Mapping drug biology to disease genetics to discover drug impacts on the human phenome.

Motivation: Medications can have unexpected effects on disease, including not only harmful drug side effects, but also beneficial drug repurposing. These effects on disease may result from hidden influences of drugs on disease gene networks. Then, discovering how biological effects of drugs relate to disease biology can both provide insight into the mechanism of latent drug effects, and can help predict new effects. Results: Here, we develop Draphnet, a model that integrates molecular data on 429 drugs and gene associations of nearly 200 common phenotypes to learn a network that explains drug effects on disease in terms of these molecular signals. We present evidence that our method can both predict drug effects, and can provide insight into the biology of unexpected drug effects on disease. Using Draphnet to map a drug's known molecular effects to downstream effects on the disease genome, we put forward disease genes impacted by drugs, and we suggest a new grouping of drugs based on shared effects on the disease genome. Our approach has multiple applications, including predicting drug uses and learning drug biology, with implications for personalized medicine. Availability and implementation: Code to reproduce the analysis is available at https://github.com/RDMelamed/drug-phenome.

Evaluating the concordance between International Classification of Diseases, Tenth Revision Code and stroke severity as measured by the National Institutes of Health Stroke Scale.

Background: The National Institutes of Health Stroke Scale (NIHSS) scores have been used to evaluate acute ischaemic stroke (AIS) severity in clinical settings. Through the International Classification of Diseases, Tenth Revision Code (ICD-10), documentation of NIHSS scores has been made possible for administrative purposes and has since been increasingly adopted in insurance claims. Per Centres for Medicare & Medicaid Services guidelines, the stroke ICD-10 diagnosis code must be documented by the treating physician. Accuracy of the administratively collected NIHSS compared with expert clinical evaluation as documented in the Paul Coverdell registry is however still uncertain. Methods: Leveraging a linked dataset comprised of the Paul Coverdell National Acute Stroke Program (PCNASP) clinical registry and matched individuals on Medicare Claims data, we sampled patients aged 65 and above admitted for AIS across nine states, from January 2017 to December 2020. We excluded those lacking documentation for either clinical or ICD-10-based NIHSS scores. We then examined score concordance from both databases and measured discordance as the absolute difference between the PCNASP and ICD-10-based NIHSS scores. Results: Among 87 996 matched patients, mean NIHSS scores for PCNASP and Medicare ICD-10 were 7.19 (95% CI 7.14 to 7.24) and 7.32 (95% CI 7.27 to 7.37), respectively. Concordance between the two scores was high as indicated by an intraclass correlation coefficient of 0.93. Conclusion: The high concordance between clinical and ICD-10 NIHSS scores highlights the latter's potential as measure of stroke severity derived from structured claims data.