Statistical Genomics

Draft Proposal for a Course

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Course Scheduling

   First Meeting  Friday 4 September, 11am, room 351 Plant Sciences
   Credits        1 (participate/present chapters) or 2 (extra project)
   Class Number   Stat 698 (Cr/NC) or Stat 699 (A-F)
   Class Hours    once per week, 75min per class
   World Wide Web http://www.stat.wisc.edu/~yandell/statgen/

   Instructor     Brian Yandell, 4367 CSSC, 262-1157
                  yandell@stat.wisc.edu
Interested students should send email to yandell@stat.wisc.edu so that we can anticipate class size. Please indicate (briefly) your statistical and biological background, in terms of courses, degrees or practical experience. If you want to register, I will need your ID number.

Objective

The objective of this course is to familiarize students with state-of-the-art statistical methods for analyzing experiments involving genomic data in the form of molecular markers, genetic linkage maps and complex phenotypic (quantitative) traits. This is sometimes termed statistical genetics or classical genomics. Construction and comparison of linkage maps, and use of such maps to infer quantitative trait loci (QTL) will be covered. Issues involving whole-genome analysis will be highlighted.

Prerequisites

Biology students should have a year sequence in statistical methods (Stat/For/Hort 571-572 or equivalent) and a readiness to learn. Statistics students should have an appreciation for data analysis in biology. A general introduction to concepts of Mendelian inheritance is assumed (Genetics 466 or equivalent).

Rationale for a Reading Course

This course is not on the books and has never been taught. However, we are starting a reading course beginning this Fall 1998 using Ben Hui Liu's new book, Statistical Genomics. Consult his web page (http://www4.ncsu.edu/~benliu/) for features, table of contents, and how to order. While the title includes the term genomics, the focus of this book and this reading course is on classical genomics, often referred to as statistical genetics. Genome informatics is an important topic area that is beyond our scope (and not covered in this book either).

Several students have requested such a course, and we have started to organize this as a reading course for 1998-99. The plan as currently envisioned is to read through the first half (ch. 1-11) this Fall, and continue with QTL mapping (ch. 12-17, 19) in the Spring. I think we can handle 10-40 students. Course number (either 875 or 698/699) and department (stat? hort?) is being worked out. Some faculty in PBPG, animal breeding and genetics, and statistics/biostatistics have expressed interest in participating at some level. It is expected that students have a decent stat background (571-572) and some exposure to genetics (466).

Many students want to learn about computer tools (ch. 18). Our intent is to introduce some of these about the middle of the Fall, and encourage hands-on projects. Volunteers to help load software are appreciated.

Please note that this constitutes an overload, but that many faculty recognize the need for such a course. If you are interested please email yandell@stat.wisc.edu.

Last modified: Fri Oct 23 18:59:06 1998 by Brian Yandell (yandell@stat.wisc.edu)