Analysis of Genotyping Results

Advances in high throughput genotyping, as exemplified by the Illumina system in use by our facility, have resulted in very large data sets that can comprise hundreds of thousands of genotypes. Effective statistical analysis of these data is an ongoing challenge. The UC Davis Genome Center is attempting to address this need through services provided by the Bioinformatics Core. This core is directed by Dawei Lin (lhslin@ucdavis.edu) and he is in the process of setting up analytical and educational resources to enable the campus community (and others) to derive useful information from the data generated by high throughput genotyping approaches.  These approaches are not necessarily limited to data sets generated on platforms in use by the DNA Technologies Core.  Dr. Lin is always interested in hearing from researchers about what services they feel would be most valuable so please don't hesitate to contact him.

Software

Genetic Analysis Software   Computer software on the following topics are included in this giant resource of nearly 400 programs: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics.  Originally created by Wentian Li and currently housed at the North Shore LIJ Research Institute, this list is offered as a service to the gene mapping community.

NCBI Genetic Analysis Software  This page briefly summarizes several ongoing projects and provides hyperlinks to more detailed pages about each project, downloadable software, and references for papers.

The Human Genetic Analysis Resource  H.G.A.R. is an NIH supported resource that provides services and expertise in the form of collaborative associations and through the distribution of the Statistical Analysis for Genetic Epidemiology (S.A.G.E. - Principal Investigator, Robert C. Elston) software package. The Resource entertains requests for collaboration from research workers who are collecting pedigree data and wish to have their data analyzed by appropriate statistical methods. 

Michelmore Lab tools  An interesting locally developed set of programs for genetic analysis can be found on Richard Michelmore's web site.  Several of these programs are distinguished by powerful graphical representations of complex genetic data sets.

 

This is just a sampling of many of the available tools for genetic analysis found via the internet. Please feel free to let us know about any other particularly interesting or useful resources that you find, and we can add them to this page.