We are building a new computer program, GENINFER, to assist genetic counselors in evaluating the risk of recurrence of genetic disorders based on the analysis of family pedigrees. The present version of the program integrates a convenient graphical interface that permits counselors to draw, examine and modify family pedigrees and to enter information relevant to risk analysis. It also includes a general-purpose Bayesian inference mechanism that permits the rapid calculation and display of probabilities of various genotypes, for the consultand and all other pedigree members. This is possible even in the presence of complex pedigrees with multiple consanguineous matings. The ability to support rapid calculation also enables the user to perform sensitivity analyses. Limitations of the prototype include a restriction to single-locus Mendelian disorders and an inability to make use of information from RFLP markers. Planned extensions include remedying these limitations, the incorporation of an algorithm for automated reformatting (layout) of an existing pedigree, improvements in the population genetic models used by the program, and connections to external databases for acquiring data on disease incidence, patterns of inheritance, mutation rates, penetrance, etc.

A discussion of the original version of the program is contained in a paper presented at MEDINFO-92, Pedigree Analysis for Genetic Counseling (or postscript version).

Current Effort

Ms. Rayka Yokoo has been implementing a new version of the Geninfer program intended to run as a signed Java applet, so that it can be made available to anyone on the Web.  As a part-time effort, it is not yet finished, not polished, and not fully debugged.  Nevertheless, you may be interested in trying it, in which case instructions may be found here.  In order to allow an applet to write files (containing disease models and family pedigrees) to your local hard disk, the default security sandbox of Java needs to be overridden, hence some complexities in installation.  Once the applet runs, you can create a disease model, then a family pedigree, and draw probabilistic inferences from the known genotypes and phenotypes of  some individuals to the unknown ones of others.

[GM Picture]
Gregor Mendel

[TB Picture]
Thomas Bayes

Geninfer Personnel

Geninfer is a collaborative effort between Peter Szolovits (principal investigator) of the Clinical Decision-Making Group of the Laboratory for Computer Science of the Massachusetts Institute of Technology and Susan Pauker, M.D., of the Harvard Community Health Plan. Many students have worked on various aspects of the program since its inception, including: Nomi Harris, Ed Yampratoom, William Stewart, Jennifer Wu, Jervis Lui, Jason Miller, and Rayka Yokoo.

Last modified: July 24, 2002

Peter Szolovits <>

CDM Projects