Potential of whole-genome sequencing-based pharmacogenetic profiling

Assessment of the current status of real-world pharmacogenomic testing: informed consent, patient education, and related practices

Introduction: The practice of informed consent (IC) for pharmacogenomic testing in clinical settings varies, and there is currently no consensus on which elements of IC to provide to patients. This study aims to assess current IC practices for pharmacogenomic testing. Methods: An online survey was developed and sent to health providers at institutions that offer clinical germline pharmacogenomic testing to assess current IC practices. Results: Forty-six completed surveys representing 43 clinical institutions offering pharmacogenomic testing were received. Thirty-two (74%) respondents obtain IC from patients with variability in elements incorporated. Results revealed that twenty-nine (67%) institutions discuss the benefits, description, and purpose of pharmacogenomic testing with patients. Less commonly discussed elements included methodology and accuracy of testing, and laboratory storage of samples. Discussion: IC practices varied widely among survey respondents. Most respondents desire the establishment of consensus IC recommendations from a trusted pharmacogenomics organization to help address these disparities.

Should secondary pharmacogenomic variants be actively screened and reported when diagnostic genome-wide sequencing is performed in a child?

This white paper was prepared by the Global Alliance for Genomics and Health Regulatory and Ethics Work Stream's Pediatric Task Team to review and provide perspective with respect to ethical, legal, and social issues regarding the return of secondary pharmacogenomic variants in children who have a serious disease or developmental disorder and are undergoing exome or genome sequencing to identify a genetic cause of their condition. We discuss actively searching for and reporting pharmacogenetic/genomic variants in pediatric patients, different methods of returning secondary pharmacogenomic findings to the patient/parents and/or treating clinicians, maintaining these data in the patient's health record over time, decision supports to assist using pharmacogenetic results in future treatment decisions, and sharing information in public databases to improve the clinical interpretation of pharmacogenetic variants identified in other children. We conclude by presenting a series of points to consider for clinicians and policymakers regarding whether, and under what circumstances, routine screening and return of pharmacogenomic variants unrelated to the indications for testing is appropriate in children who are undergoing genome-wide sequencing to assist in the diagnosis of a suspected genetic disease.

HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing

MOTIVATION

In diploid organisms, phasing is the problem of assigning the alleles at heterozygous variants to one of two haplotypes. Reads from PacBio HiFi sequencing provide long, accurate observations that can be used as the basis for both calling and phasing variants. HiFi reads also excel at calling larger classes of variation, such as structural or tandem repeat variants. However, current phasing tools typically only phase small variants, leaving larger variants unphased.

RESULTS

We developed HiPhase, a tool that jointly phases SNVs, indels, structural, and tandem repeat variants. The main benefits of HiPhase are (i) dual mode allele assignment for detecting large variants, (ii) a novel application of the A*-algorithm to phasing, and (iii) logic allowing phase blocks to span breaks caused by alignment issues around reference gaps and homozygous deletions. In our assessment, HiPhase produced an average phase block NG50 of 480 kb with 929 switchflip errors and fully phased 93.8% of genes, improving over the current state of the art. Additionally, HiPhase jointly phases SNVs, indels, structural, and tandem repeat variants and includes innate multi-threading, statistics gathering, and concurrent phased alignment output generation.

AVAILABILITY AND IMPLEMENTATION

HiPhase is available as source code and a pre-compiled Linux binary with a user guide at https://github.com/PacificBiosciences/HiPhase.

PharmVar Tutorial on CYP2D6 Structural Variation Testing and Recommendations on Reporting

The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus and a comprehensive summary of structural variation. CYP2D6 contributes to the metabolism of numerous drugs and, thus, genetic variation in its gene impacts drug efficacy and safety. To accurately predict a patient's CYP2D6 phenotype, testing must include structural variants including gene deletions, duplications, hybrid genes, and combinations thereof. This tutorial offers a comprehensive overview of CYP2D6 structural variation, terms, and definitions, a review of methods suitable for their detection and characterization, and practical examples to address the lack of standards to describe CYP2D6 structural variants or any other pharmacogene. This PharmVar tutorial offers practical guidance on how to detect the many, often complex, structural variants, as well as recommends terms and definitions for clinical and research reporting. Uniform reporting is not only essential for electronic health record-keeping but also for accurate translation of a patient's genotype into phenotype which is typically utilized to guide drug therapy.

Current status of the analytical validation of next generation sequencing applications for pharmacogenetic profiling

BACKGROUND

Analytical validity is a prerequisite to use a next generation sequencing (NGS)-based application as an in vitro diagnostic test or a companion diagnostic in clinical practice. Currently, in the United States and the European Union, the intended use of such NGS-based tests does not refer to guided drug therapy on the basis of pharmacogenetic profiling of drug metabolizing enzymes, although the value of pharmacogenetic testing has been reported. However, in research, a large variety of NGS-based tests are used and have been confirmed to be at least comparable to array-based testing.

METHODS AND RESULTS

A systematic evaluation was performed screening and assessing published literature on analytical validation of NGS applications for pharmacogenetic profiling of CYP2C9, CYP2C19, CYP2D6, VKORC1 and/or UGT1A1. Although NGS applications are also increasingly used for implementation assessments in clinical practice, we show in the present systematic literature evaluation that published information on the current status of analytical validation of NGS applications targeting drug metabolizing enzymes is scarce. Furthermore, a comprehensive performance evaluation of whole exome and whole genome sequencing with the intended use for pharmacogenetic profiling has not been published so far.

CONCLUSIONS

A standard in reporting on analytical validation of NGS-based tests is not in place yet. Therefore, many relevant performance criteria are not addressed in published literature. For an appropriate analytical validation of an NGS-based qualitative test for pharmacogenetic profiling at least accuracy, precision, limit of detection and specificity should be addressed to facilitate the implementation of such tests in clinical use.

Probiotic and Safety Evaluation of Twelve Lactic Acid Bacteria as Future Probiotics

The human gut flora is highly diverse. Most lactic acid bacteria (LAB) are widely used as probiotics in human and animal husbandry and have a variety of physiological benefits. This article mainly studied the bacteriostatic ability of LAB against four pathogenic bacteria, gastrointestinal environment tolerance, and adhesion ability to Caco-2 cells. The genome of Lactiplantibacillus plantarum L461 was sequenced and analyzed. The results showed that strains F512, L461, and D469 had the most significant inhibitory effects on Escherichia coli, Salmonella enterica B, Staphylococcus aureus, and Listeria monocytogenes. In addition, strains L461, C502, and P231 showed good tolerance after exposure to simulated gastric fluid for 0-4 h. Strains C502, H781, and L461 showed good tolerance in simulated intestinal fluid. Strains L461 and H781 showed good adhesion to Caco-2 cells. The number of viable bacteria was more than 60. Therefore, we screened L. plantarum L461 from 12 LAB strains through three aspects of evaluation, and conducted whole genome sequencing and analysis. Sequencing results showed that L. plantarum L461 had more defense mechanisms and phage annotation genes than L. plantarum WCFS1. Virulence factor studies showed that L. plantarum L461 has iron absorption system and adhesion-related gene annotation, indicating that L. plantarum L461 has survival advantage in intestinal tract. The predicted results showed that there were eight phages with phage resistance in L. plantarum L461. L. plantarum L461 is sensitive to several antibiotics, notably penicillin and oxacillin. In summary, the results of this study prove that L. plantarum L461 has good prebiotic function and is safe. Therefore, L. plantarum L461 can be safely used as a potential functional probiotic.

Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques

Molecular and genomic approaches have revolutionized medical microbiology by offering faster and more accurate diagnostic techniques for infectious diseases. Traditional methods, which include culturing microbes and biochemical testing, are time-consuming and may not detect antibiotic-resistant strains. In contrast, molecular and genomic methods, including polymerase chain reaction (PCR)-based techniques and whole-genome sequencing, provide rapid and precise detection of pathogens, early-stage diseases, and antibiotic-resistant strains. These approaches have advantages such as high sensitivity and specificity, the potential for targeted therapies, and personalized medicine. However, implementing molecular and genomic techniques faces challenges related to cost, equipment, expertise, and data analysis. Ethical and legal considerations regarding patient privacy and genetic data usage also arise. Nonetheless, the future of medical microbiology lies in the widespread adoption of molecular and genomic approaches, which can lead to improved patient outcomes and the identification of antibiotic-resistant strains. Continued advancements, education, and exploration of ethical implications are necessary to fully harness the potential of molecular and genomic techniques in medical microbiology.

Unexpected High Need for Genetic Testing in Rheumatology: A Cross-Sectional Cohort Study

BACKGROUND

Genetic testing may provide information for diagnostic, prognostic and pharmacogenetic purposes. The PREPARE study recently showed that the number of clinically relevant adverse drug reactions could be reduced via genotype-guided treatment. The aim of this work was to assess the relevance of genetic testing and its actual use in consecutive rheumatic outpatients.

METHODS

A retrospective cross-sectional analysis was performed with data from a prospectively designed observational project with outpatients consecutively recruited from a university clinic of rheumatology.

RESULTS

In this cohort of 2490 patients, the potential need for genetic testing is immense, with 57.3% of patients having the potential to benefit from genetic testing according to their diagnosis and treatment and 53.3% of patients with actually performed genetic testing for diagnostic, prognostic or pharmacogenetic purposes. In detail, patients would potentially benefit from genetic testing especially for therapeutic (28.0%) and diagnostic (26.9%) purposes. Genetic testing was performed for diagnostic purposes in 51.6% of subjects, for pharmacogenetic purposes in 3.7% and for prognostic purposes in 0.1%. The ratio between the number of patients who had had tests performed to those with a potential need for genetic testing decreased with age, from 127.1% for 20 to <30-year-old patients to 46.1% for 80 to <90-year-old patients. Pharmacogenetic testing was only performed for disease-related medications.

CONCLUSIONS

Genetic testing is frequently needed in patients with rheumatic diseases. The value of pharmacogenetic testing is certainly underestimated, especially in case of medications for comorbidities.

Characterization of pharmacogenomic variants in a Brazilian admixed cohort of elderly individuals based on whole-genome sequencing data

Introduction: Research in the field of pharmacogenomics (PGx) aims to identify genetic variants that modulate response to drugs, through alterations in their pharmacokinetics (PK) or pharmacodynamics (PD). The distribution of PGx variants differs considerably among populations, and whole-genome sequencing (WGS) plays a major role as a comprehensive approach to detect both common and rare variants. This study evaluated the frequency of PGx markers in the context of the Brazilian population, using data from a population-based admixed cohort from Sao Paulo, Brazil, which includes variants from WGS of 1,171 unrelated, elderly individuals. Methods: The Stargazer tool was used to call star alleles and structural variants (SVs) from 38 pharmacogenes. Clinically relevant variants were investigated, and the predicted drug response phenotype was analyzed in combination with the medication record to assess individuals potentially at high-risk of gene-drug interaction. Results: In total, 352 unique star alleles or haplotypes were observed, of which 255 and 199 had a frequency < 0.05 and < 0.01, respectively. For star alleles with frequency > 5% (n = 97), decreased, loss-of-function and unknown function accounted for 13.4%, 8.2% and 27.8% of alleles or haplotypes, respectively. Structural variants (SVs) were identified in 35 genes for at least one individual, and occurred with frequencies >5% for CYP2D6, CYP2A6, GSTM1, and UGT2B17. Overall 98.0% of the individuals carried at least one high risk genotype-predicted phenotype in pharmacogenes with PharmGKB level of evidence 1A for drug interaction. The Electronic Health Record (EHR) Priority Result Notation and the cohort medication registry were combined to assess high-risk gene-drug interactions. In general, 42.0% of the cohort used at least one PharmGKB evidence level 1A drug, and 18.9% of individuals who used PharmGKB evidence level 1A drugs had a genotype-predicted phenotype of high-risk gene-drug interaction. Conclusion: This study described the applicability of next-generation sequencing (NGS) techniques for translating PGx variants into clinically relevant phenotypes on a large scale in the Brazilian population and explores the feasibility of systematic adoption of PGx testing in Brazil.

Pharmacogenetic Gene-Drug Associations in Pediatric Burn and Surgery Patients

Management of critically ill patients requires simultaneous administration of many medications. Treatment for patient comorbidities may lead to drug-drug interactions which decrease drug efficacy or increase adverse reactions. Current practices rely on a one-size-fits-all dosing approach. Pharmacogenetic testing is generally reserved for addressing problems rather than used proactively to optimize care. We hypothesized that burn and surgery patients will have one or more genetic variants in drug metabolizing pathways used by one or more medications administered during the patient's hospitalization. The aim of this study was to determine the frequency of variants with abnormal function in the primary drug pathways and identify which medications may be impacted. Genetic (19 whole exome and 11 whole genome) and medication data from 30 pediatric burn and surgery patients were analyzed to identify pharmacogene-drug associations. Nineteen patients were identified with predicted altered function in one or more of the following genes: CYP2C9, CYP2C19, CYP2D6, and CYP3A4. The majority had decreased function, except for several patients with CYP2C19 rapid or ultrarapid variants. Some drugs administered during hospitalization that rely on these pathways include hydrocodone, oxycodone, methadone, ibuprofen, ketorolac, celecoxib, diazepam, famotidine, diphenhydramine, and glycopyrrolate. Approximately one-third of the patients tested had functionally impactful genotypes in each of the primary drug metabolizing pathways. This study suggests that genetic variants may in part explain the vast variability in drug efficacy and suggests that future pharmacogenetics research may optimize dosing regimens.

Detection of relevant pharmacogenetic information through exome sequencing in oncology

Background: Germline sequencing of individual genomes can detect alleles responsible for adverse drug reactions (ADRs) in relation to chemotherapy, targeted agents, antiemetics or pain treatment. Materials & methods: To evaluate the interest of such pharmacogenetic information, the authors retrospectively analyzed genes known to have an impact on cancer therapy in a cohort of 445 solid cancers patients. Results: Six patients treated with 5-fluorouracil carrying one DPYD variant classified as 1A showed decreased drug mean clearance (p = 0.01). Regarding CYP2D6, all patients (n = 5) with predicted CYP2D6 poor or ultra-rapid metabolizer status experienced adverse drug reactions related to opioid therapy. Conclusion: Genomic germline sequencing performed for theragnostic issues in patients with a solid tumor, can provide relevant information about common pharmacogenetic alleles.

Artificial Intelligence, Healthcare, Clinical Genomics, and Pharmacogenomics Approaches in Precision Medicine

Precision medicine has greatly aided in improving health outcomes using earlier diagnosis and better prognosis for chronic diseases. It makes use of clinical data associated with the patient as well as their multi-omics/genomic data to reach a conclusion regarding how a physician should proceed with a specific treatment. Compared to the symptom-driven approach in medicine, precision medicine considers the critical fact that all patients do not react to the same treatment or medication in the same way. When considering the intersection of traditionally distinct arenas of medicine, that is, artificial intelligence, healthcare, clinical genomics, and pharmacogenomics—what ties them together is their impact on the development of precision medicine as a field and how they each contribute to patient-specific, rather than symptom-specific patient outcomes. This study discusses the impact and integration of these different fields in the scope of precision medicine and how they can be used in preventing and predicting acute or chronic diseases. Additionally, this study also discusses the advantages as well as the current challenges associated with artificial intelligence, healthcare, clinical genomics, and pharmacogenomics.

A population study of clinically actionable genetic variation affecting drug response from the Middle East

Clinical implementation of pharmacogenomics will help in personalizing drug prescriptions and alleviate the personal and financial burden due to inefficacy and adverse reactions to drugs. However, such implementation is lagging in many parts of the world, including the Middle East, mainly due to the lack of data on the distribution of actionable pharmacogenomic variation in these ethnicities. We analyzed 6,045 whole genomes from the Qatari population for the distribution of allele frequencies of 2,629 variants in 1,026 genes known to affect 559 drugs or classes of drugs. We also performed a focused analysis of genotypes or diplotypes of 15 genes affecting 46 drugs, which have guidelines for clinical implementation and predicted their phenotypic impact. The allele frequencies of 1,320 variants in 703 genes affecting 299 drugs or class of drugs were significantly different between the Qatari population and other world populations. On average, Qataris carry 3.6 actionable genotypes/diplotypes, affecting 13 drugs with guidelines for clinical implementation, and 99.5% of the individuals had at least one clinically actionable genotype/diplotype. Increased risk of simvastatin-induced myopathy could be predicted in ~32% of Qataris from the diplotypes of SLCO1B1, which is higher compared to many other populations, while fewer Qataris may need tacrolimus dosage adjustments for achieving immunosuppression based on the CYP3A5 diplotypes compared to other world populations. Distinct distribution of actionable pharmacogenomic variation was also observed among the Qatari subpopulations. Our comprehensive study of the distribution of actionable genetic variation affecting drugs in a Middle Eastern population has potential implications for preemptive pharmacogenomic implementation in the region and beyond.

DNA sequencing: an overview of solid-state and biological nanopore-based methods

The field of sequencing is a topic of significant interest since its emergence and has become increasingly important over time. Impressive achievements have been obtained in this field, especially in relations to DNA and RNA sequencing. Since the first achievements by Sanger and colleagues in the 1950s, many sequencing techniques have been developed, while others have disappeared. DNA sequencing has undergone three generations of major evolution. Each generation has its own specifications that are mentioned briefly. Among these generations, nanopore sequencing has its own exciting characteristics that have been given more attention here. Among pioneer technologies being used by the third-generation techniques, nanopores, either biological or solid-state, have been experimentally or theoretically extensively studied. All sequencing technologies have their own advantages and disadvantages, so nanopores are not free from this general rule. It is also generally pointed out what research has been done to overcome the obstacles. In this review, biological and solid-state nanopores are elaborated on, and applications of them are also discussed briefly.

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review

Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.