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BackgroundAdvances in next generation sequencing technologies have revolutionized our ability to discover the causes of rare genetic diseases. However, developing treatments for these diseases remains challenging. In fact, when we systematically analyze the US FDA orphan drug list, we find that only 8% of rare diseases have an FDA-designated drug. Our approach leverages three primary insights: first, diseases with gain-of-function mutations and late onset are more likely to have drug options; second, drugs are more often inhibitors than activators; and third, some disease-causing proteins can be rescued by allosteric activators in diseases due to loss-of-function mutations.ResultsWe have developed a pipeline that combines natural language processing and human curation to mine promising targets for drug development from the Online Mendelian Inheritance in Man (OMIM) database. This pipeline targets diseases caused by well-characterized gain-of-function mutations or loss-of-function proteins with known allosteric activators. Applying this pipeline across thousands of rare genetic diseases, we discover 34 rare genetic diseases that are promising candidates for drug development.ConclusionOur analysis has revealed uneven coverage of rare diseases in the current US FDA orphan drug space. Diseases with gain-of-function mutations or loss-of-function mutations and known allosteric activators should be prioritized for drug treatments.Electronic supplementary materialThe online version of this article (doi:10.1186/s13023-017-0614-4) contains supplementary material, which is available to authorized users.
BackgroundAdvances in next generation sequencing technologies have revolutionized our ability to discover the causes of rare genetic diseases. However, developing treatments for these diseases remains challenging. In fact, when we systematically analyze the US FDA orphan drug list, we find that only 8% of rare diseases have an FDA-designated drug. Our approach leverages three primary insights: first, diseases with gain-of-function mutations and late onset are more likely to have drug options; second, drugs are more often inhibitors than activators; and third, some disease-causing proteins can be rescued by allosteric activators in diseases due to loss-of-function mutations.ResultsWe have developed a pipeline that combines natural language processing and human curation to mine promising targets for drug development from the Online Mendelian Inheritance in Man (OMIM) database. This pipeline targets diseases caused by well-characterized gain-of-function mutations or loss-of-function proteins with known allosteric activators. Applying this pipeline across thousands of rare genetic diseases, we discover 34 rare genetic diseases that are promising candidates for drug development.ConclusionOur analysis has revealed uneven coverage of rare diseases in the current US FDA orphan drug space. Diseases with gain-of-function mutations or loss-of-function mutations and known allosteric activators should be prioritized for drug treatments.Electronic supplementary materialThe online version of this article (doi:10.1186/s13023-017-0614-4) contains supplementary material, which is available to authorized users.
ObjectiveRecognizing what physicians know and do not know about a particular disease is one of the keys to designing clinical decision support systems, since these systems can fulfill complementary role by recognizing this boundary. To our knowledge, however, no study has attempted to quantify how many diseases physicians actually know and thus the boundary is unclear. This study explores a method to solve this problem by investigating whether the vocabulary assessment techniques developed in the linguistics field can be applied to assess physicians’ knowledge.MethodsThe test design required us to pay special attention to disease knowledge assessment. First, to avoid imposing unnecessary burdens on the physicians, we chose a self-assessment questionnaire that was straightforward to fill out. Second, to prevent overestimation, we used a “pseudo-word” approach: fictitious diseases were included in the questionnaire, and positive responses to them were penalized. Third, we used paper-based tests, rather than computer-based ones, to further prevent participants from cheating by using a search engine. Fourth, we selectively used borderline diseases, i.e., diseases that physicians might or might not know about, rather than well-known or little-known diseases, in the questionnaire.ResultsWe collected 102 valid answers from 109 physicians who attended the seminars we conducted. On the basis of these answers, we estimated that the average physician knew of 2008 diseases (95% confidence interval: (1939, 2071)). This preliminary estimation agrees with the guideline for the national license examination in Japan, suggesting that this vocabulary assessment was able to evaluate physicians’ knowledge. The survey included physicians with various backgrounds, but there were no significant differences between subgroups. Other implication for researches on clinical decision support and limitation of the sampling method adopted in this study are also discussed, toward more rigorous estimation in future surveys.
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