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bioRxiv · 10.1101/2020.07.22.215426

A novel PS4 criterion approach based on symptoms of rare diseases and in-house frequency data in a Bayesian framework.

Cho, Y. K.·Won, D.-g.·Keum, C.·Seo, G. H.·Lee, B. H.·Lee, B.-C.
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Abstract

The American College of Medical Genetics (ACMG) and Genomics/Association for Molecular Pathology (AMP) previously reported standardized guidance for the assessment of genetic variants. One of the criteria regarding the prevalence in a case-control study, PS4, is important due to its evidence of pathogenicity. Despite recent studies approaching gene- and disease-specific probands, interpretation of a variant to PS4 still has certain limitations for rare variants. Here, we suggest a generalized method, Bayesian odds ratio (BayesianOR), applicable to PS4 via decomposing a disease to its symptoms and applying a Bayesian framework. Using this approach, we demonstrate reproducibility of the calculation of the original odds ratio from well-studied epilepsy data and verify the applicability to in-house frequencies for various rare diseases. In addition, BayesianOR showed a significant difference in tendency with different ClinVar pathogenicity, using in-house data. Thus, the novel method described here should provide an improved interpretation of sequence variants. Furthermore, we anticipate that it will enhance the diagnosis of patients with rare diseases.

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Cho, Y. K., Won, D.-g., Keum, C., Seo, G. H., Lee, B. H., Lee, B.-C.. 2020-07-24. A novel PS4 criterion approach based on symptoms of rare diseases and in-house frequency data in a Bayesian framework.. https://doi.org/10.1101/2020.07.22.215426

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