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Pharmacogenomics and Population Genetics: Personalized Medicine in Ethnically Diverse Population
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Pharmacogenomics and Population Genetics: Personalized Medicine in Ethnically Diverse Population

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (15 April 2024) | Viewed by 3828

Special Issue Editor

Dr. Zhuo (Shawn) Shao
*
E-Mail
Guest Editor
Department of Pediatrics and Genetics Program, North York General Hospital, University of Toronto, 4001 Leslie St, Toronto, ON M2K 1E1, Canada
Interests: personalized medicine; genomic medicine; pharmacogenetics; therapeutics for genetic disorders; gene therapy; oligoneucliotide therapy
* M.D., C.M., Ph.D., FRCPC, FCCMG, Clinical Geneticist, Assistant Professor

Special Issue Information

Dear Colleagues,

Pharmacogenomics (PGx) studies drug responsiveness based on the genomic make-up of an individual. Previous pharmacogenetic researches focused on common nucleotide polymorphisms and their influence on pharmacokinetics and pharmacodynamics of medications already approved by regulatory agencies. Lack of evidence in the superiority of PGx-guided prescribing has delayed the implementation of PGx in routine clinical care. Furthermore, lack of knowledge translation has created another barrier for medical practitioners to incorporate PGx-guided prescribing in their clinical practices.

With the increased size of population genomic data base, low frequency loss of function variants in PGx-related genes has been identified, but their clinical significance in drug metabolism is yet to be confirmed. Further research into these variants is an emerging field of PGx-related research.

Emerging evidence has pointed to racial inequality in health care. This radial inequality is partially attributed to the lack of studies in the efficacy and dosing of medications in minority populations. Due to the diver distribution of PGx related nucleotide polymorphisms in different ethnic populations, the prescription guideline based on clinical trials conducted in predominantly European participants may not be applicable to other racial groups. Further investigation of this structural inequality is urgently required.

This Special Issue of Genes aims to promote and explore pharmacogenomic research in ethnically diverse populations by way of original research articles, reviews, and short communications. We look forward to submissions that describe basic science, translational, epidemiological, and clinical research. We are also looking for perspectives that provide unique viewpoints on the role of how PGx may be a tool to address racial inequality.

Dr. Zhuo (Shawn) Shao
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • pharmacogenomics
  • presciption medication
  • racial inequality
  • pharmacokinetics
  • pharmacodynamics
  • genome analysis

Published Papers (3 papers)

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13 pages, 2280 KiB  
Article
A New Cloud-Native Tool for Pharmacogenetic Analysis
by David Yu Yuan, Jun Hyuk Park, Zhenyu Li, Rohan Thomas, David M. Hwang and Lei Fu
Genes 2024, 15(3), 352; https://0-doi-org.brum.beds.ac.uk/10.3390/genes15030352 - 11 Mar 2024
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Abstract
Background: The advancement of next-generation sequencing (NGS) technologies provides opportunities for large-scale Pharmacogenetic (PGx) studies and pre-emptive PGx testing to cover a wide range of genotypes present in diverse populations. However, NGS-based PGx testing is limited by the lack of comprehensive computational tools [...] Read more.
Background: The advancement of next-generation sequencing (NGS) technologies provides opportunities for large-scale Pharmacogenetic (PGx) studies and pre-emptive PGx testing to cover a wide range of genotypes present in diverse populations. However, NGS-based PGx testing is limited by the lack of comprehensive computational tools to support genetic data analysis and clinical decisions. Methods: Bioinformatics utilities specialized for human genomics and the latest cloud-based technologies were used to develop a bioinformatics pipeline for analyzing the genomic sequence data and reporting PGx genotypes. A database was created and integrated in the pipeline for filtering the actionable PGx variants and clinical interpretations. Strict quality verification procedures were conducted on variant calls with the whole genome sequencing (WGS) dataset of the 1000 Genomes Project (G1K). The accuracy of PGx allele identification was validated using the WGS dataset of the Pharmacogenetics Reference Materials from the Centers for Disease Control and Prevention (CDC). Results: The newly created bioinformatics pipeline, Pgxtools, can analyze genomic sequence data, identify actionable variants in 13 PGx relevant genes, and generate reports annotated with specific interpretations and recommendations based on clinical practice guidelines. Verified with two independent methods, we have found that Pgxtools consistently identifies variants more accurately than the results in the G1K dataset on GRCh37 and GRCh38. Conclusions: Pgxtools provides an integrated workflow for large-scale genomic data analysis and PGx clinical decision support. Implemented with cloud-native technologies, it is highly portable in a wide variety of environments from a single laptop to High-Performance Computing (HPC) clusters and cloud platforms for different production scales and requirements. Full article
(This article belongs to the Special Issue Pharmacogenomics and Population Genetics: Personalized Medicine in Ethnically Diverse Population)
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9 pages, 243 KiB  
Brief Report
CYP2D6 and CYP2C19 Variant Coverage of Commercial Antidepressant Pharmacogenomic Testing Panels Available in Victoria, Australia
by Malcolm Forbes, Mal Hopwood and Chad A. Bousman
Genes 2023, 14(10), 1945; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14101945 - 16 Oct 2023
Viewed by 1218
Abstract
Pharmacogenomic (PGx) testing to inform antidepressant medication selection and dosing is gaining attention from healthcare professionals, patients, and payors in Australia. However, there is often uncertainty regarding which test is most suitable for a particular patient. Here, we identified and evaluated the coverage [...] Read more.
Pharmacogenomic (PGx) testing to inform antidepressant medication selection and dosing is gaining attention from healthcare professionals, patients, and payors in Australia. However, there is often uncertainty regarding which test is most suitable for a particular patient. Here, we identified and evaluated the coverage of CYP2D6 and CYP2C19 variants in commercial antidepressant PGx testing panels in Victoria, a large and ethnically diverse state of Australia. Test characteristics and star alleles tested for both genes were obtained directly from pathology laboratories offering PGx testing and compared against the Association of Molecular Pathology’s recommended minimum (Tier 1) and extended (Tier 2) allele sets. Although all tests covered the minimum recommended alleles for CYP2C19, this was not the case for CYP2D6. This study emphasizes that PGx tests might not be suitable for all individuals in Australia due to the limited range of star alleles assessed. Inadequate haplotype coverage may risk misclassification of an individual’s predicted metabolizer phenotype, which has ramifications for depression medication selection and dosage. This study underscores the urgent need for greater standardization in PGx testing and emphasizes the importance of considering genetic ancestry when choosing a PGx testing panel to ensure optimal clinical applicability. Full article
(This article belongs to the Special Issue Pharmacogenomics and Population Genetics: Personalized Medicine in Ethnically Diverse Population)
11 pages, 873 KiB  
Perspective
Population Pharmacogenomics for Health Equity
by I. King Jordan, Shivam Sharma and Leonardo Mariño-Ramírez
Genes 2023, 14(10), 1840; https://doi.org/10.3390/genes14101840 - 22 Sep 2023
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Abstract
Health equity means the opportunity for all people and populations to attain optimal health, and it requires intentional efforts to promote fairness in patient treatments and outcomes. Pharmacogenomic variants are genetic differences associated with how patients respond to medications, and their presence can [...] Read more.
Health equity means the opportunity for all people and populations to attain optimal health, and it requires intentional efforts to promote fairness in patient treatments and outcomes. Pharmacogenomic variants are genetic differences associated with how patients respond to medications, and their presence can inform treatment decisions. In this perspective, we contend that the study of pharmacogenomic variation within and between human populations—population pharmacogenomics—can and should be leveraged in support of health equity. The key observation in support of this contention is that racial and ethnic groups exhibit pronounced differences in the frequencies of numerous pharmacogenomic variants, with direct implications for clinical practice. The use of race and ethnicity to stratify pharmacogenomic risk provides a means to avoid potential harm caused by biases introduced when treatment regimens do not consider genetic differences between population groups, particularly when majority group genetic profiles are assumed to hold for minority groups. We focus on the mitigation of adverse drug reactions as an area where population pharmacogenomics can have a direct and immediate impact on public health. Full article
(This article belongs to the Special Issue Pharmacogenomics and Population Genetics: Personalized Medicine in Ethnically Diverse Population)
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