Navigating pleiotropy in precision medicine: pharmacogenes from trauma to behavioral health

CYP2C19 genotype-guided antiplatelet therapy: promises and pitfalls

Pharmacogenetic variants can alter the mechanism of action (pharmacodynamic gene variants) or kinetic processes such as absorption, distribution, metabolism and elimination (pharmacokinetic gene variants). Many initial successes in precision medicine occurred in the context of genes encoding the cytochromes P450 (CYP enzymes). CYP2C19 activates the antiplatelet drug clopidogrel, and polymorphisms in the CYP2C19 gene are known to alter the outcome for patients taking clopidogrel in the context of cardiovascular disease. CYP2C19 loss-of-function alleles are specifically associated with increased risk for coronary stent thrombosis and major adverse cardiovascular events in patients taking clopidogrel following percutaneous coronary intervention. We explore successes and challenges encountered as the clinical and scientific communities advance CYP2C19 genotyping in the context of routine patient care.

Application of pharmacogenomics for trauma and critical care patients: A case report

Background

Pharmacogenomics is increasingly becoming a valuable tool for improving health outcomes, reducing health care costs and avoiding adverse drug reactions. While application of pharmacogenomics is quite common in oncology and cardiology, routine use of this technology is rare in certain other fields including Trauma and Critical Care Surgery. We are testing feasibility of applying pharmacogenomic testing to improve therapeutic outcomes of trauma and acute care patients at MercyOne Medical Center in Des Moines, IA.

Methods

Trauma patients admitted to the hospital with projected stay of >5 days, or with admission extended due to failed multiple trials of medication volunteered to participate in this IRB-approved study. Effectiveness of medical therapy was evaluated using standard pain scores recorded prior to admission of any pain medication to conscious and competent patients. Pharmacogenomic results were obtained from commercial providers within 3–5 days and used to alter medical therapy as needed.

Results

An 18-year-old African American male, admitted for gunshot wounds to the neck, exhibited an ASIA A spinal cord injury, with no sensation or movement of his extremities, persistent nausea with emesis and a history of depression. He also developed gastritis with hematemesis. In addition to all standard trauma procedures, he received standard doses of tramadol, oxycodone or hydrocodone, ondansetron, citalopram, and intravenous protonix daily. He reported no pain relief. The patient's pharmacogenomic analysis revealed his ultrarapid and rapid genotype for CYP2D6 and CYP2C19 respectively, allowing us to choose dilaudid resulting in immediate improvement of his pain scores. Additionally, using metoclopramide, duloxetine and famotidine led to immediate improvement or complete resolution of symptoms.

Conclusion

Pharmacogenomics testing is a useful tool for selecting appropriate pain management of trauma patients with expected hospital stay ≥5 days. Additionally, standard pharmacogenomic panels allow tailoring medical therapy to common conditions associated with traumatic injury.

PleioNet: a web-based visualization tool for exploring pleiotropy across complex traits

SUMMARY

Pleiotropy plays an important role in furthering our understanding of the shared genetic architecture of different human diseases and traits. However, exploring and visualizing pleiotropic information with currently publicly available tools is limiting and challenging. To aid researchers in constructing and digesting pleiotropic networks, we present PleioNet, a web-based visualization tool for exploring this information across human diseases and traits. This program provides an intuitive and interactive web interface that seamlessly integrates large database queries with visualizations that enable users to quickly explore complex high-dimensional pleiotropic information. PleioNet works on all modern computer and mobile web browsers, making pleiotropic information readily available to a broad range of researchers and clinicians with diverse technical backgrounds. We expect that PleioNet will be an important tool for studying the underlying pleiotropic connections among human diseases and traits.

AVAILABILITY AND IMPLEMENTATION

PleioNet is hosted on Google cloud and freely available at http://www.pleionet.com/.

Implementation of wide-scale pharmacogenetic testing in primary care

The convergence of translational genomics and biomedical informatics has changed healthcare delivery. Institutional consortia have begun implementing lab testing and decision support for drug–gene interactions. Aggregate datasets are now revealing the impact of clinical decision support for drug–gene interactions. Given the pleiotropic nature of pharmacogenes, interdisciplinary teams and robust clinical decision support tools must exist within an informatics framework built to be flexible and capable of cross-talk between clinical specialties. Navigation of the challenges presented with the implementation of five steps to build a genetics program infrastructure requires the expertise of multiple healthcare professionals. Ultimately, this manuscript describes our efforts to place pharmacogenomics in the hands of the primary care provider integrating this information into a patient’s healthcare over their lifetime.

CYP2C19 genotype, physician prescribing pattern, and risk for long QT on serotonin selective reuptake inhibitors

Aim: To examine the impact of CYP2C19 genotype on selective serotonin reuptake inhibitor (SSRI) prescribing patterns. Patients & methods: Observational cohort containing 507 unique individuals receiving an SSRI prescription with CYP2C19 genotype already in their electronic medical record. Genotype was distributed as follows: n = 360 (71%) had no loss of function alleles, 136 (26.8%) had one loss of function allele and 11 (2.2%) had two loss of function alleles. Results & conclusion: For poor metabolizers exposed to sertraline, citalopram or escitalopram, providers changed prescribing patterns in response to alerts in the electronic medical record by either changing the drug, changing the dose or monitoring serial EKGs longitudinally. For intermediate metabolizers exposed to sertraline, citalopram or escitalopram, no alert was needed (mean QTc = 440.338 ms [SD = 31.1273] for CYP2C19*1/*1, mean QTc = 440.371 ms [SD = 29.2706] for CYP2C19*1/*2; p = 0.995).

Precision medicine review: rare driver mutations and their biophysical classification

How can biophysical principles help precision medicine identify rare driver mutations? A major tenet of pragmatic approaches to precision oncology and pharmacology is that driver mutations are very frequent. However, frequency is a statistical attribute, not a mechanistic one. Rare mutations can also act through the same mechanism, and as we discuss below, “latent driver” mutations may also follow the same route, with “helper” mutations. Here, we review how biophysics provides mechanistic guidelines that extend precision medicine. We outline principles and strategies, especially focusing on mutations that drive cancer. Biophysics has contributed profoundly to deciphering biological processes. However, driven by data science, precision medicine has skirted some of its major tenets. Data science embodies genomics, tissue- and cell-specific expression levels, making it capable of defining genome- and systems-wide molecular disease signatures. It classifies cancer driver genes/mutations and affected pathways, and its associated protein structural data guide drug discovery. Biophysics complements data science. It considers structures and their heterogeneous ensembles, explains how mutational variants can signal through distinct pathways, and how allo-network drugs can be harnessed. Biophysics clarifies how one mutation—frequent or rare—can affect multiple phenotypic traits by populating conformations that favor interactions with other network modules. It also suggests how to identify such mutations and their signaling consequences. Biophysics offers principles and strategies that can help precision medicine push the boundaries to transform our insight into biological processes and the practice of personalized medicine. By contrast, “phenotypic drug discovery,” which capitalizes on physiological cellular conditions and first-in-class drug discovery, may not capture the proper molecular variant. This is because variants of the same protein can express more than one phenotype, and a phenotype can be encoded by several variants.