor

Department of Ecology and Evolutionary Biology

The University of Connecticut

Storrs, CT

Dr. Trudy F. C. Mackay, William Neal Reynolds Professor of Genetics

Department of Genetics, NC State University

Dr. Eden R. Martin, Associate in Medicine

Department of Medicine, Section of Medical Genetics

Duke University

Durham, NC

Dr. Lauren M. McIntyre, Assistant Research Professor

Duke University Medical Center

Durham, NC

Dr. Spencer V. Muse, Assistant Professor

Program in Statistical Genetics, Department of Statistics, NC State University

Dr. Ian S. Painter, Research Scientist

Talaria Inc.

Seattle WA

Dr. Michael D. Purugganan, Assistant Professor

Department of Genetics, NC State University

Dr. Katy L. Simonsen, Assistant Professor

Department of Statistics

Purdue University

West Lafayette, IN

Dr. Jeffrey L. Thorne, Assistant Professor

Program in Statistical Genetics, Department of Statistics, NC State University

Dr. Marta L. Wayne, Assistant Professor

Department of Biology

Florida State University

Gainesville, FL

Dr. Bruce S. Weir, William Neal Reynolds Professor of Statistics and Genetics

Program in Statistical Genetics, Department of Statistics, NC State University

Dr. Brian Yandell, Professor

Department of Statistics

University of Wisconsin

Madison, WI

Dr. Zhao-Bang Zeng, Research Associate Professor of Statistics

Program in Statistical Genetics, Department of Statistics, NC State University

Application Procedure

Space will be limited in each module, with no guarantees of availability for applications received later than March 31, 1998. A fee of $25 must accompany all applications. This fee is not refundable, unless space is not available. The balance of tuition fees are due by the beginning of each module. Take advantage of $50 discount if full payment received prior to April 30, 1999. Payment can be made by institutional purchase order, cash, or by check or money order drawn on a US bank and made payable to "North Carolina State University."

Applications should be sent to:

Ms Debra Hibbard
Summer Institute in Statistical Genetics
Department of Statistics
North Carolina State University
Raleigh NC 27695-8203
Phone: (919) 515-1932
FAX: (919) 515-7315
e-mail: hibbard@stat.ncsu.edu

Courier Address:
Room 220 Patterson Hall
NC State University
Raleigh NC 27695-8203

Instructional Program and Fees

Module 1. Genetics for Statisticians. ($300)

Instructors: T. H. Emigh and M. D. Purugganan

Dates: May 26, 27, 28

Syllabus: This module is targeted at statisticians and covers Mendel's laws, DNA as genetic material, the central dogma, organization and transmission of nuclear and cytoplasmic genomes, and mutation. Techniques for detecting and characterizing allelic variation, especially at the DNA level via restriction enzymes and PCR will be described. Laboratory visits are included. The module serves as a foundation for all later modules, except modules 2, 3, and 4.

Text: Gonick and Wheelis, "The Cartoon Guide to Genetics," Harper.

Module 2. Statistics for Geneticists I ($300)

Instructors: D. D. Boos and J. Hughes-Oliver

Dates: May 26, 27, 28

Syllabus: This module covers the laws of probability and the basic probability distributions: binomial, multinomial and normal. Methods of inference include maximum likelihood, confidence intervals, numerical resampling, exact and permutation tests, and chi-square tests. Software developed by the instructors is used to illustrate the methods taught. The module serves as a foundation for all later modules, except module 3.

Text: Gonick and Smith, "The Cartoon Guide to Statistics," Harper.

Module 3. Forensic and Paternity Data Analysis ($300)

Instructors: J. Buckleton and B. S. Weir

Dates: May 26, 27, 28

Syllabus: This module is aimed at a specialist audience, although some evolutionary biologists have taken it in previous years because it covers several population genetic topics. There is a growing use of DNA profiles for identification by seed companies and wildlife protection agencies, for example. It covers Bayes' theorem, genotype probabilities for one and two individuals, interpretation of matching genetic profiles from one or more contributors, paternity index calculations, and the effects of relatives and population structure. It is designed to stand alone, but can also be taken in conjunction with any of the other modules.

Text: Evett and Weir, "Interpreting DNA Evidence," Sinauer

Module 4. Statistics for Geneticists II. ($300)

Instructors: M. Davidian and T. B. Kepler

Dates: May 30, 31, June 1

Syllabus: This module is designed especially as a foundation for the quantitative genetics and QTL mapping modules. It covers regression, analysis of variance and variance components and can either be taken as a first module or following module 2. The material covered is assumed in modules 6, 8, 10, 13.

Text: Gonick and Smith, "The Cartoon Guide to Statistics," Harper.

Module 5. Population Genetic Data Analysis ($300)

Instructors: B. S. Weir, P. O. Lewis, I. S. Painter

Dates: May 30, 31, June 1

Syllabus: This module covers estimation of allele frequencies, inferences about disequilibrium

and population structure, linkage estimation and linkage disequilibrium mapping. Participants will gain experience with the GDA software package, designed to accompany the text and written by P. O. Lewis and D. Zaykin. Lewis and Zaykin will teach the computer labs for these modules. Assumes the material in Modules 1 and 2.

Text: B.S. Weir "Genetic Data Analysis II," Sinauer.

Module 6. Principles of Quantitative Genetics ($300)

Instructors: T. F. C. Mackay, P. Keightley, and J. Fry

Dates: May 30, 31, June 1

Syllabus: This module covers quantitative trait models, variances and covariances of relatives, estimation of variance components, response to selection and the effects of mutation. The module can stand alone but the material covered is necessary fro understanding modules 9, 10, and 13. Assumes the material in modules 1, 2, and 4.

Text: Falconer and Mackay, "Introduction to Quantitative Genetics (4th Edition)," Longman.

Module 7. Population Genetic Data Analysis (duplicates Module 5) ($300)

Instructors: B. S. Weir, P. O. Lewis, I. S. Painter

Dates: June 2, 3, 4

Syllabus: This module covers estimation of allele frequencies, inferences about disequilibrium and population structure, linkage estimation and linkage disequilibrium mapping. Participants will gain experience with the GDA software package, designed to accompany the text and written by P. O. Lewis and D. Zaykin. Lewis and Zaykin will teach the computer labs for these modules. Assumes the material in Modules 1 and 2.

Text: B.S. Weir "Genetic Data Analysis II," Sinauer.

Module 8: Quantitative Trait Gene Mapping I

Instructors: Z-B. Zeng, C. J. Basten, and R. Doerge

Dates: June 2, 3, 4

Syllabus: This module covers linkage map construction, single-marker analyses, multiple and partial regression methods, internval and composite-interval mapping. Attention is paid to determining significance levels. Participants will use Zeng and Basten's QTL-CARTOGRAPHER computer package. Assumes the material in modules 1, 2, 4, and 6.

Text: Lynch and Walsh, "Genetics and Analysis of Quantitative Traits," Sinauer.

Module 9: Human Disease Gene Mapping

Instructors: L. B. Jorde, E. R. Martin, B. S. Weir, J. C. Brocklebank

Dates: June 6, 7, 8

Syllabus: This module covers both the statistical aspects of tests such as case-control comparisons, the TDT test and the population-genetic models that lead to association. Extensions to quantitative traits are covered. Data mining. Assumes the material in modules 1 and 2. Modules 5 or 7 would be helpful but not necessary.

Text: Weir, "Genetic Data Analysis," Sinauer.

Module 10: Quantitative Trait Gene Mapping I (duplicates Module 8)

Instructors: Z-B. Zeng, C. J. Basten, B. Yandell and R. Doerge

Dates: June 6, 7, 8

Syllabus: This module covers linkage map construction, single-marker analyses, multiple and partial regression methods, interval and composite-interval mapping. Attention is paid to determining significance levels. Participants will use Zeng and Basten's QTL-CARTOGRAPHER computer package. Assumes the material in modules 1, 2, 4, and 6.

Text: Lynch and Walsh, "Genetics and Analysis of Quantitative Traits," Sinauer.

Module 11: Molecular Evolution

Instructors: J. L. Thorne, S. V. Muse, B. S. Gaut, K. L. Simonsen, M. L. Wayne

June 6, 7, 8

Syllabus: This module gives an overview of methods for studying evolution with DNA and protein sequence data. Statistical methodology is emphasized and computational algorithms and software implementations will also be introduced. Module topics include: phylogeny reconstruction, molecular evolution, and molecular population genetics. Software tutorials will be interwoven throughout the module. An evening session gives students the opportunity to seek assistance in analyzing their own data as well as the chance to pursue the topics in evolution that most interest them. Assumes the material in modules 1 and 2. Material in modules 5 or 7 would be helpful, but not necessary.

Text: Li, "Molecular Evolution," Sinauer.

Module 12: Quantitative Trait Gene Mapping II

Instructors: Z-B Zeng, C. J. Basten, B. Yandell and I. Hoeschele

June 9, 10, 11

Syllabus: This second QTL module is designed for participants with stronger statistical skills. Epistatic models and the application of Bayesian methods will be covered. Use software for multiple interval mapping technique, with inclusion of epistatic interactions among multiple QTLs. Assumes the material in modules 1, 2, 4 and 9 or 10.

Text: Lynch and Walsh, "Genetics and Analysis of Quantitative Traits," Sinauer.

Module 13: Bioinformatics

Instructors: S. V. Muse, J. L. Thorne, J. J. Hein, C. E. Lawrence

Syllabus: This module will cover alignment, database searching,and protein structure. Assumes materials in modules 1 and 2.

Text: Durbin, Eddy, Krogh and Mitchison, "Biological Sequence Analysis," Cambridge University Press.

Daily Schedule

Each day will cover four instructional periods:

Period I 8:30 a.m. - 10:00 a.m.

Break 10:00 a.m. - 10:30 a.m.

Period II 10:30 a.m. - 12:00 Noon

LUNCH 12:00 Noon - 1:30 p.m.

Period III 1:30 p.m. - 3:00 p.m.

Break 3:00 p.m. -- 3:30 p.m.

Period IV 3:30 p.m. - 5:00 p.m.

Some modules may schedule evening discussion sessions. Breaks and lunches are included in tuition fees.

Enquiries

Enquiries should be addressed to Dr B.S. Weir at the same address as Ms Hibbard, or to weir@stat.ncsu.edu. For further information about the Program in Statistical Genetics at NC State University, please see our web page (http://stat.ncsu.edu/).

1999 SUMMER INSTITUTE IN STATISTICAL GENETICS