Brcapro Software Download

BRCAPRO is a statistical model, with associated software, for assessing the probability that an individual carries a germline deleterious mutation of the BRCA1. BRCAPro does perform well in certain. Dec 1, 2009 - 809 Downloads; 5 Citations. BRCA1 BRCA2 BRCAPRO Mutation Myriad II Probability model Unclassified variants. Calculated with the CancerGene software package from the University of Texas Southwestern Medical.

BRCAPRO is a widely used model for genetic risk prediction of breast cancer. It is a function within the R package BayesMendel and is used to calculate the probabilities of being a carrier of a deleterious mutation in one or both of the BRCA genes, as well as the probability of being affected with breast and ovarian cancer within a defined time window. Both predictions are based on information contained in the counselee’s family history of cancer. During the last decade, BRCAPRO has undergone several rounds of successive refinements: the current version is part of release 2.1 of BayesMendel. In this review, we showcase some of the most notable features of the software resulting from these recent changes. We provide examples highlighting each feature, using artificial pedigrees motivated by complex clinical examples.

We illustrate how BRCAPRO is a comprehensive software for genetic risk prediction with many useful features that allow users the flexibility to incorporate varying amounts of available information. Introduction: Background The BRCAPRO genetic risk prediction model is widely used in genetic counseling and is freely available through the open source R package BayesMendel and through a web based risk service interface. Genetic counseling packages Cancer-Gene and HughesRiskApps (HRA) also embed BRCAPRO calculations. BayesMendel is a statistical package designed to calculate Mendelian risk prediction of different types of inherited disease, according to the family history provided as an input. It includes several modules: BRCAPRO [breast and ovarian cancer (BC and OC)], MMRpro (colorectal and endometrial cancer), PancPRO (pancreatic cancer), and MelaPRO (melanoma) models, as well as the functionality to adapt these models to specific populations and to develop new Mendelian risk prediction models for other syndromes.

The BayesMendel R package has been consistently updated during the last decade: 11 versions were released from 2004 to 2007 (versions 1.1–15 to 1.4–3). These versions allowed input of family history up through relatives of first and second degree to the counselee. Starting with version 2.0 in 2008, relatives of any degree could be included in the family history, and 11 versions of BayesMendel were released from 2008 to 2014 (versions 2.0–1 to the currently available 2.1–1).

The different risk modules of the BayesMendel package, in general, return as output •. The future risk of OC for an unaffected counselee. As it will be shown in one example, the standard time window used for the risk prediction is 5 years, but this can be modified by the user to any value. Here we review some of the most useful features that have been incorporated in the recent releases of BayesMendel, focusing only on BRCAPRO, and illustrating each feature with examples. Only in one case we will refer directly to the output of the R version of BRCAPRO for listing the results that the software returns under different scenarios. The same results are provided by CancerGene, HRA, and the online risk service.

In fact, CancerGene and HRA are directly used for counseling, while the role of the R version is at the back-end of these tools, to supply the numerical results only. Thus, these clinical tools are better equipped with counseling-friendly features such as graphs and tables showing various diagnosis and risks to help make clinical decisions.

Here we focus on illustrating various features of the R package directly, rather than specific outputs of CancerGene and HRA. Methods For the purpose of illustration, we use artificially generated families.

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In these examples, we consider “large” (29 individuals or more) as well as “small” (10 individuals or less) families. We have chosen families with different types and numbers of members to illustrate variations in the distributions of the diseases and age of onset across the family members. Software aplikasi antrian. Specifically, we include families with occurrence of BC only, families with BC and OC diagnoses, a family with no cancer diagnoses, a family with one BC within a pair of twin sisters, and a family including rare occurrence of male BC. These choices allow us to give a more complete description of the software capabilities, and show how its applicability is not restricted to family with a specific size or structure. From a computational standpoint, we note that BRCAPRO results are not affected by the size or type of the pedigree, but it is reasonable to expect that the accuracy of the risk estimates will increase with more information (including size) on the pedigree if that information is correct. In a few examples, we modify some of the information in a pedigree to demonstrate specific features of BRCAPRO.

BRCAPRO is a statistical model, with associated software, for assessing the probability that an individual carries a germline deleterious mutation of the BRCA1. BRCAPro does perform well in certain. Dec 1, 2009 - 809 Downloads; 5 Citations. BRCA1 BRCA2 BRCAPRO Mutation Myriad II Probability model Unclassified variants. Calculated with the CancerGene software package from the University of Texas Southwestern Medical.

BRCAPRO is a widely used model for genetic risk prediction of breast cancer. It is a function within the R package BayesMendel and is used to calculate the probabilities of being a carrier of a deleterious mutation in one or both of the BRCA genes, as well as the probability of being affected with breast and ovarian cancer within a defined time window. Both predictions are based on information contained in the counselee’s family history of cancer. During the last decade, BRCAPRO has undergone several rounds of successive refinements: the current version is part of release 2.1 of BayesMendel. In this review, we showcase some of the most notable features of the software resulting from these recent changes. We provide examples highlighting each feature, using artificial pedigrees motivated by complex clinical examples.

We illustrate how BRCAPRO is a comprehensive software for genetic risk prediction with many useful features that allow users the flexibility to incorporate varying amounts of available information. Introduction: Background The BRCAPRO genetic risk prediction model is widely used in genetic counseling and is freely available through the open source R package BayesMendel and through a web based risk service interface. Genetic counseling packages Cancer-Gene and HughesRiskApps (HRA) also embed BRCAPRO calculations. BayesMendel is a statistical package designed to calculate Mendelian risk prediction of different types of inherited disease, according to the family history provided as an input. It includes several modules: BRCAPRO [breast and ovarian cancer (BC and OC)], MMRpro (colorectal and endometrial cancer), PancPRO (pancreatic cancer), and MelaPRO (melanoma) models, as well as the functionality to adapt these models to specific populations and to develop new Mendelian risk prediction models for other syndromes.

The BayesMendel R package has been consistently updated during the last decade: 11 versions were released from 2004 to 2007 (versions 1.1–15 to 1.4–3). These versions allowed input of family history up through relatives of first and second degree to the counselee. Starting with version 2.0 in 2008, relatives of any degree could be included in the family history, and 11 versions of BayesMendel were released from 2008 to 2014 (versions 2.0–1 to the currently available 2.1–1).

The different risk modules of the BayesMendel package, in general, return as output •. The future risk of OC for an unaffected counselee. As it will be shown in one example, the standard time window used for the risk prediction is 5 years, but this can be modified by the user to any value. Here we review some of the most useful features that have been incorporated in the recent releases of BayesMendel, focusing only on BRCAPRO, and illustrating each feature with examples. Only in one case we will refer directly to the output of the R version of BRCAPRO for listing the results that the software returns under different scenarios. The same results are provided by CancerGene, HRA, and the online risk service.

In fact, CancerGene and HRA are directly used for counseling, while the role of the R version is at the back-end of these tools, to supply the numerical results only. Thus, these clinical tools are better equipped with counseling-friendly features such as graphs and tables showing various diagnosis and risks to help make clinical decisions.

Here we focus on illustrating various features of the R package directly, rather than specific outputs of CancerGene and HRA. Methods For the purpose of illustration, we use artificially generated families.

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In these examples, we consider “large” (29 individuals or more) as well as “small” (10 individuals or less) families. We have chosen families with different types and numbers of members to illustrate variations in the distributions of the diseases and age of onset across the family members. Software aplikasi antrian. Specifically, we include families with occurrence of BC only, families with BC and OC diagnoses, a family with no cancer diagnoses, a family with one BC within a pair of twin sisters, and a family including rare occurrence of male BC. These choices allow us to give a more complete description of the software capabilities, and show how its applicability is not restricted to family with a specific size or structure. From a computational standpoint, we note that BRCAPRO results are not affected by the size or type of the pedigree, but it is reasonable to expect that the accuracy of the risk estimates will increase with more information (including size) on the pedigree if that information is correct. In a few examples, we modify some of the information in a pedigree to demonstrate specific features of BRCAPRO.