Frequencies of pharmacogenomic alleles across biogeographic groups in a large-scale biobank

Pharmacogenomics (PGx) is an integral part of precision medicine and contributes to the maximization of drug efficacy and reduction of adverse drug event risk. Accurate information on PGx allele frequencies improves the implementation of PGx. Nonetheless, curating such information from published allele data is time and resource intensive. The limited number of allelic variants in most studies leads to an underestimation of certain alleles. We applied the Pharmacogenomics Clinical Annotation Tool (PharmCAT) on an integrated 200K UK Biobank genetic dataset (N = 200,044). Based on PharmCAT results, we estimated PGx frequencies (alleles, diplotypes, phenotypes, and activity scores) for 17 pharmacogenes in five biogeographic groups: European, Central/South Asian, East Asian, Afro-Caribbean, and Sub-Saharan African. PGx frequencies were distinct for each biogeographic group. Even biogeographic groups with similar proportions of phenotypes were driven by different sets of dominant PGx alleles. PharmCAT also identified "no-function" alleles that were rare or seldom tested in certain groups by previous studies, e.g., SLCO1B1∗31 in the Afro-Caribbean (3.0%) and Sub-Saharan African (3.9%) groups. Estimated PGx frequencies are disseminated via the PharmGKB (The Pharmacogenomics Knowledgebase: www.pharmgkb.org). We demonstrate that genetic biobanks such as the UK Biobank are a robust resource for estimating PGx frequencies. Improving our understanding of PGx allele and phenotype frequencies provides guidance for future PGx studies and clinical genetic test panel design, and better serves individuals from wider biogeographic backgrounds.

An Evidence-Based Framework for Evaluating Pharmacogenomics Knowledge for Personalized Medicine

Clinical annotations are one of the most popular resources available on the Pharmacogenomics Knowledgebase (PharmGKB). Each clinical annotation summarizes the association between variant‐drug pairs, shows relevant findings from the curated literature, and is assigned a level of evidence (LOE) to indicate the strength of support for that association. Evidence from the pharmacogenomic literature is curated into PharmGKB as variant annotations, which can be used to create new clinical annotations or added to existing clinical annotations. This means that the same clinical annotation can be worked on by multiple curators over time. As more evidence is curated into PharmGKB, the task of maintaining consistency when assessing all the available evidence and assigning an LOE becomes increasingly difficult. To remedy this, a scoring system has been developed to automate LOE assignment to clinical annotations. Variant annotations are scored according to certain attributes, including study size, reported P value, and whether the variant annotation supports or fails to find an association. Clinical guidelines or US Food and Drug Administration (FDA)‐approved drug labels which give variant‐specific prescribing guidance are also scored. The scores of all annotations attached to a clinical annotation are summed together to give a total score for the clinical annotation, which is used to calculate an LOE. Overall, the system increases transparency, consistency, and reproducibility in LOE assignment to clinical annotations. In combination with increased standardization of how clinical annotations are written, use of this scoring system helps to ensure that PharmGKB clinical annotations continue to be a robust source of pharmacogenomic information.

Genomewide Association Study of Platelet Reactivity and Cardiovascular Response in Patients Treated With Clopidogrel: A Study by the International Clopidogrel Pharmacogenomics Consortium

Antiplatelet response to clopidogrel shows wide variation, and poor response is correlated with adverse clinical outcomes. CYP2C19 loss‐of‐function alleles play an important role in this response, but account for only a small proportion of variability in response to clopidogrel. An aim of the International Clopidogrel Pharmacogenomics Consortium (ICPC) is to identify other genetic determinants of clopidogrel pharmacodynamics and clinical response. A genomewide association study (GWAS) was performed using DNA from 2,750 European ancestry individuals, using adenosine diphosphate‐induced platelet reactivity and major cardiovascular and cerebrovascular events as outcome parameters. GWAS for platelet reactivity revealed a strong signal for CYP2C19*2 (P value = 1.67e−33). After correction for CYP2C19*2 no other single‐nucleotide polymorphism reached genomewide significance. GWAS for a combined clinical end point of cardiovascular death, myocardial infarction, or stroke (5.0% event rate), or a combined end point of cardiovascular death or myocardial infarction (4.7% event rate) showed no significant results, although in coronary artery disease, percutaneous coronary intervention, and acute coronary syndrome subgroups, mutations in SCOS5P1, CDC42BPA, and CTRAC1 showed genomewide significance (lowest P values: 1.07e−09, 4.53e−08, and 2.60e−10, respectively). CYP2C19*2 is the strongest genetic determinant of on‐clopidogrel platelet reactivity. We identified three novel associations in clinical outcome subgroups, suggestive for each of these outcomes.

Life beyond kinases: structure-based discovery of sorafenib as nanomolar antagonist of 5-HT receptors

Of great interest in recent years has been computationally predicting the novel polypharmacology of drug molecules. Here, we applied an "induced-fit" protocol to improve the homology models of 5-HT(2A) receptor, and we assessed the quality of these models in retrospective virtual screening. Subsequently, we computationally screened the FDA approved drug molecules against the best induced-fit 5-HT(2A) models and chose six top scoring hits for experimental assays. Surprisingly, one well-known kinase inhibitor, sorafenib, has shown unexpected promiscuous 5-HTRs binding affinities, K(i) = 1959, 56, and 417 nM against 5-HT(2A), 5-HT(2B), and 5-HT(2C), respectively. Our preliminary SAR exploration supports the predicted binding mode and further suggests sorafenib to be a novel lead compound for 5HTR ligand discovery. Although it has been well-known that sorafenib produces anticancer effects through targeting multiple kinases, carefully designed experimental studies are desirable to fully understand whether its "off-target" 5-HTR binding activities contribute to its therapeutic efficacy or otherwise undesirable side effects.

The BioPAX community standard for pathway data sharing

BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.

Clinical assessment incorporating a personal genome

BACKGROUND

The cost of genomic information has fallen steeply, but the clinical translation of genetic risk estimates remains unclear. We aimed to undertake an integrated analysis of a complete human genome in a clinical context.

METHODS

We assessed a patient with a family history of vascular disease and early sudden death. Clinical assessment included analysis of this patient's full genome sequence, risk prediction for coronary artery disease, screening for causes of sudden cardiac death, and genetic counselling. Genetic analysis included the development of novel methods for the integration of whole genome and clinical risk. Disease and risk analysis focused on prediction of genetic risk of variants associated with mendelian disease, recognised drug responses, and pathogenicity for novel variants. We queried disease-specific mutation databases and pharmacogenomics databases to identify genes and mutations with known associations with disease and drug response. We estimated post-test probabilities of disease by applying likelihood ratios derived from integration of multiple common variants to age-appropriate and sex-appropriate pre-test probabilities. We also accounted for gene-environment interactions and conditionally dependent risks.

FINDINGS

Analysis of 2.6 million single nucleotide polymorphisms and 752 copy number variations showed increased genetic risk for myocardial infarction, type 2 diabetes, and some cancers. We discovered rare variants in three genes that are clinically associated with sudden cardiac death-TMEM43, DSP, and MYBPC3. A variant in LPA was consistent with a family history of coronary artery disease. The patient had a heterozygous null mutation in CYP2C19 suggesting probable clopidogrel resistance, several variants associated with a positive response to lipid-lowering therapy, and variants in CYP4F2 and VKORC1 that suggest he might have a low initial dosing requirement for warfarin. Many variants of uncertain importance were reported.

INTERPRETATION

Although challenges remain, our results suggest that whole-genome sequencing can yield useful and clinically relevant information for individual patients.

FUNDING

National Institute of General Medical Sciences; National Heart, Lung And Blood Institute; National Human Genome Research Institute; Howard Hughes Medical Institute; National Library of Medicine, Lucile Packard Foundation for Children's Health; Hewlett Packard Foundation; Breetwor Family Foundation.

Predicting new molecular targets for known drugs

Whereas drugs are intended to be selective, at least some bind to several physiologic targets, explaining both side effects and efficacy. As many drug-target combinations exist, it would be useful to explore possible interactions computationally. Here, we compared 3,665 FDA-approved and investigational drugs against hundreds of targets, defining each target by its ligands. Chemical similarities between drugs and ligand sets predicted thousands of unanticipated associations. Thirty were tested experimentally, including the antagonism of the β₁ receptor by the transporter inhibitor Prozac, the inhibition of the 5-HT transporter by the ion channel drug Vadilex, and antagonism of the histamine H₄ receptor by the enzyme inhibitor Rescriptor. Overall, 23 new drug-target associations were confirmed, five of which were potent (< 100 nM). The physiological relevance of one such, the drug DMT on serotonergic receptors, was confirmed in a knock-out mouse. The chemical similarity approach is systematic and comprehensive, and may suggest side-effects and new indications for many drugs.

The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge

PharmGKB is a knowledge base that captures the relationships between drugs, diseases/phenotypes and genes involved in pharmacokinetics (PK) and pharmacodynamics (PD). This information includes literature annotations, primary data sets, PK and PD pathways, and expert-generated summaries of PK/PD relationships between drugs, diseases/phenotypes and genes. PharmGKB's website is designed to effectively disseminate knowledge to meet the needs of our users. PharmGKB currently has literature annotations documenting the relationship of over 500 drugs, 450 diseases and 600 variant genes. In order to meet the needs of whole genome studies, PharmGKB has added new functionalities, including browsing the variant display by chromosome and cytogenetic locations, allowing the user to view variants not located within a gene. We have developed new infrastructure for handling whole genome data, including increased methods for quality control and tools for comparison across other data sources, such as dbSNP, JSNP and HapMap data. PharmGKB has also added functionality to accept, store, display and query high throughput SNP array data. These changes allow us to capture more structured information on phenotypes for better cataloging and comparison of data. PharmGKB is available at www.pharmgkb.org.

Antiemetic efficacy of granisetron plus dexamethasone in bone marrow transplant patients receiving chemotherapy and total body irradiation

Few trials exist regarding the antiemetic efficacy of granisetron in bone marrow transplant (BMT) recipients conditioned with high-dose chemotherapy and total body irradiation (TBI). In this single-center, open-label, prospective, trial, the antiemetic efficacy and safety of granisetron plus dexamethasone were evaluated in 26 patients conditioned with cyclophosphamide-containing regimens (the majority receiving 60 mg/kg per day on 2 consecutive days), and TBI (12 Gy divided over 4 days). Daily intravenous doses of granisetron 1 mg plus dexamethasone 10 mg were given 30 min prior to chemotherapy or radiation, and continued for 24 h after the last conditioning treatment for a median of 6 days (range 3-9). Emetic control was defined by the number of emetic episodes occurring within a 24 h period, or the requirement for rescue medication for nausea or vomiting. A total of 25 patients completed 186 evaluable treatment days. Response (emetic control by treatment days) was complete in 50% of patients, major in 48%, minor in 2%, and there were no failures. Adverse effects were minor, with diarrhea (15%), headache (14%), and constipation (11%) reported most often. Based on these results, the antiemetic regimen of granisetron plus dexamethasone appears effective and well tolerated during BMT conditioning with high-dose cyclophosphamide and TBI.

The correlation between neuropsychological and neuroanatomic changes over time in asymptomatic and symptomatic HIV-1-infected individuals

To determine the relationship between neuroanatomic and neuropsychological changes in both asymptomatic and symptomatic HIV-1-infected individuals, we conducted a longitudinal study of 47 HIV-infected individuals, 15 of whom were asymptomatic and 32 of whom had either AIDS-related complex or AIDS. To measure neuroanatomic change over a 30-month period, we conducted quantitative MRI measures of bicaudate/brain ratio (BCR) and bifrontal/ brain ratio. A comparison of change over time between BCR and neuropsychological performance showed a correlation between increase in atrophy and worsening in certain cognitive functions. The correlation held for both asymptomatic and symptomatic groups, with more pronounced changes in the symptomatic group.

Vitamin B12 deficiency and nervous system disease in HIV infection

BACKGROUND

Vitamin B12 deficiency may result in a number of neurological and neuropsychiatric disorders. Patients with human immunodeficiency virus type 1 (HIV-1) infection may have a high rate of vitamin B12 deficiency and nervous system disease. Vitamin B12 deficiency may contribute to neurological disease in HIV-1-infected individuals.

OBJECTIVE

To evaluate the possible contribution of vitamin B12 deficiency to neurological disease in HIV-1-infected individuals.

MAIN OUTCOME MEASURES

Comparison of serum vitamin B12 levels with neurological, neuropsychological, and mood state abnormalities in 153 HIV-1-positive subjects and 57 high-risk seronegative controls. A subgroup of 67 subjects underwent additional extensive clinical neurophysiological, cerebrospinal fluid, and magnetic resonance imaging evaluations.

RESULTS

No statistically significant relationships were noted between vitamin B12 levels and abnormalities on any of the measures examined.

CONCLUSIONS

This study does not indicate an important role for vitamin B12 deficiency in the neurological disease of HIV-1 infection.

Pegademase bovine: replacement therapy for severe combined immunodeficiency disease

Severe combined immunodeficiency (SCID) represents a syndrome characterized by abnormal function of cellular and humoral immunity. Of the various types of SCID, approximately one-fourth are associated with adenosine deaminase (ADA) deficiency. Treatment consists of bone marrow transplantation, red blood cell transfusions, enzyme replacement, and, more recently, gene therapy. Pegademase bovine is the sole agent available for enzyme replacement therapy of SCID associated with ADA deficiency. The drug is administered intramuscularly to infants from birth and to children of any age at time of diagnosis. At present, few adverse effects or drug interactions have been documented. Although it is expensive (approximately $60,000 annually), pegademase bovine offers an alternative to standard means of therapy.

Clustering a large number of compounds. 2. Using the Connection Machine

About 230,000 compounds in the National Cancer Institute Repository are available for screening under a new protocol. This paper is the second on an project to extract a representative sample of these compounds by clustering. The clustering program was implemented on the Connection Machine, a massively parallel computer with 16K processing elements. This implementation reduced a formidable task to a relatively routine run.

Complications following transfemoral cerebral angiography for cerebral ischemia. Report of 159 angiograms and correlation with surgical risk

One hundred fifty-nine transfemoral cerebral angiograms for patients with carotid stenosis who subsequently underwent carotid endarterectomy were reviewed. No patient with an asymptomatic carotid bruit developed cerebrovascular complications during angiography. Patients with transient ischemic attacks (TIAs) had a 4.5% incidence of complications. Patients with stroke in evolution had a complication rate of 7.7%. Patients with completed strokes had no angiographic complications. No complication lasted more than 1 hour; all occurred during angiography or immediately afterwards. Stroke in progress has too high a surgical and angiographic risk to warrant study. Transient ischemic attacks have an acceptable morbidity both surgically and angiographically.

Anomalous exit of the C-6 nerve root via the C-6, C-7 foramen

We report a case of the anomalous exit of the C-6 nerve root at the C-6, C-7 foramen. This caused intense radicular and cervical pain in a 25-year-old woman. At myelography, the 5th and 6th cervical roots appeared conjoined, and at operation the C-6 root and ganglion were found to turn acutely downward, lateral to the pedicle of C-6, and then to exit with the C-7 nerve root through the C-6, C-7 foramen. The ganglion of C-6 was placed nearly parallel to the dural sac and tethered at its origin on the dural sac and at the exit foramen with the C-7 root. The pedicle of C-6 was interposed between the dural sac and the ganglion of C-6. Cervical hemilaminectomy and resection of the pedicle of C-6 defined the anatomy and resulted in a clinical cure. The radiological features are described and contrasted with those of other anomalies. To our knowledge, this is the first report of such an anomalous course of exit of a cervical root.

The relative roles of neurological examination, functional abilities, and computed tomography in the definition of treatment failure in patients with anaplastic gliomas

Forty-one patients with anaplastic gliomas undergoing postoperative treatment and evaluation underwent bimonthly evaluation of the following indices of treatment failure: neurological examination; Karnofsky functional rating; and computed tomography (CT) brain scanning. Treatment failure was declared when neurological examination or Karnofsky rating showed increased impairment or when CT scan revealed an increase in tumor sizes. Most often, all three indices simultaneously indicated treatment failure. In only 6 of 41 cases the CT scan alone was the first indication of treatment failure. During the first 6 months of follow-up, tumor enlargement on CT scan as a sole index of treatment failure occurred in only 3 of 26 cases that showed evidence of treatment failure during that time. For patients with glioblastoma, about 6% of treatment failures within 6 months are predicted to be missed by Karnofsky rating plus neurological examination, whereas CT scan alone is predicted to miss about 30%. It would seem reasonable to rely on the neurological examination and Karnofsky rating for follow-up during the first 6 months after surgery, without routine serial CT scanning during that time.