Julia Krushkal
Linkage Analysis, LINKAGE and RH Map Construction:
a Tutorial for Students
This page was created as a by-product of bioinformatics courses I teach, when I was searching for materials to offer to students that would be related to linkage and RH analysis. This is not a comprehensive list, as other resources for linkage and RH mapping exist.
This session will allow a student to achieve the following goals:
1. Get familiar with resources for linkage analysis;
- Learn about LINKAGE
format, a common format in genetic linkage analysis;
- Learn how to build a
genetic linkage map using an array of microsatellite markers;
- Learn how to build a
radiation hybrid map using an array of radiation hybrid markers
- View a sample
software that visualizes plant crosses
- (Added at a later
time) Run a linkage analysis program via the Web.
1. Let us first learn about available resources for linkage analysis.
Go to http://linkage.rockefeller.edu/
This is a Web site of the research group of Dr. J. Ott at Rockefeller University, which contains excellent resources for linkage analysis.
First, follow a link to the list of available genetic analysis programs. View this list.
Next, return to the previous page and explore three links under Linkage bibliography:
Sibpair analysis and
Allele-sharing method
Variance components of
quantitative traits
Linkage algorithms
This is a great place to learn about current literature on linkage analysis.
2. Now, let us learn about the LINKAGE format. Return to http://linkage.rockefeller.edu/ and follow the link to GENEHUNTER, or go directly to http://linkage.rockefeller.edu/soft/gh/
GENEHUNTER is a program for non-parametric multipoint linkage analysis, but it uses a standard LINKAGE format. Follow the links to SCAN PEDIGREES and LOAD MARKERS to learn about the structure of the pedigree file data and the marker data.
3. Now, let us try to build some genetic maps of markers. First, let us try to insert a marker into an existing map of markers. Go to http://linkage.rockefeller.edu:1802/mapomat/
Select "ALL" on the left hand side and proceed to run ALL demo. Follow the instructions and click "Do calculation". View the results and click "Get Map Distances" to evaluate the map distances.
Next, let us choose a different approach - build a map de novo using existing information about marker locations. Go to Marshfield Center:
http://research.marshfieldclinic.org/genetics/Map_Markers/mapmaker/MapFormFrames.html
Proceed to sample input and output. View comprehensive maps.
4. We will now proceed to build radiation hybrid maps. Go to http://www.cs.technion.ac.il/Labs/cbl/CGI/rh-wizard.pl
Follow the link to the Whitehead file format to see how the data looks like. Now return to the previous page and type in your e-mail address. Click "Continue".
Now we will look at another RH mapping resource: http://rhbase.med.upenn.edu/rh/
You will need to select a user ID and a password. Note that this site, although very helpful for RH learning, may not be appropriate for a large class where many students may need to log in simultaneously.
To view how the RH data should look like, go to
http://www.jax.org/resources/documents/cmdata/rhmap/rh.html (view data for chromosome 1)
http://waldo.wi.mit.edu/mouse_rh/ (look at release 9 text file New)
5. To view plant crosses, go to http://jiio5.jic.bbsrc.ac.uk:8000/newframe.html Look at the map of plant loci.
6. This link was provided to me at a time after the tutorial, and it allows one to run a linkage program via the Web as described in several papers by Zhao et al. (the references are provided on the Web site):
http://cougar.fhcrc.org/~filq/html/main.htm
Acknowledgements:
Thanks to Drs. C. Letondal, D. Duffy, and A. Alavizadeh for assistance with some of these links.
Disclaimer
The information in this page is provided as a courtesy by the author. The author expressly disclaims any representation or warranty express or implied concerning the accuracy, completeness or fitness for a particular purpose of the information. Persons accessing this information assume full responsibility for the use of the information and understand and agree that the author is not responsible or liable for any claim, loss or damage arising from the use of the information. Reference to specific products, processes, or services do not constitute or imply recommendation or endorsement by the author. This information is designed for educational purposes only and is not provided as a professional service or as medical advice for specific patients.
This page last updated: 05-05-2003