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. 2004:3:Article21.
doi: 10.2202/1544-6115.1063. Epub 2004 Sep 17.

BayesMendel: an R environment for Mendelian risk prediction

Sining Chen  1 , Wenyi Wang, Karl W Broman, Hormuzd A Katki, Giovanni Parmigiani
Affiliations

BayesMendel: an R environment for Mendelian risk prediction

Sining Chen et al. Stat Appl Genet Mol Biol. 2004.

Abstract

Several important syndromes are caused by deleterious germline mutations of individual genes. In both clinical and research applications it is useful to evaluate the probability that an individual carries an inherited genetic variant of these genes, and to predict the risk of disease for that individual, using information on his/her family history. Mendelian risk prediction models accomplish these goals by integrating Mendelian principles and state-of-the-art statistical models to describe phenotype/genotype relationships. Here we introduce an R library called BayesMendel that allows implementation of Mendelian models in research and counseling settings. BayesMendel is implemented in an object-oriented structure in the language R and distributed freely as an open source library. In its first release, it includes two major cancer syndromes: the breast-ovarian cancer syndrome and the hereditary non-polyposis colorectal cancer syndrome, along with up-to-date estimates of penetrance and prevalence for the corresponding genes. Input genetic parameters can be easily modified by users. BayesMendel can also serve as a generic tool for genetic epidemiologists to flexibly implement their own Mendelian models for novel syndromes and local subpopulations, without reprogramming complex statistical analyses and prediction tools.

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Figures

Figure 1
Figure 1
An example suspected HNPCC syndrome pedigree. The arrow indicates the individual to be counseled (counselee). The counselee can be either a man or a woman. A man is indicated by a square and a woman by a circle. For each relative, cancer of the colorectum (CRC) or endometrium (EC) are indicated by a solid square or circle with the type of cancer, age at onset and microsatellite status (MSI for microsatellite instability, MSS for microsatellite stability) below it. Boldface numbers on the left correspond to the relative ID’s in Figure 2. Other numbers are ages.
Figure 2
Figure 2
Pedigree information matrix corresponding to the family of Figure 1.
See this image and copyright information in PMC

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