December 6, 2016. Finding mutations in transcription factor binding sites with MutationForecaster

Genome-scale transcription factor binding site analysis now available on MutationForecaster:
Cytognomix‘s goal is to enable complete gene or genome bioinformatic mutation interpretation for our customers and partners. We will be introducing multiple new types of mutation analyses to our MutationForecaster ® product over the coming year.

We are excited to announce the first of these innovations is now available. It uses the Shannon pipeline framework to present results of genome-wide variant analysis, except in additon to splicing mutations it will identify transcription factor binding site mutations in gene promoters. Genome-scale variants can now be examined for changes in 94 primary and 23 cofactor transcription factor binding motifs to discover mutations in binding sites based on their effects on binding affinity to these factors.  We have recently published 2 large patient-based studies where we have prioritized these and other types mutations for inherited breast cancer:
Caminsky NG, Mucaki EJ, Perri AM, Lu R, Knoll JHM and Rogan PK. Prioritizing variants in complete Hereditary Breast and Ovarian Cancer (HBOC) genes in patients lacking known BRCA mutations. Human Mutation, 37:640-52, 2016.
Mucaki, E*, Caminsky N*, Perri A, Lu R, Laederach A, Halvorsen, M, Knoll, JHM, Rogan PK. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer, BMC Medical Genomics, 9:19, 2016.
The information theory based models of these transcription factor binding sites have been validated by 4 different experimentally-derived, statistical, and thermodynamic approaches. These are described in this recently published article:
Lu R, Mucaki EJ and Rogan PK. Discovery and validation of information theory-based transcription factor and cofactor binding site motifs. Nucleic Acids Res. Advance online publication. doi:10.1093/nar/gkw1036
A reminder that Cytognomix continues to offer a free trial of this new tool and the majority of our MutationForecaster® genome interpretation suite to all registrants. No subscription is required to examine sample data from any of our software tools. Trial users are provided with the same datasets that we have analyzed in our peer-reviewed publications.

Once you see the discoveries that only MutationForecaster® can make, we are confident that you will sign up for a subscription to analyze your own data.

Contact us if you have questions.

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