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Singh J, Wilkins G, Goodman-Vincent E, Chishti S, Bonilla Guerrero R, McFadden L, Zahavi Z, Santosh P. Co-Occurring Methylenetetrahydrofolate Reductase ( MTHFR) rs1801133 and rs1801131 Genotypes as Associative Genetic Modifiers of Clinical Severity in Rett Syndrome. Brain Sci 2024; 14:624. [PMID: 39061365 PMCID: PMC11275218 DOI: 10.3390/brainsci14070624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
AIM Remethylation disorders such as 5,10-methylenetetrahydrofolate reductase (MTHFR) deficiency reduce the remethylation of homocysteine to methionine. The resulting hyperhomocysteinemia can lead to serious neurological consequences and multisystem toxicity. The role of MTHFR genotypes has not been investigated in patients with Rett Syndrome (RTT). In this study, we sought to assess the impact of co-occurring MTHFR genotypes on symptom profiles in RTT. METHOD Using pharmacogenomic (PGx) testing, the MTHFR genetic polymorphisms rs1801133 (c.665C>T mutation) and rs1801131 (c.1286A>C mutation) were determined in 65 patients (18.7 years ± 12.1 [mean ± standard deviation]) with RTT as part of routine clinical care within the Centre for Interventional Paediatric Psychopharmacology (CIPP) Rett Centre, a National and Specialist Child and Adolescent Mental Health Service (CAMHS) in the UK. The clinical severity of patients was assessed using the RTT-anchored Clinical Global Impression Scale (RTT-CGI). RESULTS The clinical severity symptom distribution varied between the homozygous and heterozygous MTHFR rs1801133 and rs1801131 genotypes. Those with the homozygous genotype had a narrower spread of severity scores across several domains (language and communication, ambulation, hand-use and eye contact clinical domains). Patients with the homozygous genotype had statistically significantly greater CGI-Severity scores than individuals with a non-homozygous MTHFR genotype (Z = -2.44, p = 0.015). When comparing the ratings of moderately impaired (4), markedly impaired (5), severely impaired (6) and extremely impaired (7), individuals with the homozygous MTHFR genotype were more impaired than those with the non-homozygous MTHFR genotype (Z = -2.06, p = 0.039). There was no statistically significant difference in the number of prescribed anti-epileptic drugs between the genotypes. CONCLUSIONS Our findings show that in those with a pathogenic RTT genetic variant, co-occurring homozygotic MTHFR rs1801133 and rs1801131 polymorphisms may act as associative genetic modifiers of clinical severity in a subset of patients. Profiling of rs1801133 and rs1801131 in RTT may therefore be useful, especially for high-risk patients who may be at the most risk from symptom deterioration.
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Affiliation(s)
- Jatinder Singh
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK; (J.S.); (G.W.); (E.G.-V.); (S.C.); (L.M.)
- Centre for Interventional Paediatric Psychopharmacology and Rare Diseases (CIPPRD), South London and Maudsley NHS Foundation Trust, London SE5 8AZ, UK
- Centre for Interventional Paediatric Psychopharmacology (CIPP) Rett Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Georgina Wilkins
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK; (J.S.); (G.W.); (E.G.-V.); (S.C.); (L.M.)
- Centre for Interventional Paediatric Psychopharmacology and Rare Diseases (CIPPRD), South London and Maudsley NHS Foundation Trust, London SE5 8AZ, UK
- Centre for Interventional Paediatric Psychopharmacology (CIPP) Rett Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Ella Goodman-Vincent
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK; (J.S.); (G.W.); (E.G.-V.); (S.C.); (L.M.)
- Centre for Interventional Paediatric Psychopharmacology and Rare Diseases (CIPPRD), South London and Maudsley NHS Foundation Trust, London SE5 8AZ, UK
- Centre for Interventional Paediatric Psychopharmacology (CIPP) Rett Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Samiya Chishti
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK; (J.S.); (G.W.); (E.G.-V.); (S.C.); (L.M.)
- Centre for Interventional Paediatric Psychopharmacology and Rare Diseases (CIPPRD), South London and Maudsley NHS Foundation Trust, London SE5 8AZ, UK
- Centre for Interventional Paediatric Psychopharmacology (CIPP) Rett Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | | | - Leighton McFadden
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK; (J.S.); (G.W.); (E.G.-V.); (S.C.); (L.M.)
- Centre for Interventional Paediatric Psychopharmacology and Rare Diseases (CIPPRD), South London and Maudsley NHS Foundation Trust, London SE5 8AZ, UK
- Centre for Interventional Paediatric Psychopharmacology (CIPP) Rett Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Zvi Zahavi
- Myogenes Limited, Borehamwood WD6 4PJ, UK;
| | - Paramala Santosh
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK; (J.S.); (G.W.); (E.G.-V.); (S.C.); (L.M.)
- Centre for Interventional Paediatric Psychopharmacology and Rare Diseases (CIPPRD), South London and Maudsley NHS Foundation Trust, London SE5 8AZ, UK
- Centre for Interventional Paediatric Psychopharmacology (CIPP) Rett Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
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Lenz C, Narang A, Bousman CA. Pharmacogenomic allele coverage of genome-wide genotyping arrays: a comparative analysis. Pharmacogenet Genomics 2024; 34:130-134. [PMID: 38359167 DOI: 10.1097/fpc.0000000000000523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The use of genome-wide genotyping arrays in pharmacogenomics (PGx) research and clinical implementation applications is increasing but it is unclear which arrays are best suited for these applications. Here, we conduct a comparative coverage analysis of PGx alleles included on genome-wide genotyping arrays, with an emphasis on alleles in genes with PGx-based prescribing guidelines. Genomic manifest files for seven arrays including the Axiom Precision Medicine Diversity Array (PMDA), Axiom PMDA Plus, Axiom PangenomiX, Axiom PangenomiX Plus, Infinium Global Screening Array, Infinium Global Diversity Array (GDA) and Infinium GDA with enhanced PGx (GDA-PGx) Array, were evaluated for coverage of 523 star alleles across 19 pharmacogenes included in prescribing guidelines developed by the Clinical Pharmacogenetic Implementation Consortium and Dutch Pharmacogenomics Working Group. Specific attention was given to coverage of the Association of Molecular Pathology's Tier 1 and Tier 2 allele sets for CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, NUDT15, TPMT and VKORC1 . Coverage of the examined PGx alleles was highest for the Infinium GDA-PGx (88%), Axiom PangenomiX Plus (77%), Axiom PangenomiX (72%) and Axiom PMDA Plus (70%). Three arrays (Infinium GDA-PGx, Axiom PangenomiX Plus and Axiom PMDA Plus) fully covered the Tier 1 alleles and the Axiom PangenomiX array provided full coverage of Tier 2 alleles. In conclusion, PGx allele coverage varied by gene and array. A superior array for all PGx applications was not identified. Future comparative analyses of genotype data produced by these arrays are needed to determine the robustness of the reported coverage estimates.
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Affiliation(s)
| | | | - Chad A Bousman
- Alberta Children's Hospital Research Institute
- Department of Medical Genetics
- The Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Cumming School of Medicine
- Departments of Psychiatry
- Physiology and Pharmacology
- Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
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Bhalla M, Mittal R, Kumar M, Bhatia R, Kushwah AS. Metabolomics: A Tool to Envisage Biomarkers in Clinical Interpretation of Cancer. Curr Drug Res Rev 2024; 16:333-348. [PMID: 37702236 DOI: 10.2174/2589977516666230912120412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/22/2023] [Accepted: 07/20/2023] [Indexed: 09/14/2023]
Abstract
BACKGROUND Cancer is amongst the most dreadful ailments of modern times, and its impact continuously worsens global health systems. Early diagnosis and suitable therapeutic agents are the prime keys to managing this disease. Metabolomics deals with the complete profiling of cells and physiological phenomena in their organelles, thus helping in keen knowledge of the pathological status of the disease. It has been proven to be one of the best strategies in the early screening of cancer. OBJECTIVE This review has covered the recent updates on the promising role of metabolomics in the identification of significant biochemical markers in cancer-prone individuals that could lead to the identification of cancer in the early stages. METHODS The literature was collected through various databases, like Scopus, PubMed, and Google Scholar, with stress laid on the last ten years' publications. CONCLUSION It was assessed in this review that early recognition of cancerous growth could be achieved via complete metabolic profiling in association with transcriptomics and proteomics. The outcomes are rooted in various clinical studies that anticipated various biomarkers like tryptophan, phenylalanine, lactates, and different metabolic pathways associated with the Warburg effect. This metabolite imaging has been a fundamental step for the target acquisition, evaluation of predictive cancer biomarkers for early detection, and outlooks into cancer therapy along with critical evaluation. Significant efforts should be made to make this technique most reliable and easy.
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Affiliation(s)
- Medha Bhalla
- Department of Pharmacology, Amar Shaheed Baba Ajit Singh Jujhar Singh Memorial College of Pharmacy, Ropar, 140111, India
| | - Roopal Mittal
- Department of Pharmacology, IKG Punjab Technical University, Jalandhar, 144601, India
- Department of Pharmacology, R.K.S.D. College of Pharmacy, Kaithal, 136027, India
| | - Manish Kumar
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, 140401, India
| | - Rohit Bhatia
- Department of Pharmaceutical Chemistry, Indo Soviet Friendship College of Pharmacy, Moga, 142001, India
| | - Ajay Singh Kushwah
- Department of Pharmacology, Amar Shaheed Baba Ajit Singh Jujhar Singh Memorial College of Pharmacy, Ropar, 140111, India
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Ahmed Z. Precision medicine with multi-omics strategies, deep phenotyping, and predictive analysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 190:101-125. [DOI: 10.1016/bs.pmbts.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Piriyapongsa J, Sukritha C, Kaewprommal P, Intarat C, Triparn K, Phornsiricharoenphant K, Chaosrikul C, Shaw PJ, Chantratita W, Mahasirimongkol S, Tongsima S. PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation. J Pers Med 2021; 11:1230. [PMID: 34834582 PMCID: PMC8618518 DOI: 10.3390/jpm11111230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/17/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
The increasing availability of next generation sequencing (NGS) for personal genomics could promote pharmacogenomics (PGx) discovery and application. However, current tools for analysis and interpretation of pharmacogenomic variants from NGS data are inadequate, as none offer comprehensive analytic functions in a simple, web-based platform. In addition, no tools exist to analyze human leukocyte antigen (HLA) genes for determining potential risks of immune-mediated adverse drug reaction (IM-ADR). We describe PharmVIP, a web-based PGx tool, for one-stop comprehensive analysis and interpretation of genome-wide variants obtained from NGS platforms. PharmVIP comprises three main interpretation modules covering analyses of pharmacogenes involved in pharmacokinetics, pharmacodynamics and IM-ADR. The Guideline module provides Clinical Pharmacogenetics Implementation Consortium (CPIC) drug guideline recommendations based on the translation of genotypic data in genes having guidelines. The HLA module reports HLA genotypes, potential adverse drug reactions, and the relevant drug guidelines. The Pharmacogenes module is employed for prioritizing variants according to variant effect on gene function. Detailed, customizable reports are provided as exportable files and as an interactive web version. PharmVIP is a new integrated NGS workflow for the PGx community to facilitate discovery and clinical application.
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Affiliation(s)
- Jittima Piriyapongsa
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Chanathip Sukritha
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Pavita Kaewprommal
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Chalermpong Intarat
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Kwankom Triparn
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Krittin Phornsiricharoenphant
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Chadapohn Chaosrikul
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Philip J. Shaw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand;
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Phayathai, Bangkok 10400, Thailand;
| | - Surakameth Mahasirimongkol
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand;
| | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
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Linskey DW, Linskey DC, McLeod HL, Luzum JA. The need to shift pharmacogenetic research from candidate gene to genome-wide association studies. Pharmacogenomics 2021; 22:1143-1150. [PMID: 34608812 DOI: 10.2217/pgs-2021-0108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The primary research approach in pharmacogenetics has been candidate gene association studies (CGAS), but pharmacogenomic genome-wide association studies (GWAS) are becoming more common. We are now at a critical juncture when the results of those two research approaches, CGAS and GWAS, can be compared in pharmacogenetics. We analyzed publicly available databases of pharmacogenetic CGAS and GWAS (i.e., the Pharmacogenomics Knowledgebase [PharmGKB®] and the NHGRI-EBI GWAS catalog) and the vast majority of variants (98%) and genes (94%) discovered in pharmacogenomic GWAS were novel (i.e., not previously studied CGAS). Therefore, pharmacogenetic researchers are not selecting the right candidate genes in the vast majority of CGAS, highlighting a need to shift pharmacogenetic research efforts from CGAS to GWAS.
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Affiliation(s)
- Derek W Linskey
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | | | - Howard L McLeod
- Precision Medicine, Geriatric Oncology Consortium, Tampa, FL 33609, USA
| | - Jasmine A Luzum
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
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PharmaKU: A Web-Based Tool Aimed at Improving Outreach and Clinical Utility of Pharmacogenomics. J Pers Med 2021; 11:jpm11030210. [PMID: 33809530 PMCID: PMC7998233 DOI: 10.3390/jpm11030210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022] Open
Abstract
With the tremendous advancements in genome sequencing technology in the field of pharmacogenomics, data have to be made accessible to be more efficiently utilized by broader clinical disciplines. Physicians who require the drug–genome interactome information, have been challenged by the complicated pharmacogenomic star-based classification system. We present here an end-to-end web-based pharmacogenomics tool, PharmaKU, which has a comprehensive easy-to-use interface. PharmaKU can help to overcome several hurdles posed by previous pharmacogenomics tools, including input in hg38 format only, while hg19/GRCh37 is now the most popular reference genome assembly among clinicians and geneticists, as well as the lack of clinical recommendations and other pertinent dosage-related information. This tool extracts genetic variants from nine well-annotated pharmacogenes (for which diplotype to phenotype information is available) from whole genome variant files and uses Stargazer software to assign diplotypes and apply prescribing recommendations from pharmacogenomic resources. The tool is wrapped with a user-friendly web interface, which allows for choosing hg19 or hg38 as the reference genome version and reports results as a comprehensive PDF document. PharmaKU is anticipated to enable bench to bedside implementation of pharmacogenomics knowledge by bringing precision medicine closer to a clinical reality.
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Update on next generation sequencing of pharmacokinetics-related genes: Development of the PKseq panel, a platform for amplicon sequencing of drug-metabolizing enzyme and drug transporter genes. Drug Metab Pharmacokinet 2020; 37:100370. [PMID: 33508759 DOI: 10.1016/j.dmpk.2020.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/01/2020] [Accepted: 11/18/2020] [Indexed: 02/08/2023]
Abstract
Genetic variation in pharmacokinetics (PK)-related genes encoding drug metabolizing enzymes or drug transporters is one of the most practical pharmacogenetic biomarkers for the prediction or explanation of an individual's response to drugs. Many pharmacogenomic variations are identified using targeted, whole-exome, and whole-genome sequencing, and the number of known novel variations and alleles in PK-related genes is increasing. The high homology of sequences among PK-related genes is suspected to lead to potential read misalignment and genotyping errors when short-read sequencing was performed. Therefore, highly efficient and accurate next generation sequencing (NGS) platforms for the sequencing of PK-related genes are needed. We have developed PKseq, a targeted sequencing panel based on multiplex PCR, which targets the coding regions of 37 drug transporters, 30 cytochrome P450 isoforms, 10 UDP-glucuronosyltransferases, 5 flavin-containing monooxygenases, 4 glutathione S-transferases, 4 sulfotransferases, and 10 other genes. In this review, we describe the current NGS platforms for the sequencing of PK-related genes. The NGS platforms, including the PKseq panel, will be useful not only for the identification of all the variants of PK-related genes associated with adverse drug reactions and drug efficacy, but also for clinical sequencing to achieve pharmacogenomics-based stratified medicine.
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Zaid N, Limami Y, Senhaji N, Errafiy N, Khalki L, Bakri Y, Zaid Y, Amzazi S. Coverage rate of ADME genes from commercial sequencing arrays. Medicine (Baltimore) 2019; 98:e13975. [PMID: 30653102 PMCID: PMC6370070 DOI: 10.1097/md.0000000000013975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Pharmacogenomics offers remarkable potential for the rapid translation of discoveries into changes in clinical practice. In the present work, we are interested in evaluating the ability of commercially available genome-wide association sequencing chips to cover genes that have high pharmacogenomics potential.We used a set of 2794 variations within 369 absorption, distribution, metabolism, and elimination (ADME) genes of interest, as previously defined in collaboration with the Pharma ADME consortium. We have compared the Illumina TrueSeq and both Agilent SureSelect and HaloPlex sequencing technologies. We have developed Python scripts to evaluate the coverage for each of these products. In particular, we considered a specific list of 155 allelic variants in 34 genes which present high pharmacogenomics potential. Both the theoretical and practical coverage was assessed.Given the need to have a good coverage to establish confidently the functionality of an enzyme, the observed rates are unlikely to provide sufficient evidence for pharmacogenomics studies. We assessed the coverage using enrichment technology for exome sequencing using the Illumina Trueseq exome, Agilent SureSelectXT1 V4 and V5, and Haloplex exome, which offer a coverage of 96.12%, 91.61%, and 88.38%, respectively.Although pharmacogenomic advances had been limited in the past due in part to the lack of coverage of commercial genotyping chips, it is anticipated that future studies that make use of new sequencing technologies should offer a greater potential for discovery.
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Affiliation(s)
- Nabil Zaid
- Faculty of Sciences, Mohammed V University, Rabat
- Biochemistry and Immunology Laboratory, Rabat
| | - Youness Limami
- Research Center, Abulcasis University of Health Sciences, Rabat
| | - Nezha Senhaji
- Faculty of Medicine and Pharmacy of Casablanca, Laboratory of Genetics and Molecular pathologies, Hassan II University
| | - Nadia Errafiy
- Mohammed VI University of Health Sciences (UM6SS), Casablanca
| | - Loubna Khalki
- Mohammed VI University of Health Sciences (UM6SS), Casablanca
| | - Youssef Bakri
- Faculty of Sciences, Laboratory of Biology of Human Pathology, Center of Genomics of Human Pathologies, Mohammed V University, Rabat, Morocco
| | - Younes Zaid
- Research Center, Abulcasis University of Health Sciences, Rabat
| | - Saaid Amzazi
- Faculty of Sciences, Mohammed V University, Rabat
- Biochemistry and Immunology Laboratory, Rabat
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Lemieux Perreault LP, Zaïd N, Cameron M, Mongrain I, Dubé MP. Pharmacogenetic content of commercial genome-wide genotyping arrays. Pharmacogenomics 2018; 19:1159-1167. [DOI: 10.2217/pgs-2017-0129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Aim: We have evaluated the pharmacogenetic content of commercial human genome-wide genotyping arrays, as it is a critical determinant to enabling pharmacogenomic discoveries. Methods: Using bioinformatics approaches, we assessed 27,811 genetic variants in 3146 genes for their presence in 18 Illumina and 15 Affymetrix genome-wide arrays. Results: The pharmacogenetic content of the arrays varied greatly. The combination of the Affymetrix precision medicine array and PharmacoScan arrays (Affymetrix) had the highest coverage for a set of clinically actionable absorption, distribution, metabolism and excretion (ADME) variants, single nucleotide ADME variants and ADME insertions/deletions, with a physical coverage of 125/130 (96.2%), 9924/24,138 (41.1%) and 2252/3994 (56.4%), respectively. Conclusion: The combination of the Affymetrix precision medicine array and PharmacoScan arrays provided both genome-wide and pharmacogene coverage, which is crucial in the discovering of new variants responsible for drug adverse effects. These results will help in the design of pharmacogenomic studies and will enable a critical review of results from past studies.
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Affiliation(s)
- Louis-Philippe Lemieux Perreault
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Nabil Zaïd
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Université Mohammed V – Faculté des Sciences, Avenue des Nations Unies, Agdal, Rabat Morocco
| | - Michel Cameron
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- BiogeniQ, 4105-G Boulevard Matte, Brossard, J4Y 2P4, Canada
| | - Ian Mongrain
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Marie-Pierre Dubé
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Université de Montréal, Faculty of Medicine, 2900 Boulevard Edouard-Montpetit, Montreal, H3T 1J4, Canada
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DMET™ (Drug Metabolism Enzymes and Transporters): a pharmacogenomic platform for precision medicine. Oncotarget 2018; 7:54028-54050. [PMID: 27304055 PMCID: PMC5288240 DOI: 10.18632/oncotarget.9927] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/29/2016] [Indexed: 02/07/2023] Open
Abstract
In the era of personalized medicine, high-throughput technologies have allowed the investigation of genetic variations underlying the inter-individual variability in drug pharmacokinetics/pharmacodynamics. Several studies have recently moved from a candidate gene-based pharmacogenetic approach to genome-wide pharmacogenomic analyses to identify biomarkers for selection of patient-tailored therapies. In this aim, the identification of genetic variants affecting the individual drug metabolism is relevant for the definition of more active and less toxic treatments. This review focuses on the potentiality, reliability and limitations of the DMET™ (Drug Metabolism Enzymes and Transporters) Plus as pharmacogenomic drug metabolism multi-gene panel platform for selecting biomarkers in the final aim to optimize drugs use and characterize the individual genetic background.
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Puchades-Carrasco L, Pineda-Lucena A. Metabolomics Applications in Precision Medicine: An Oncological Perspective. Curr Top Med Chem 2017; 17:2740-2751. [PMID: 28685691 PMCID: PMC5652075 DOI: 10.2174/1568026617666170707120034] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 04/03/2017] [Accepted: 04/11/2017] [Indexed: 12/17/2022]
Abstract
Nowadays, cancer therapy remains limited by the conventional one-size-fits-all approach. In this context, treatment decisions are based on the clinical stage of disease but fail to ascertain the individual´s underlying biology and its role in driving malignancy. The identification of better therapies for cancer treatment is thus limited by the lack of sufficient data regarding the characterization of specific biochemical signatures associated with each particular cancer patient or group of patients. Metabolomics approaches promise a better understanding of cancer, a disease characterized by significant alterations in bioenergetic metabolism, by identifying changes in the pattern of metabolite expression in addition to changes in the concentration of individual metabolites as well as alterations in biochemical pathways. These approaches hold the potential of identifying novel biomarkers with different clinical applications, including the development of more specific diagnostic methods based on the characterization of metabolic subtypes, the monitoring of currently used cancer therapeutics to evaluate the response and the prognostic outcome with a given therapy, and the evaluation of the mechanisms involved in disease relapse and drug resistance. This review discusses metabolomics applications in different oncological processes underlining the potential of this omics approach to further advance the implementation of precision medicine in the oncology area.
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Affiliation(s)
- Leonor Puchades-Carrasco
- Joint Research Unit in Clinical Metabolomics, Centro de Investigación Príncipe Felipe / Instituto de Investigación Sanitaria La Fe, Valencia. Spain
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Bekri S. The role of metabolomics in precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2016.1273067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Soumeya Bekri
- Department of Metabolic Biochemistry, Rouen University Hospital, Rouen 76000, France
- Normandie Univ, UNIROUEN, INSERM, CHU Rouen, IRIB, INSERM U1245, Rouen 76000, France
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Sivadas A, Salleh MZ, Teh LK, Scaria V. Genetic epidemiology of pharmacogenetic variants in South East Asian Malays using whole-genome sequences. THE PHARMACOGENOMICS JOURNAL 2016; 17:461-470. [PMID: 27241059 DOI: 10.1038/tpj.2016.39] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 03/16/2016] [Accepted: 05/02/2016] [Indexed: 12/28/2022]
Abstract
Expanding the scope of pharmacogenomic research by including multiple global populations is integral to building robust evidence for its clinical translation. Deep whole-genome sequencing of diverse ethnic populations provides a unique opportunity to study rare and common pharmacogenomic markers that often vary in frequency across populations. In this study, we aim to build a diverse map of pharmacogenetic variants in South East Asian (SEA) Malay population using deep whole-genome sequences of 100 healthy SEA Malay individuals. We investigated the allelic diversity of potentially deleterious pharmacogenomic variants in SEA Malay population. Our analysis revealed 227 common and 466 rare potentially functional single nucleotide variants (SNVs) in 437 pharmacogenomic genes involved in drug metabolism, transport and target genes, including 74 novel variants. This study has created one of the most comprehensive maps of pharmacogenetic markers in any population from whole genomes and will hugely benefit pharmacogenomic investigations and drug dosage recommendations in SEA Malays.
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Affiliation(s)
- A Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - M Z Salleh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM) Malaysia, Puncak Alam, Selangor, Malaysia.,Faculty of Pharmacy, Universiti Teknologi MARA (UiTM) Malaysia, Puncak Alam, Selangor, Malaysia
| | - L K Teh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM) Malaysia, Puncak Alam, Selangor, Malaysia.,Faculty of Pharmacy, Universiti Teknologi MARA (UiTM) Malaysia, Puncak Alam, Selangor, Malaysia
| | - V Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
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Huang MC, Chuang TP, Chen CH, Wu JY, Chen YT, Li LH, Yang HC. An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation population-optimized human arrays. BMC Genomics 2016; 17:266. [PMID: 27029637 PMCID: PMC4815280 DOI: 10.1186/s12864-016-2478-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/16/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Affymetrix Axiom single nucleotide polymorphism (SNP) arrays provide a cost-effective, high-density, and high-throughput genotyping solution for population-optimized analyses. However, no public software is available for the integrated genomic analysis of hybridization intensities and genotypes for this new-generation population-optimized genotyping platform. RESULTS A set of statistical methods was developed for an integrated analysis of allele frequency (AF), allelic imbalance (AI), loss of heterozygosity (LOH), long contiguous stretch of homozygosity (LCSH), and copy number variation or alteration (CNV/CNA) on the basis of SNP probe hybridization intensities and genotypes. This study analyzed 3,236 samples that were genotyped using different SNP platforms. The proposed AF adjustment method considerably increased the accuracy of AF estimation. The proposed quick circular binary segmentation algorithm for segmenting copy number reduced the computation time of the original segmentation method by 30-67 %. The proposed CNV/CNA detection, which integrates AI and LOH/LCSH detection, had a promising true positive rate and well-controlled false positive rate in simulation studies. Moreover, our real-time quantitative polymerase chain reaction experiments successfully validated the CNVs/CNAs that were identified in the Axiom data analyses using the proposed methods; some of the validated CNVs/CNAs were not detected in the Affymetrix Array 6.0 data analysis using the Affymetrix Genotyping Console. All the analysis functions are packaged into the ALICE (AF/LOH/LCSH/AI/CNV/CNA Enterprise) software. CONCLUSIONS ALICE and the used genomic reference databases, which can be downloaded from http://hcyang.stat.sinica.edu.tw/software/ALICE.html , are useful resources for analyzing genomic data from the Axiom and other SNP arrays.
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Affiliation(s)
- Mei-Chu Huang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan.,Institute of Statistical Science, Academia Sinica, No 128, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 112, Taiwan
| | - Tzu-Po Chuang
- Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Ling-Hui Li
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan.
| | - Hsin-Chou Yang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan. .,Institute of Statistical Science, Academia Sinica, No 128, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan. .,Institute of Public Health, National Yang Ming University, Taipei, 112, Taiwan. .,Department of Statistics, National Cheng Kung University, Tainan, 701, Taiwan. .,Institute of Statistics, National Tsing Hua University, Hsinchu, 300, Taiwan. .,School of Public Health, National Defense Medical Center, Taipei, 114, Taiwan.
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Wishart DS. Emerging applications of metabolomics in drug discovery and precision medicine. Nat Rev Drug Discov 2016; 15:473-84. [PMID: 26965202 DOI: 10.1038/nrd.2016.32] [Citation(s) in RCA: 879] [Impact Index Per Article: 109.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Metabolomics is an emerging 'omics' science involving the comprehensive characterization of metabolites and metabolism in biological systems. Recent advances in metabolomics technologies are leading to a growing number of mainstream biomedical applications. In particular, metabolomics is increasingly being used to diagnose disease, understand disease mechanisms, identify novel drug targets, customize drug treatments and monitor therapeutic outcomes. This Review discusses some of the latest technological advances in metabolomics, focusing on the application of metabolomics towards uncovering the underlying causes of complex diseases (such as atherosclerosis, cancer and diabetes), the growing role of metabolomics in drug discovery and its potential effect on precision medicine.
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Affiliation(s)
- David S Wishart
- Department of Biological Sciences, CW 405, Biological Sciences Building, University of Alberta, Edmonton, Alberta, Canada T6G 2E9.,Department of Computing Science, 2-21 Athabasca Hall University of Alberta, Edmonton, Alberta, Canada T6G 2E8.,National Institute of Nanotechnology, National Research Council, Edmonton, Alberta, Canada T6G 2M9
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Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. THE PHARMACOGENOMICS JOURNAL 2016; 17:137-145. [PMID: 26856248 PMCID: PMC4980276 DOI: 10.1038/tpj.2015.93] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 11/06/2015] [Accepted: 11/13/2015] [Indexed: 12/15/2022]
Abstract
Variation in the expression level and activity of genes involved in drug disposition and action (‘pharmacogenes') can affect drug response and toxicity, especially when in tissues of pharmacological importance. Previous studies have relied primarily on microarrays to understand gene expression differences, or have focused on a single tissue or small number of samples. The goal of this study was to use RNA-sequencing (RNA-seq) to determine the expression levels and alternative splicing of 389 Pharmacogenomics Research Network pharmacogenes across four tissues (liver, kidney, heart and adipose) and lymphoblastoid cell lines, which are used widely in pharmacogenomics studies. Analysis of RNA-seq data from 139 different individuals across the 5 tissues (20–45 individuals per tissue type) revealed substantial variation in both expression levels and splicing across samples and tissue types. Comparison with GTEx data yielded a consistent picture. This in-depth exploration also revealed 183 splicing events in pharmacogenes that were previously not annotated. Overall, this study serves as a rich resource for the research community to inform biomarker and drug discovery and use.
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Wassenaar CA, Zhou Q, Tyndale RF. CYP2A6 genotyping methods and strategies using real-time and end point PCR platforms. Pharmacogenomics 2015; 17:147-62. [PMID: 26670214 DOI: 10.2217/pgs.15.156] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
CYP2A6 genotyping is of clinical importance--CYP2A6 gene variants influence nicotine metabolism and are associated with nicotine dependence, cigarettes per day, smoking cessation and the risk for tobacco-associated cancers. CYP2A6 gene variants also influence the metabolism of therapeutic drugs, such as the anticancer agents, tegafur and letrozole. Over the years, CYP2A6 genotyping methods have evolved to incorporate novel gene variants and to circumvent genotyping errors resulting from the high degree of homology between CYP2A6 and neighboring CYP2A genes. Herein, CYP2A6 genotyping strategies are described for commonly genotyped functionally significant alleles including SNPs, small insertions/deletions and more complex structural variants. The methods presented utilize higher throughput SYBR green real-time PCR technology in addition to standard thermocycling.
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Affiliation(s)
- Catherine A Wassenaar
- Department of Pharmacology & Toxicology, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8 ON, Canada
| | - Qian Zhou
- Department of Pharmacology & Toxicology, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8 ON, Canada
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction & Mental Health (CAMH), Departments of Pharmacology & Toxicology & Psychiatry, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8 ON, Canada
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Mizzi C, Peters B, Mitropoulou C, Mitropoulos K, Katsila T, Agarwal MR, van Schaik RHN, Drmanac R, Borg J, Patrinos GP. Personalized pharmacogenomics profiling using whole-genome sequencing. Pharmacogenomics 2015; 15:1223-34. [PMID: 25141897 DOI: 10.2217/pgs.14.102] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIM Pharmacogenomics holds promise to rationalize drug use by minimizing drug toxicity and at the same time increase drug efficacy. There are currently several assays to screen for known pharmacogenomic biomarkers for the most commonly prescribed drugs. However, these genetic screening assays cannot account for other known or novel pharmacogenomic markers. MATERIALS & METHODS We analyzed whole-genome sequences of 482 unrelated individuals of various ethnic backgrounds to obtain their personalized pharmacogenomics profiles. RESULTS Bioinformatics analysis revealed 408,964 variants in 231 pharmacogenes, from which 26,807 were residing on exons and proximal regulatory sequences, whereas 16,487 were novel. In silico analyses indicated that 1012 novel pharmacogene-related variants possibly abolish protein function. We have also performed whole-genome sequencing analysis in a seven-member family of Greek origin in an effort to explain the variable response rate to acenocoumarol treatment in two family members. CONCLUSION Overall, our data demonstrate that whole-genome sequencing, unlike conventional genetic screening methods, is necessary to determine an individual's pharmacogenomics profile in a more comprehensive manner, which, combined with the gradually decreasing whole-genome sequencing costs, would expedite bringing personalized medicine closer to reality.
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Affiliation(s)
- Clint Mizzi
- Laboratory of Molecular Genetics, Department of Physiology & Biochemistry, University of Malta, Msida, Malta
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Abdo N, Xia M, Brown CC, Kosyk O, Huang R, Sakamuru S, Zhou YH, Jack JR, Gallins P, Xia K, Li Y, Chiu WA, Motsinger-Reif AA, Austin CP, Tice RR, Rusyn I, Wright FA. Population-based in vitro hazard and concentration-response assessment of chemicals: the 1000 genomes high-throughput screening study. ENVIRONMENTAL HEALTH PERSPECTIVES 2015; 123:458-66. [PMID: 25622337 PMCID: PMC4421772 DOI: 10.1289/ehp.1408775] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 01/12/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Understanding of human variation in toxicity to environmental chemicals remains limited, so human health risk assessments still largely rely on a generic 10-fold factor (10½ each for toxicokinetics and toxicodynamics) to account for sensitive individuals or subpopulations. OBJECTIVES We tested a hypothesis that population-wide in vitro cytotoxicity screening can rapidly inform both the magnitude of and molecular causes for interindividual toxicodynamic variability. METHODS We used 1,086 lymphoblastoid cell lines from the 1000 Genomes Project, representing nine populations from five continents, to assess variation in cytotoxic response to 179 chemicals. Analysis included assessments of population variation and heritability, and genome-wide association mapping, with attention to phenotypic relevance to human exposures. RESULTS For about half the tested compounds, cytotoxic response in the 1% most "sensitive" individual occurred at concentrations within a factor of 10½ (i.e., approximately 3) of that in the median individual; however, for some compounds, this factor was > 10. Genetic mapping suggested important roles for variation in membrane and transmembrane genes, with a number of chemicals showing association with SNP rs13120371 in the solute carrier SLC7A11, previously implicated in chemoresistance. CONCLUSIONS This experimental approach fills critical gaps unaddressed by recent large-scale toxicity testing programs, providing quantitative, experimentally based estimates of human toxicodynamic variability, and also testable hypotheses about mechanisms contributing to interindividual variation.
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Affiliation(s)
- Nour Abdo
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Haga SB, Allen LaPointe NM, Moaddeb J. Challenges to integrating pharmacogenetic testing into medication therapy management. J Manag Care Spec Pharm 2015; 21:346-52. [PMID: 25803768 PMCID: PMC4522310 DOI: 10.18553/jmcp.2015.21.4.346] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Some have proposed the integration of pharmacogenetic (PGx) testing into medication therapy management (MTM) to enable further refinement of treatments to reduce risk of adverse responses and improve efficacy. PGx testing involves the analysis of genetic variants associated with therapeutic or adverse response and may be useful in enhancing the ability to identify ineffective and/or harmful drugs or drug combinations. This "enhanced" MTM might also reduce patient concerns about side effects and increase confidence that the medication is effective, addressing 2 key factors that impact patient adherence: concern and necessity. However, the feasibility and effectiveness of the integration of PGx testing into MTM in clinical practice has not yet been determined. In this commentary, we consider some of the challenges to the integration and delivery of PGx testing in MTM services.
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Affiliation(s)
- Susanne B Haga
- Duke University School of Medicine, 304 Research Dr., Box 90141, Durham, NC 27708.
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Katsila T, Patrinos GP. Whole genome sequencing in pharmacogenomics. Front Pharmacol 2015; 6:61. [PMID: 25859217 PMCID: PMC4374451 DOI: 10.3389/fphar.2015.00061] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/09/2015] [Indexed: 11/13/2022] Open
Abstract
Pharmacogenomics aims to shed light on the role of genes and genomic variants in clinical treatment response. Although, several drug-gene relationships are characterized to date, many challenges still remain toward the application of pharmacogenomics in the clinic; clinical guidelines for pharmacogenomic testing are still in their infancy, whereas the emerging high throughput genotyping technologies produce a tsunami of new findings. Herein, the potential of whole genome sequencing on pharmacogenomics research and clinical application are highlighted.
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Affiliation(s)
- Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras Patras, Greec
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras Patras, Greec
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Gamazon ER, Perera M. Genome-wide approaches in pharmacogenomics: heritability estimation and pharmacoethnicity as primary challenges. Pharmacogenomics 2013; 13:1101-4. [PMID: 22909197 DOI: 10.2217/pgs.12.88] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Innocenti F. Moving away from candidate genes: a 'genome-wise' discovery of gemcitabine myelotoxicity. Pharmacogenomics 2013; 13:1113-4. [PMID: 22909200 DOI: 10.2217/pgs.12.96] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Federico Innocenti
- University of North Carolina at Chapel Hill, Institute for Pharmacogenomics & Individualized Therapy, Eshelman School of Pharmacy, School of Medicine, Chapel Hill, NC 27599-7361, USA.
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Pharmacogenomics in children: advantages and challenges of next generation sequencing applications. Int J Pediatr 2013; 2013:136524. [PMID: 23401694 PMCID: PMC3562678 DOI: 10.1155/2013/136524] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 12/20/2012] [Indexed: 12/31/2022] Open
Abstract
Pharmacogenetics is considered as a prime example of how personalized medicine nowadays can be put into practice. However, genotyping to guide pharmacological treatment is relatively uncommon in the routine clinical practice. Several reasons can be found why the application of pharmacogenetics is less than initially anticipated, which include the contradictory results obtained for certain variants and the lack of guidelines for clinical implementation. However, more reproducible results are being generated, and efforts have been made to establish working groups focussing on evidence-based clinical guidelines. For another pharmacogenetic hurdle, the speed by which a pharmacogenetic profile for a certain drug can be obtained in an individual patient, there has been a revolution in molecular genetics through the introduction of next generation sequencing (NGS), making it possible to sequence a large number of genes up to the complete genome in a single reaction. Besides the enthusiasm due to the tremendous increase of our sequencing capacities, several considerations need to be made regarding quality and interpretation of the sequence data as well as ethical aspects of this technology. This paper will focus on the different NGS applications that may be useful for pharmacogenomics in children and the challenges that they bring on.
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Cavallari LH, Momary K. Pharmacogenetics in Cardiovascular Diseases. Pharmacogenomics 2013. [DOI: 10.1016/b978-0-12-391918-2.00005-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Cavallari LH, Perera MA. The future of warfarin pharmacogenetics in under-represented minority groups. Future Cardiol 2012; 8:563-76. [PMID: 22871196 DOI: 10.2217/fca.12.31] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Genotype-based dosing recommendations are provided in the US FDA-approved warfarin labeling. However, data that informed these recommendations were from predominately Caucasian populations. Studies show that variants contributing to warfarin dose requirements in Caucasians provide similar contributions to dose requirements in US Hispanics, but significantly lesser contributions in African-Americans. Further data demonstrate that variants occurring commonly in individuals of African ancestry, but rarely in other racial groups, significantly influence dose requirements in African-Americans. These data suggest that it is important to consider variants specific for African-Americans when implementing genotype-guided warfarin dosing in this population.
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Affiliation(s)
- Larisa H Cavallari
- Department of Pharmacy Practice, University of Illinois at Chicago, College of Pharmacy, 833 South Wood Street, Chicago, IL 60612-7230, USA.
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Justenhoven C. Polymorphisms of Phase I and Phase II Enzymes and Breast Cancer Risk. Front Genet 2012; 3:258. [PMID: 23226154 PMCID: PMC3508624 DOI: 10.3389/fgene.2012.00258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 11/05/2012] [Indexed: 12/21/2022] Open
Abstract
Breast cancer is a complex disease which is provoked by a multitude of exogenous and endogenous factors including genetic variations. Recent genome-wide association studies identified a set of more than 18 novel low penetrant susceptibility loci, however, a limitation of this powerful approach is the hampered analysis of polymorphisms in DNA sequences with a high degree of similarity to other genes or pseudo genes. Since this common feature affects the majority of the highly polymorphic genes encoding phase I and II enzymes the retrieval of specific genotype data requires adapted amplification methods. With regard to breast cancer these genes are of certain interest due to their involvement in the metabolism of carcinogens like exogenous genotoxic compounds or steroid hormones. The present review summarizes the observed effects of functional genetic variants of phase I and II enzymes in well designed case control studies to shed light on their contribution to breast cancer risk.
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Affiliation(s)
- Christina Justenhoven
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology Stuttgart, Germany ; University of Tübingen Tübingen, Germany
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Abstract
A new generation of technologies commonly named omics permits assessment of the entirety of the components of biological systems and produces an explosion of data and a major shift in our concepts of disease. These technologies will likely shape the future of health care. One aspect of these advances is that the data generated document the uniqueness of each human being in regard to disease risk and treatment response. These developments have reemphasized the concept of personalized medicine. Here we review the impact of omics technologies on one key aspect of personalized medicine: the individual drug response. We describe how knowledge of different omics may affect treatment decisions, namely drug choice and drug dose, and how it can be used to improve clinical outcomes.
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Affiliation(s)
- Urs A Meyer
- Division of Pharmacology and Neurobiology, Biozentrum of the University of Basel, CH-4056 Basel, Switzerland.
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