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Mohamed ME, Saqr A, Staley C, Onyeaghala G, Teigen L, Dorr CR, Remmel RP, Guan W, Oetting WS, Matas AJ, Israni AK, Jacobson PA. Pharmacomicrobiomics: Immunosuppressive Drugs and Microbiome Interactions in Transplantation. Transplantation 2024:00007890-990000000-00663. [PMID: 38361239 DOI: 10.1097/tp.0000000000004926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The human microbiome is associated with human health and disease. Exogenous compounds, including pharmaceutical products, are also known to be affected by the microbiome, and this discovery has led to the field of pharmacomicobiomics. The microbiome can also alter drug pharmacokinetics and pharmacodynamics, possibly resulting in side effects, toxicities, and unanticipated disease response. Microbiome-mediated effects are referred to as drug-microbiome interactions (DMI). Rapid advances in the field of pharmacomicrobiomics have been driven by the availability of efficient bacterial genome sequencing methods and new computational and bioinformatics tools. The success of fecal microbiota transplantation for recurrent Clostridioides difficile has fueled enthusiasm and research in the field. This review focuses on the pharmacomicrobiome in transplantation. Alterations in the microbiome in transplant recipients are well documented, largely because of prophylactic antibiotic use, and the potential for DMI is high. There is evidence that the gut microbiome may alter the pharmacokinetic disposition of tacrolimus and result in microbiome-specific tacrolimus metabolites. The gut microbiome also impacts the enterohepatic recirculation of mycophenolate, resulting in substantial changes in pharmacokinetic disposition and systemic exposure. The mechanisms of these DMI and the specific bacteria or communities of bacteria are under investigation. There are little or no human DMI data for cyclosporine A, corticosteroids, and sirolimus. The available evidence in transplantation is limited and driven by small studies of heterogeneous designs. Larger clinical studies are needed, but the potential for future clinical application of the pharmacomicrobiome in avoiding poor outcomes is high.
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Affiliation(s)
- Moataz E Mohamed
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN
| | - Abdelrahman Saqr
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN
| | | | - Guillaume Onyeaghala
- Hennepin Healthcare Research Institute, Minneapolis, MN
- Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Levi Teigen
- Department of Food Science and Nutrition, University of Minnesota, St Paul, MN
| | - Casey R Dorr
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN
- Hennepin Healthcare Research Institute, Minneapolis, MN
- Department of Medicine, University of Minnesota, Minneapolis, MN
- Department of Medicine, Hennepin Healthcare, Minneapolis, MN
| | - Rory P Remmel
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN
| | - Arthur J Matas
- Department of Surgery, University of Minnesota, Minneapolis, MN
| | - Ajay K Israni
- Hennepin Healthcare Research Institute, Minneapolis, MN
- Department of Medicine, Hennepin Healthcare, Minneapolis, MN
- Department of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN
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Capps B, Chadwick R, Lederman Z, Lysaght T, Mills C, Mulvihill JJ, Oetting WS, Winship I. The Human Genome Organisation (HUGO) and a vision for Ecogenomics: the Ecological Genome Project. Hum Genomics 2023; 17:115. [PMID: 38111041 PMCID: PMC10726505 DOI: 10.1186/s40246-023-00560-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND The following outlines ethical reasons for widening the Human Genome Organisation's (HUGO) mandate to include ecological genomics. MAIN: The environment influences an organism's genome through ambient factors in the biosphere (e.g. climate and UV radiation), as well as the agents it comes into contact with, i.e. the epigenetic and mutagenic effects of inanimate chemicals and pollution, and pathogenic organisms. Emerging scientific consensus is that social determinants of health, environmental conditions and genetic factors work together to influence the risk of many complex illnesses. That paradigm can also explain the environmental and ecological determinants of health as factors that underlie the (un)healthy ecosystems on which communities rely. We suggest that The Ecological Genome Project is an aspirational opportunity to explore connections between the human genome and nature. We propose consolidating a view of Ecogenomics to provide a blueprint to respond to the environmental challenges that societies face. This can only be achieved by interdisciplinary engagement between genomics and the broad field of ecology and related practice of conservation. In this respect, the One Health approach is a model for environmental orientated work. The idea of Ecogenomics-a term that has been used to relate to a scientific field of ecological genomics-becomes the conceptual study of genomes within the social and natural environment. CONCLUSION The HUGO Committee on Ethics, Law and Society (CELS) recommends that an interdisciplinary One Health approach should be adopted in genomic sciences to promote ethical environmentalism. This perspective has been reviewed and endorsed by the HUGO CELS and the HUGO Executive Board.
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Affiliation(s)
- Benjamin Capps
- Department of Bioethics, Dalhousie University, 5849 University Avenue, CRC Building, Room C-312, PO Box 15000, Halifax, NS, B3H 4R2, Canada.
| | | | | | - Tamra Lysaght
- National University of Singapore, Singapore, Singapore
| | | | - John J Mulvihill
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
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Brown JT, Sorge LA, Oetting WS, Jacobson PA, Pereira C. Meeting the New AACP Competencies in Genetics and Clinical Pharmacogenomics at the University of Minnesota. Innov Pharm 2023; 14:10.24926/iip.v14i4.5142. [PMID: 38495355 PMCID: PMC10939494 DOI: 10.24926/iip.v14i4.5142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
Objective: Pharmacogenomics (PGx) is increasingly being used for creating individualized treatments for patient care. Healthcare professionals, especially pharmacists, need to understand how genetic variation impacts the efficacy and toxicity of medications. Due to the breadth and complexity of PGx-related information, it has been challenging to determine what information should be included in pharmacy curricula and how best to educate students. Methods: The University of Minnesota College of Pharmacy recently began the process of incorporating into the curriculum expanded competencies for PGx from the American Association of Colleges of Pharmacy (AACP) Pharmacogenomics Special Interest Group (PGx-SIG). We evaluated our curriculum for PGx content, determined what was currently being taught and identified educational gaps. Results: A review of our Doctor of Pharmacy curriculum showed substantial PGx content, although it was inconsistently taught throughout the required courses and in some courses absent. We revised the content of existing courses incorporating content that meet most of the PGx-SIG recommended competencies. Conclusion: There are and will be major changes in our understanding of the influences of PGx on individualized medical treatment. As our understanding grows, information on PGx in pharmacy curriculums will need to keep pace with these changes. We have begun this process at the University of Minnesota by doing a full review of PGx related information and making appropriate revisions in the pharmacy curriculum.
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Loftus SK, Gillis MF, Lundh L, Baxter LL, Wedel JC, Watkins-Chow DE, Donovan FX, Sergeev YV, Oetting WS, Pavan WJ, Adams DR. Haplotype-based analysis resolves missing heritability in oculocutaneous albinism type 1B. Am J Hum Genet 2023; 110:1123-1137. [PMID: 37327787 PMCID: PMC10357474 DOI: 10.1016/j.ajhg.2023.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/18/2023] Open
Abstract
Oculocutaneous albinism (OCA) is a rare disorder of pigment production. Affected individuals have variably decreased global pigmentation and visual-developmental changes that lead to low vision. OCA is notable for significant missing heritability, particularly among individuals with residual pigmentation. Tyrosinase (TYR) is the rate-limiting enzyme in melanin pigment biosynthesis and mutations that decrease enzyme function are one of the most common causes of OCA. We present the analysis of high-depth short-read TYR sequencing data for a cohort of 352 OCA probands, ∼50% of whom were previously sequenced without yielding a definitive diagnostic result. Our analysis identified 66 TYR single-nucleotide variants (SNVs) and small insertion/deletions (indels), 3 structural variants, and a rare haplotype comprised of two common frequency variants (p.Ser192Tyr and p.Arg402Gln) in cis-orientation, present in 149/352 OCA probands. We further describe a detailed analysis of the disease-causing haplotype, p.[Ser192Tyr; Arg402Gln] ("cis-YQ"). Haplotype analysis suggests that the cis-YQ allele arose by recombination and that multiple cis-YQ haplotypes are segregating in OCA-affected individuals and control populations. The cis-YQ allele is the most common disease-causing allele in our cohort, representing 19.1% (57/298) of TYR pathogenic alleles in individuals with type 1 (TYR-associated) OCA. Finally, among the 66 TYR variants, we found several additional alleles defined by a cis-oriented combination of minor, potentially hypomorph-producing alleles at common variant sites plus a second, rare pathogenic variant. Together, these results suggest that identification of phased variants for the full TYR locus are required for an exhaustive assessment for potentially disease-causing alleles.
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Affiliation(s)
- Stacie K Loftus
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Meredith F Gillis
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Linnea Lundh
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julia C Wedel
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank X Donovan
- Cancer Genomics Unit, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuri V Sergeev
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Reininger KA, Onyeaghala G, Anderson-Haag T, Schladt DS, Wu B, Guan W, Dorr CR, Remmel RP, Mannon R, Matas AJ, Oetting WS, Stahler P, Israni AK, Jacobson PA. Higher number of tacrolimus dose adjustments in kidney transplant recipients who are extensive and intermediate CYP3A5 metabolizers. Clin Transplant 2023; 37:e14893. [PMID: 36571802 PMCID: PMC10089949 DOI: 10.1111/ctr.14893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022]
Abstract
Kidney transplant recipients carrying the CYP3A5*1 allele have lower tacrolimus troughs, and higher dose requirements compared to those with the CYP3A5*3/*3 genotype. However, data on the effect of CYP3A5 alleles on post-transplant tacrolimus management are lacking. The effect of CYP3A5 metabolism phenotypes on the number of tacrolimus dose adjustments and troughs in the first 6 months post-transplant was evaluated in 78 recipients (64% Caucasians). Time to first therapeutic concentration, percentage of time in therapeutic range (TTR), and estimated glomerular filtration rate (eGFR) were also evaluated. Fifty-five kidney transplant recipients were CYP3A5 poor metabolizers (PM), 17 were intermediate metabolizers (IM), and 6 were extensive metabolizers (EM). Compared to PMs, EMs/IMs had significantly more dose adjustments (6.1 vs. 8.1, p = .015). Overall, 33.82% of trough measurements resulted in a dose change. There was no difference in the number of tacrolimus trough measurements between PMs and EM/IMs. The total daily tacrolimus dose requirements were higher in EMs and IMs compared to PMs (<.001). TTR was ∼50% in the PMs and EMs/IMs groups. CYP3A5 EM/IM metabolizers have more tacrolimus dose changes and higher dose requirements which increases clinical management complexity. Larger studies are needed to assess the cost and benefits of including genotyping data to improve clinical management.
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Affiliation(s)
- Kevin A Reininger
- Department of Pharmacy, Hennepin County Medical Center, Minneapolis, Minnesota, USA
| | - Guillaume Onyeaghala
- Hennepin Healthcare Research Institute, Minneapolis, Minnesota, USA
- Division of Nephrology, Hennepin Healthcare, University of Minnesota, Minneapolis, Minnesota, USA
| | - Teresa Anderson-Haag
- Department of Pharmacy, Hennepin County Medical Center, Minneapolis, Minnesota, USA
| | - David S Schladt
- Hennepin Healthcare Research Institute, Minneapolis, Minnesota, USA
| | - Baolin Wu
- Department of Biostatistics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Weihua Guan
- Department of Biostatistics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Casey R Dorr
- Hennepin Healthcare Research Institute, Minneapolis, Minnesota, USA
- Division of Nephrology, Hennepin Healthcare, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rory P Remmel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Roslyn Mannon
- Division of Nephrology, University of Nebraska, Omaha, Nebraska, USA
| | - Arthur J Matas
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Paul Stahler
- Division of Surgery, Hennepin Healthcare, Minneapolis, Minnesota, USA
| | - Ajay K Israni
- Division of Nephrology, Hennepin Healthcare, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA
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Wen YF, Jacobson PA, Oetting WS, Pereira C, Brown JT. Knowledge and attitudes of incoming pharmacy students toward pharmacogenomics and survey reliability. Pharmacogenomics 2022; 23:873-885. [DOI: 10.2217/pgs-2022-0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Aims: To assess knowledge and attitudes toward pharmacogenomics (PGx) of incoming doctoral pharmacy students, to evaluate the internal structure and reliability of the PGx survey and to identify variables associated with the different responses. Methods: A PGx survey based on the core pharmacist competencies in PGx was created. Results: Of 83.2% analyzable responses, 91% believed PGx is a useful tool and relevant to future practice but over 70% stated they lack confidence in clinical PGx knowledge. This 38-item PGx survey included three factors showing high reliability. Prior genetic/PGx testing and unsatisfactory medication experiences were associated with a more positive attitude toward PGx. Conclusion: The majority of students have positive attitudes toward PGx, but lack knowledge in genetic concepts and clinical PGx.
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Affiliation(s)
- Ya-Feng Wen
- Department of Experimental & Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Pamala A Jacobson
- Department of Experimental & Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - William S Oetting
- Department of Experimental & Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chrystian Pereira
- Department of Pharmaceutical Care & Health Systems, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jacob T Brown
- Department of Pharmacy Practice & Pharmaceutical Sciences, College of Pharmacy, University of Minnesota, Duluth, MN 55812, USA
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Arthur VL, Li Z, Cao R, Oetting WS, Israni AK, Jacobson PA, Ritchie MD, Guan W, Chen J. A Multi-Marker Test for Analyzing Paired Genetic Data in Transplantation. Front Genet 2021; 12:745773. [PMID: 34721531 PMCID: PMC8548646 DOI: 10.3389/fgene.2021.745773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/23/2021] [Indexed: 12/02/2022] Open
Abstract
Emerging evidence suggests that donor/recipient matching in non-HLA (human leukocyte antigen) regions of the genome may impact transplant outcomes and recognizing these matching effects may increase the power of transplant genetics studies. Most available matching scores account for either single-nucleotide polymorphism (SNP) matching only or sum these SNP matching scores across multiple gene-coding regions, which makes it challenging to interpret the association findings. We propose a multi-marker Joint Score Test (JST) to jointly test for association between recipient genotype SNP effects and a gene-based matching score with transplant outcomes. This method utilizes Eigen decomposition as a dimension reduction technique to potentially increase statistical power by decreasing the degrees of freedom for the test. In addition, JST allows for the matching effect and the recipient genotype effect to follow different biological mechanisms, which is not the case for other multi-marker methods. Extensive simulation studies show that JST is competitive when compared with existing methods, such as the sequence kernel association test (SKAT), especially under scenarios where associated SNPs are in low linkage disequilibrium with non-associated SNPs or in gene regions containing a large number of SNPs. Applying the method to paired donor/recipient genetic data from kidney transplant studies yields various gene regions that are potentially associated with incidence of acute rejection after transplant.
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Affiliation(s)
- Victoria L. Arthur
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Zhengbang Li
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
- Departments of Statistics, Central China Normal University, Wuhan, China
| | - Rui Cao
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, United States
| | - Ajay K. Israni
- Minneapolis Medical Research Foundation, Minneapolis, MN, United States
- Department of Medicine, Hennepin County Medical Center, Minneapolis, MN, United States
- Department of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, United States
| | - Pamala A. Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, United States
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Jinbo Chen
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
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Al-Kofahi M, Oetting WS, Schladt DP, Remmel RP, Guan W, Wu B, Dorr CR, Mannon RB, Matas AJ, Israni AK, Jacobson PA. Precision Dosing for Tacrolimus Using Genotypes and Clinical Factors in Kidney Transplant Recipients of European Ancestry. J Clin Pharmacol 2021; 61:1035-1044. [PMID: 33512723 DOI: 10.1002/jcph.1823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022]
Abstract
Genetic variation in the CYP3A4 and CYP3A5 (CYP3A4/5) genes, which encode the key enzymes in tacrolimus metabolism, is associated with tacrolimus clearance and dose requirements. Tacrolimus has a narrow therapeutic index with high intra- and intersubject variability, in part because of genetic variation. High tacrolimus clearance and low trough concentration are associated with a greater risk for rejection, whereas high troughs are associated with calcineurin-induced toxicity. The objective of this study was to develop a model of tacrolimus clearance with a dosing equation accounting for genotypes and clinical factors in adult kidney transplant recipients of European ancestry that could preemptively guide dosing. Recipients receiving immediate-release tacrolimus for maintenance immunosuppression from 2 multicenter studies were included. Participants in the GEN03 study were used for tacrolimus model development (n = 608 recipients) and was validated by prediction performance in the DeKAF Genomics study (n = 1361 recipients). Nonlinear mixed-effects modeling was used to develop the apparent oral tacrolimus clearance (CL/F) model. CYP3A4/5 genotypes and clinical covariates were tested for their influence on CL/F. The predictive performance of the model was determined by assessing the bias (median prediction error [ME] and median percentage error [MPE]) and the precision (root median squared error [RMSE]) of the model. CYP3A5*3, CYP3A4*22, corticosteroids, calcium channel blocker and antiviral drug use, age, and diabetes significantly contributed to the interindividual variability of oral tacrolimus apparent clearance. The bias (ME, MPE) and precision (RMSE) of the final model was good, 0.49 ng/mL, 6.5%, and 3.09 ng/mL, respectively. Prospective testing of this equation is warranted.
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Affiliation(s)
- Mahmoud Al-Kofahi
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, USA
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, USA
| | - David P Schladt
- Hennepin Health Research Institute, Minneapolis, Minnesota, USA
| | - Rory P Remmel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Weihua Guan
- Department of Biostatistics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Baolin Wu
- Department of Biostatistics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Casey R Dorr
- Hennepin Health Research Institute, Minneapolis, Minnesota, USA
- Department of Medicine, Hennepin Healthcare, University of Minnesota, Minneapolis, Minnesota, USA
| | - Roslyn B Mannon
- Division of Nephrology, University of Nebraska, Omaha, Nebraska, USA
| | - Arthur J Matas
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ajay K Israni
- Hennepin Health Research Institute, Minneapolis, Minnesota, USA
- Department of Medicine, Hennepin Healthcare, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Epidemiology & Community Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, USA
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Loftus SK, Lundh L, Watkins-Chow DE, Baxter LL, Pairo-Castineira E, Nisc Comparative Sequencing Program, Jackson IJ, Oetting WS, Pavan WJ, Adams DR. A custom capture sequence approach for oculocutaneous albinism identifies structural variant alleles at the OCA2 locus. Hum Mutat 2021; 42:1239-1253. [PMID: 34246199 DOI: 10.1002/humu.24257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/02/2021] [Accepted: 06/24/2021] [Indexed: 11/09/2022]
Abstract
Oculocutaneous albinism (OCA) is a heritable disorder of pigment production that manifests as hypopigmentation and altered eye development. Exon sequencing of known OCA genes is unsuccessful in producing a complete molecular diagnosis for a significant number of affected individuals. We sequenced the DNA of individuals with OCA using short-read custom capture sequencing that targeted coding, intronic, and noncoding regulatory regions of known OCA genes, and genome-wide association study-associated pigmentation loci. We identified an OCA2 complex structural variant (CxSV), defined by a 143 kb inverted segment reintroduced in intron 1, upstream of the native location. The corresponding CxSV junctions were observed in 11/390 probands screened. The 143 kb CxSV presents in one family as a copy number variant duplication for the 143 kb region. In the remaining 10/11 families, the 143 kb CxSV acquired an additional 184 kb deletion across the same region, restoring exons 3-19 of OCA2 to a copy-number neutral state. Allele-associated haplotype analysis found rare SNVs rs374519281 and rs139696407 are linked with the 143 kb CxSV in both OCA2 alleles. For individuals in which customary molecular evaluation does not reveal a biallelic OCA diagnosis, we recommend preliminary screening for these haplotype-associated rare variants, followed by junction-specific validation for the OCA2 143 kb CxSV.
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Affiliation(s)
- Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Linnea Lundh
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | | | - Ian J Jackson
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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10
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Nguyen TT, Pearson RA, Mohamed ME, Schladt DP, Berglund D, Rivers Z, Skaar DJ, Wu B, Guan W, van Setten J, Keating BJ, Dorr C, Remmel RP, Matas AJ, Mannon RB, Israni AK, Oetting WS, Jacobson PA. Pharmacogenomics in kidney transplant recipients and potential for integration into practice. J Clin Pharm Ther 2020; 45:1457-1465. [PMID: 32662547 DOI: 10.1111/jcpt.13223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/14/2020] [Accepted: 06/11/2020] [Indexed: 11/29/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE Pharmacogenomic biomarkers are now used in many clinical care settings and represent one of the successes of precision medicine. Genetic variants are associated with pharmacokinetic and pharmacodynamic changes leading to medication adverse effects and changes in clinical response. Actionable pharmacogenomic variants are common in transplant recipients and have implications for medications used in transplant, but yet are not broadly incorporated into practice. METHODS From the Clinical Pharmacogenetics Implementation Consortium and Dutch Pharmacogenetics Working Group guidelines, and PharmGKB databases, 12 pharmacogenomic genes with 30 variants were selected and used to create diplotypes and actionable pharmacogenomic phenotypes. A total of 853 kidney allograft recipients who had genomic information available from a genome-wide association study were included. RESULTS Each recipient had at least one actionable pharmacogenomic diplotype/phenotype, whereas the majority (58%) had three or four actionable diplotypes/phenotypes and 17.4% had five or more among the 12 genes. The participants carried actionable diplotypes/phenotypes for multiple medications, including tacrolimus, azathioprine, clopidogrel, warfarin, simvastatin, voriconazole, antidepressants and proton-pump inhibitors. WHAT IS NEW AND CONCLUSION Pharmacogenomic variants are common in transplant recipients, and transplant recipients receive medications that have actionable variants. CLINICAL TRIAL Genomics of Transplantation, clinicaltrials.gov (NCT01714440).
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Affiliation(s)
- Tam T Nguyen
- College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | | | - Moataz E Mohamed
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA.,Department of Pharmacy Practice, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - David P Schladt
- Chronic Disease Research Group, Minneapolis Medical Research Foundation, Minneapolis, MN, USA
| | - Danielle Berglund
- Complex Care Core Analytics, Fairview University of Minnesota, Minneapolis, MN, USA
| | - Zachary Rivers
- Social and Administrative Pharmacy, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Debra J Skaar
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Baolin Wu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Brendan J Keating
- Penn Transplant Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Casey Dorr
- Minneapolis Medical Research Foundation and Division of Nephrology, Hennepin Healthcare, Minneapolis, MN, USA
| | - Rory P Remmel
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Arthur J Matas
- Department of Surgery, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Roslyn B Mannon
- Department of Nephrology, School of Medicine, University of Nebraska, Omaha, NE, USA
| | - Ajay K Israni
- Division of Nephrology, Hennepin Healthcare, Minneapolis, MN, USA.,Epidemiology & Community Health, University of Minnesota, Minneapolis, MN, USA
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
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11
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Mohamed ME, Schladt DP, Guan W, Wu B, van Setten J, Keating B, Iklé D, Remmel RP, Dorr CR, Mannon RB, Matas AJ, Israni AK, Oetting WS, Jacobson PA. Tacrolimus troughs and genetic determinants of metabolism in kidney transplant recipients: A comparison of four ancestry groups. Am J Transplant 2019; 19:2795-2804. [PMID: 30953600 PMCID: PMC6763344 DOI: 10.1111/ajt.15385] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/04/2019] [Accepted: 03/28/2019] [Indexed: 02/06/2023]
Abstract
Tacrolimus trough and dose requirements vary dramatically between individuals of European and African American ancestry. These differences are less well described in other populations. We conducted an observational, prospective, multicenter study from which 2595 kidney transplant recipients of European, African, Native American, and Asian ancestry were studied for tacrolimus trough, doses, and genetic determinants of metabolism. We studied the well-known variants and conducted a CYP3A4/5 gene-wide analysis to identify new variants. Daily doses, and dose-normalized troughs were significantly different between the four groups (P < .001). CYP3A5*3 (rs776746) was associated with higher dose-normalized tacrolimus troughs in all groups but occurred at different allele frequencies and had differing effect sizes. The CYP3A5*6 (rs10264272) and *7 (rs413003343) variants were only present in African Americans. CYP3A4*22 (rs35599367) was not found in any of the Asian ancestry samples. We identified seven suggestive variants in the CYP3A4/5 genes associated with dose-normalized troughs in Native Americans (P = 1.1 × 10-5 -8.8 × 10-6 ) and one suggestive variant in Asian Americans (P = 5.6 × 10-6 ). Tacrolimus daily doses and dose-normalized troughs vary significantly among different ancestry groups. We identified potential new variants important in Asians and Native Americans. Studies with larger populations should be conducted to assess the importance of the identified suggestive variants.
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Affiliation(s)
- Moataz E. Mohamed
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA,Department of Pharmacy Practice, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | | | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN
| | - Baolin Wu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Brendan Keating
- Department of Surgery, School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Rory P. Remmel
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Casey R. Dorr
- Hennepin Healthcare Research Institute, Minneapolis, MN, USA,Department of Medicine, University of Minnesota, Hennepin Healthcare, Minneapolis, MN
| | | | - Arthur J. Matas
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - Ajay K. Israni
- Hennepin Healthcare Research Institute, Minneapolis, MN, USA,Department of Medicine, University of Minnesota, Hennepin Healthcare, Minneapolis, MN,Department of Epidemiology & Community Health, University of Minnesota, Minneapolis, MN, USA
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - Pamala A. Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
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12
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Stapleton CP, Heinzel A, Guan W, van der Most PJ, van Setten J, Lord GM, Keating BJ, Israni AK, de Borst MH, Bakker SJ, Snieder H, Weale ME, Delaney F, Hernandez‐Fuentes MP, Reindl-Schwaighofer R, Oberbauer R, Jacobson PA, Mark PB, Chapman FA, Phelan PJ, Kennedy C, Sexton D, Murray S, Jardine A, Traynor JP, McKnight AJ, Maxwell AP, Smyth LJ, Oetting WS, Matas AJ, Mannon RB, Schladt DP, Iklé DN, Cavalleri GL, Conlon PJ. The impact of donor and recipient common clinical and genetic variation on estimated glomerular filtration rate in a European renal transplant population. Am J Transplant 2019; 19:2262-2273. [PMID: 30920136 PMCID: PMC6989089 DOI: 10.1111/ajt.15326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/22/2019] [Accepted: 02/11/2019] [Indexed: 01/25/2023]
Abstract
Genetic variation across the human leukocyte antigen loci is known to influence renal-transplant outcome. However, the impact of genetic variation beyond the human leukocyte antigen loci is less clear. We tested the association of common genetic variation and clinical characteristics, from both the donor and recipient, with posttransplant eGFR at different time-points, out to 5 years posttransplantation. We conducted GWAS meta-analyses across 10 844 donors and recipients from five European ancestry cohorts. We also analyzed the impact of polygenic risk scores (PRS), calculated using genetic variants associated with nontransplant eGFR, on posttransplant eGFR. PRS calculated using the recipient genotype alone, as well as combined donor and recipient genotypes were significantly associated with eGFR at 1-year posttransplant. Thirty-two percent of the variability in eGFR at 1-year posttransplant was explained by our model containing clinical covariates (including weights for death/graft-failure), principal components and combined donor-recipient PRS, with 0.3% contributed by the PRS. No individual genetic variant was significantly associated with eGFR posttransplant in the GWAS. This is the first study to examine PRS, composed of variants that impact kidney function in the general population, in a posttransplant context. Despite PRS being a significant predictor of eGFR posttransplant, the effect size of common genetic factors is limited compared to clinical variables.
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Affiliation(s)
- Caragh P. Stapleton
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Weihua Guan
- Department of Biostatistics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Peter J. van der Most
- Departments of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Graham M. Lord
- King’s College London, MRC Centre for Transplantation, London, UK
- NIHR Biomedical Research Centre at Guy’s and St Thomas’, NHS Foundation Trust and King’s College London, London, UK
| | - Brendan J. Keating
- Department of Surgery, Penn Transplant Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ajay K. Israni
- Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Martin H. de Borst
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Stephan J.L. Bakker
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Harold Snieder
- Departments of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michael E. Weale
- Division of Genetics & Molecular Medicine, King’s College London, London, UK
| | - Florence Delaney
- King’s College London, MRC Centre for Transplantation, London, UK
- NIHR Biomedical Research Centre at Guy’s and St Thomas’, NHS Foundation Trust and King’s College London, London, UK
| | | | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Pamala A. Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
| | - Patrick B. Mark
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | - Fiona A. Chapman
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | - Paul J. Phelan
- Department of Nephrology, Royal Infirmary of Edinburgh, NHS Lothian, UK
| | - Claire Kennedy
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Donal Sexton
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Susan Murray
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Alan Jardine
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | - Jamie P. Traynor
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, UK
| | | | | | - Laura J. Smyth
- Centre for Public Health, Queen’s University of Belfast, Belfast, UK
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
| | - Arthur J. Matas
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Roslyn B. Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | | | | | | | | | | | - Gianpiero L. Cavalleri
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Peter J. Conlon
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
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13
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Wu JF, Muthusamy A, Al-Ghalith GA, Knights D, Guo B, Wu B, Remmel RP, Schladt DP, Alegre ML, Oetting WS, Jacobson PA, Israni AK. Urinary microbiome associated with chronic allograft dysfunction in kidney transplant recipients. Clin Transplant 2018; 32:e13436. [PMID: 30372560 PMCID: PMC6984979 DOI: 10.1111/ctr.13436] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/14/2018] [Accepted: 10/21/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND We performed a study to identify differences in the urinary microbiome associated with chronic allograft dysfunction (CAD) and compared the urinary microbiome of male and female transplant recipients with CAD. METHODS This case-control study enrolled 67 patients within the Deterioration of Kidney Allograft Function (DeKAF) Genomics cohort at two transplant centers. CAD was defined as a greater than 25% rise in serum creatinine relative to a 3 month post-transplant baseline. Urine samples from patients with and without CAD were analyzed using 16S V4 bacterial ribosomal DNA sequences. RESULTS Corynebacterium was more prevalent in female and male patients with CAD compared to non-CAD female patients (P = 0.0005). A total 21 distinct Operational Taxonomic Unit (OTUs) were identified as significantly different when comparing CAD and non-CAD patients using Kruskal-Wallis (P < 0.01). A subset analysis of female patients with CAD compared to non-CAD females identified similar differentially abundant OTUs, including the genera Corynebacterium and Staphylococcus (Kruskal-Wallis; P = 0.01; P = 0.004, respectively). Male CAD vs female CAD analysis showed greater abundance of phylum Proteobacteria in males. CONCLUSION There were differences in the urinary microbiome when comparing female and male CAD patients with their female non-CAD counterparts and these differences persisted in the subset analysis limited to female patients only.
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Affiliation(s)
- Jennifer F. Wu
- Department of Medicine, Nephrology Division, Hennepin Healthcare, Minneapolis, MN
| | | | | | - Dan Knights
- Department of Computer Science and Biotechnology Institute, University of Minnesota, Minneapolis, MN
| | - Bin Guo
- Division of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Baolin Wu
- Division of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Rory P. Remmel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN
| | | | - Maria-Luisa Alegre
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN
| | - Pamala A. Jacobson
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN
| | - Ajay K. Israni
- Department of Medicine, Nephrology Division, Hennepin Healthcare, Minneapolis, MN
- Hennepin Healthcare Research Institute, Minneapolis, MN
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14
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Seibert SR, Schladt DP, Wu B, Guan W, Dorr C, Remmel RP, Matas AJ, Mannon RB, Israni AK, Oetting WS, Jacobson PA. Tacrolimus trough and dose intra-patient variability and CYP3A5 genotype: Effects on acute rejection and graft failure in European American and African American kidney transplant recipients. Clin Transplant 2018; 32:e13424. [PMID: 30318646 PMCID: PMC6317347 DOI: 10.1111/ctr.13424] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/18/2018] [Accepted: 10/08/2018] [Indexed: 02/01/2023]
Abstract
BACKGROUND Suboptimal immunosuppression after kidney transplantation contributes to toxicity and loss of efficacy. Little is known regarding the impact of intra-patient variability of tacrolimus (TAC) doses and troughs in the early post-transplant period or the influence of genetic variants on variability. METHODS Coefficients of variation (CV) of TAC troughs and doses of 1226 European American (EA) and 246 African American (AA) adult recipients enrolled in DeKAF Genomics were compared for association with acute rejection and graft failure. Additionally, the influence of recipients' number of CYP3A5 loss-of-function alleles was assessed. RESULTS Acute rejection was associated with greater CV of dose in AA (P < 0.001) and EA recipients (P = 0.012). Graft failure was associated with a greater CV of dose (P = 0.022) and trough (P < 0.001) in AA, and higher CV of trough (P = 0.024) in EA recipients. In EA, CYP3A5 loss-of-function alleles were associated with decreased CV of trough (P = 0.0042) and increased CV of dose (P < 0.0001). CONCLUSION CYP3A5 loss-of-function alleles influence intra-patient TAC trough and dose variability. High variability of TAC dose increases risk of acute rejection. High variability of TAC trough increases risk of graft failure. Early clinical recognition of TAC dose and trough variability may improve patient management and outcomes.
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Affiliation(s)
- Stephan R Seibert
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
| | - David P Schladt
- Chronic Disease Research Group, Minneapolis Medical Research Foundation, Hennepin County Medical Center, Minneapolis, Minnesota
| | - Baolin Wu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Casey Dorr
- Minneapolis Medical Research Foundation, Hennepin County Medical Center, Minneapolis, Minnesota
| | - Rory P Remmel
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
| | - Arthur J Matas
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Roslyn B Mannon
- Department of Nephrology, University of Alabama, Birmingham, Alabama
| | - Ajay K Israni
- Division of Nephrology, Hennepin County Medical Center, Epidemiology & Community Health, University of Minnesota, Minneapolis, Minnesota
| | - William S Oetting
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
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15
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Scheibner A, Remmel R, Schladt D, Oetting WS, Guan W, Wu B, Dorr C, Israni A, Jacobson PA. Tacrolimus Elimination in Four Patients With a CYP3A5*3/*3 CYP3A4*22/*22 Genotype Combination. Pharmacotherapy 2018; 38:e46-e52. [PMID: 29804290 PMCID: PMC6265082 DOI: 10.1002/phar.2131] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cytochrome P450 3A5 (CYP3A5) and cytochrome P450 3A4 (CYP3A4) are the predominate enzymes responsible for tacrolimus metabolism. The presence of CYP3A4 and CYP3A5 genetic variants significantly affects tacrolimus clearance and dose requirements. CYP3A5*3 is a loss-of-function variant resulting in no CYP3A5 enzyme production. CYP3A4*22 is a variant that reduces production of functional CYP3A4 protein. Caucasians commonly carry these variant alleles but are very rarely homozygous for both CYP3A5*3 and CYP3A4*22. This report describes four kidney transplant recipients who carry a rare genotype combination (CYP3A5*3/*3 and CYP3A4*22/*22). These patients were identified from a larger cohort of Caucasian kidney transplant recipients (n=1366). To understand the significance of this genotype combination on tacrolimus troughs and doses, we compared these patients to recipients without this combination. Patients homozygous for both variants are at risk for profound reductions in metabolism of CYP3A substrates. A 342% and a 90.6% increase in the median dose-normalized trough was observed, when the CYP3A5*3/*3 and CYP3A4*22/*22 genotype combination was compared to the CYP3A5*1/*1 and CYP3A4*1/*1 genotype combination and the CYP3A5*3/*3 and CYP3A4*1/*1 genotype combination, respectively. These four individuals only required on average 2.5 mg/day of tacrolimus. Knowledge of these genotypes would be useful in selecting appropriate tacrolimus doses to avoid overexposure.
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Affiliation(s)
- Aileen Scheibner
- University of Minnesota College of Pharmacy, Minneapolis, Minnesota
| | - Rory Remmel
- Department of Medicinal Chemistry, University of Minnesota College of Pharmacy, Minneapolis, Minnesota
| | - David Schladt
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota
| | - Weihua Guan
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota
| | - Baolin Wu
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota
| | - Casey Dorr
- Division of Nephrology, Department of Medicine, Hennepin Country Medical Center, Minneapolis, Minnesota
| | - Ajay Israni
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota.,Division of Nephrology, Department of Medicine, Hennepin Country Medical Center, Minneapolis, Minnesota.,Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, Minnesota
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, Minnesota
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16
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Snoek R, van Setten J, Keating BJ, Israni AK, Jacobson PA, Oetting WS, Matas AJ, Mannon RB, Zhang Z, Zhang W, Hao K, Murphy B, Reindl-Schwaighofer R, Heinzl A, Oberbauer R, Viklicky O, Conlon PJ, Stapleton CP, Bakker SJL, Snieder H, Peters EDJ, van der Zwaag B, Knoers NVAM, de Borst MH, van Eerde AM. NPHP1 (Nephrocystin-1) Gene Deletions Cause Adult-Onset ESRD. J Am Soc Nephrol 2018; 29:1772-1779. [PMID: 29654215 DOI: 10.1681/asn.2017111200] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/19/2018] [Indexed: 11/03/2022] Open
Abstract
Background Nephronophthisis (NPH) is the most prevalent genetic cause for ESRD in children. However, little is known about the prevalence of NPH in adult-onset ESRD. Homozygous full gene deletions of the NPHP1 gene encoding nephrocystin-1 are a prominent cause of NPH. We determined the prevalence of NPH in adults by assessing homozygous NPHP1 full gene deletions in adult-onset ESRD.Methods Adult renal transplant recipients from five cohorts of the International Genetics and Translational Research in Transplantation Network (iGeneTRAiN) underwent single-nucleotide polymorphism genotyping. After quality control, we determined autosomal copy number variants (such as deletions) on the basis of median log2 ratios and B-allele frequency patterns. The findings were independently validated in one cohort. Patients were included in the analysis if they had adult-onset ESRD, defined as start of RRT at ≥18 years old.Results We included 5606 patients with adult-onset ESRD; 26 (0.5%) showed homozygous NPHP1 deletions. No donor controls showed homozygosity for this deletion. Median age at ESRD onset was 30 (range, 18-61) years old for patients with NPH, with 54% of patients age ≥30 years old. Notably, only three (12%) patients were phenotypically classified as having NPH, whereas most patients were defined as having CKD with unknown etiology (n=11; 42%).Conclusions Considering that other mutation types in NPHP1 or mutations in other NPH-causing genes were not analyzed, NPH is a relatively frequent monogenic cause of adult-onset ESRD. Because 88% of patients had not been clinically diagnosed with NPH, wider application of genetic testing in adult-onset ESRD may be warranted.
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Affiliation(s)
- Rozemarijn Snoek
- Departments of Genetics and.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Brendan J Keating
- Department of Surgery, Penn Transplant Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ajay K Israni
- Department of Medicine, Hennepin County Medical Center
| | | | | | - Arthur J Matas
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Roslyn B Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences.,Icahn Institute for Genomics and Multiscale Biology, and
| | - Weijia Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ke Hao
- Department of Genetics and Genomic Sciences.,Icahn Institute for Genomics and Multiscale Biology, and
| | - Barbara Murphy
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andreas Heinzl
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Ondrej Viklicky
- Department of Nephrology, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Peter J Conlon
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons, Dublin, Ireland.,Department of Nephrology, Beaumont Hospital, Dublin, Ireland; and
| | - Caragh P Stapleton
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons, Dublin, Ireland
| | | | | | - Edith D J Peters
- Departments of Genetics and.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Nine V A M Knoers
- Departments of Genetics and.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Genetica, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Albertien M van Eerde
- Departments of Genetics and .,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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17
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Oetting WS, Wu B, Schladt DP, Guan W, Remmel RP, Dorr C, Mannon RB, Matas AJ, Israni AK, Jacobson PA. Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients. Pharmacogenomics 2018; 19:175-184. [PMID: 29318894 PMCID: PMC6021962 DOI: 10.2217/pgs-2017-0187] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023] Open
Abstract
AIM Multiple genetic variants have been associated with variation in tacrolimus (TAC) trough concentrations. Unfortunately, additional studies do not confirm these associations, leading one to question if a reported association is accurate and reliable. We attempted to validate 44 published variants associated with TAC trough concentrations. MATERIALS & METHODS Genotypes of the variants in our cohort of 1923 kidney allograft recipients were associated with TAC trough concentrations. RESULTS Only variants in CYP3A4 and CYP3A5 were significantly associated with variation in TAC trough concentrations in our validation. CONCLUSION There is no evidence that common variants outside the CYP3A4 and CYP3A5 loci are associated with variation in TAC trough concentrations. In the future rare variants may be important and identified using DNA sequencing.
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Affiliation(s)
- William S Oetting
- Department of Experimental & Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Baolin Wu
- Department of Biostatistics, University of Minnesota, Minneapolis, MN 55455, USA
| | - David P Schladt
- Minneapolis Medical Research Foundation, Minneapolis, MN 55404, USA
| | - Weihua Guan
- Department of Biostatistics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rory P Remmel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Casey Dorr
- Minneapolis Medical Research Foundation, Minneapolis, MN 55404, USA
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Roslyn B Mannon
- Division of Nephrology, University of Alabama, Birmingham, AL 35233, USA
| | - Arthur J Matas
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ajay K Israni
- Minneapolis Medical Research Foundation, Minneapolis, MN 55404, USA
- Department of Medicine, Hennepin County Medical Center, Minneapolis, MN 55415, USA
- Department of Epidemiology & Community Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Pamala A Jacobson
- Department of Experimental & Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
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18
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Oetting WS, Béroud C, Brenner SE, Greenblatt MS, Karchin R, Mooney SD. Methods and tools for assessing the impact of genetic variations: The 2017 Annual Scientific Meeting of the Human Genome Variation Society. Hum Mutat 2018; 39:454-458. [PMID: 29282786 DOI: 10.1002/humu.23393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 12/21/2017] [Indexed: 11/10/2022]
Affiliation(s)
- William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota
| | | | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California
| | | | - Rachel Karchin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Massachusetts.,Department of Oncology, Johns Hopkins University, Baltimore, Massachusetts.,Institute for Computational Medicine, Johns Hopkins University, Baltimore, Massachusetts
| | - Sean D Mooney
- Buck Institute for Research on Aging, Novato, California
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19
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Oetting WS, Wu B, Schladt DP, Guan W, Remmel RP, Mannon RB, Matas AJ, Israni AK, Jacobson PA. Genome-wide association study identifies the common variants in CYP3A4 and CYP3A5 responsible for variation in tacrolimus trough concentration in Caucasian kidney transplant recipients. Pharmacogenomics J 2017; 18:501-505. [PMID: 29160300 DOI: 10.1038/tpj.2017.49] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/23/2017] [Accepted: 09/18/2017] [Indexed: 12/16/2022]
Abstract
The immunosuppressant tacrolimus (TAC) is metabolized by both cytochrome P450 3A4 (CYP3A4) and CYP3A5 enzymes. It is common for European Americans (EA) to carry two CYP3A5 loss-of-function (LoF) variants that profoundly reduces TAC metabolism. Despite having two LoF alleles, there is still considerable variability in TAC troughs and identifying additional variants in genes outside of the CYP3A5 gene could provide insight into this variability. We analyzed TAC trough concentrations in 1345 adult EA recipients with two CYP3A5 LoF alleles in a genome-wide association study. Only CYP3A4*22 was identified and no additional variants were genome-wide significant. Additional high allele frequency genetic variants with strong genetic effects associated with TAC trough variability are unlikely to be associated with TAC variation in the EA population. These data suggest that low allele frequency variants, identified by DNA sequencing, should be evaluated and may identify additional variants that contribute to TAC pharmacokinetic variability.
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Affiliation(s)
- W S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - B Wu
- Department of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - D P Schladt
- Minneapolis Medical Research Foundation, Minneapolis, MN, USA
| | - W Guan
- Department of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - R P Remmel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - R B Mannon
- Division of Nephrology, University of Alabama, Birmingham, AL, USA
| | - A J Matas
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - A K Israni
- Minneapolis Medical Research Foundation, Minneapolis, MN, USA.,Department of Medicine, Hennepin County Medical Center, Minneapolis, MN, USA.,Department of Epidemiology & Community Health, University of Minnesota, Minneapolis, MN, USA
| | - P A Jacobson
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
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20
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Dorr CR, Oetting WS, Jacobson PA, Israni AK. Genetics of acute rejection after kidney transplantation. Transpl Int 2017; 31:263-277. [PMID: 29030886 DOI: 10.1111/tri.13084] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/07/2017] [Accepted: 10/09/2017] [Indexed: 01/02/2023]
Abstract
Treatment of acute rejection (AR) following kidney transplantation has improved in recent years, but there are still limitations to successful outcomes. This review article covers literature in regard to recipient and donor genetics of AR kidney and secondarily of liver allografts. Many candidate gene and some genome-wide association studies (GWASs) have been conducted for AR in kidney transplantation. Genetic associations with AR in kidney and liver are mostly weak, and in most cases, the associations have not been reproducible. A limitation in the study of AR is the lack of sufficiently large populations that account for population stratification to study the AR phenotype which in this era occurs in <10% of transplants. Furthermore, the AR phenotype has been difficult to define and the definitions of classifications have evolved over time. Literature related to the pharmacogenomics of tacrolimus is robust and has been validated in many studies. Associations between gene expression and AR are emerging as markers of outcomes and AR classification. In the future, combinations of pretransplant genotype for AR risk prediction, genotype-based immune suppressant dosing, and pharmacogenomic markers to select AR maintenance or treatment and expression markers from biopsies may provide valuable clinical tools for guiding treatment.
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Affiliation(s)
- Casey R Dorr
- Department of Nephrology, Minneapolis Medical Research Foundation, Minneapolis, MN, USA.,Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Ajay K Israni
- Department of Nephrology, Minneapolis Medical Research Foundation, Minneapolis, MN, USA.,Department of Medicine, University of Minnesota, Minneapolis, MN, USA.,Department of Medicine, Hennepin County Medical Center, Minneapolis, MN, USA
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21
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Lanting P, Oetting WS. Implementing pharmacogenomics in modern health care: The 2017 scientific meeting of the Human Genome Variation Society. Hum Mutat 2017; 38:1606-1610. [DOI: 10.1002/humu.23300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/23/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Pauline Lanting
- Department of Genetics University of Groningen University Medical Center Groningen Groningen The Netherlands
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology University of Minnesota Minneapolis Minnesota
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22
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Dorr CR, Remmel RP, Muthusamy A, Fisher J, Moriarity BS, Yasuda K, Wu B, Guan W, Schuetz EG, Oetting WS, Jacobson PA, Israni AK. CRISPR/Cas9 Genetic Modification of CYP3A5 *3 in HuH-7 Human Hepatocyte Cell Line Leads to Cell Lines with Increased Midazolam and Tacrolimus Metabolism. Drug Metab Dispos 2017; 45:957-965. [PMID: 28533324 DOI: 10.1124/dmd.117.076307] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 05/18/2017] [Indexed: 02/06/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 engineering of the CYP3A5 *3 locus (rs776746) in human liver cell line HuH-7 (CYP3A5 *3/*3) has led to three CYP3A5 *1 cell lines by deletion of the exon 3B splice junction or point mutation. Cell lines CYP3A5 *1/*3 sd (single deletion), CYP3A5 *1/*1 dd (double deletion), or CYP3A5 *1/*3 pm (point mutation) expressed the CYP3A5 *1 mRNA and had elevated CYP3A5 mRNA (P < 0.0005 for all engineered cell lines) and protein expression compared with HuH-7. In metabolism assays, HuH-7 had less tacrolimus (all P < 0.05) or midazolam (MDZ) (all P < 0.005) disappearance than all engineered cell lines. HuH-7 had less 1-OH MDZ (all P < 0.0005) or 4-OH (all P < 0.005) production in metabolism assays than all bioengineered cell lines. We confirmed CYP3A5 metabolic activity with the CYP3A4 selective inhibitor CYP3CIDE. This is the first report of genomic CYP3A5 bioengineering in human cell lines with drug metabolism analysis.
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Affiliation(s)
- Casey R Dorr
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Rory P Remmel
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Amutha Muthusamy
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - James Fisher
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Branden S Moriarity
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Kazuto Yasuda
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Baolin Wu
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Weihua Guan
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Erin G Schuetz
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - William S Oetting
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Pamala A Jacobson
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Ajay K Israni
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
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23
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Oetting WS, Jacobson PA, Israni AK. Validation Is Critical for Genome-Wide Association Study-Based Associations. Am J Transplant 2017; 17:318-319. [PMID: 27640398 PMCID: PMC5266629 DOI: 10.1111/ajt.14051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 01/25/2023]
Affiliation(s)
- William S. Oetting
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN,Corresponding author: William S. Oetting,
| | - Pamala A. Jacobson
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN
| | - Ajay K. Israni
- Minneapolis Medical Research Foundation, Minneapolis, MN,University of Minnesota, Department of Medicine, Hennepin County Medical Center, Minneapolis, MN,University of Minnesota, Department of Epidemiology & Community Health, Minneapolis MN
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24
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Oetting WS, Béroud C, Brenner SE, Greenblatt M, Karchin R, Mooney SD, Sunyaev S. Non-Coding Variation: The 2016 Annual Scientific Meeting of the Human Genome Variation Society. Hum Mutat 2017; 38:460-463. [PMID: 28054414 DOI: 10.1002/humu.23169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/02/2017] [Indexed: 11/10/2022]
Affiliation(s)
- William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota
| | | | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, California
| | - Marc Greenblatt
- Department of Medicine, University of Vermont, Burlington, Vermont
| | - Rachel Karchin
- Departments of Biomedical Engineering and Oncology, Institute for Computational Medicine, Johns Hopkins University, Baltimore, Massachusetts
| | - Sean D Mooney
- Department of Biomedical Informatics, University of Washington, Seattle, Washington
| | - Shamir Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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25
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Oetting WS, Brookes AJ, Béroud C, Taschner PE. Clinical Interpretation of Variants from Next-Generation Sequencing: The 2016 Scientific Meeting of the Human Genome Variation Society. Hum Mutat 2016; 37:1110-3. [PMID: 27492570 DOI: 10.1002/humu.23059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/23/2016] [Indexed: 11/08/2022]
Abstract
The 2016 scientific meeting of the Human Genome Variation Society (HGVS; http://www.hgvs.org) was held on the 20th of May in Barcelona, Spain, with the theme of "Clinical Interpretation of Variants from Next-Generation Sequencing."
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Affiliation(s)
- William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota.
| | - Anthony J Brookes
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | | | - Peter E Taschner
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Generade Centre of Expertise Genomics and University of Applied Sciences, Leiden, The Netherlands
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26
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Oetting WS, Brenner SE, Brookes AJ, Greenblatt MS, Hart RK, Karchin R, Sunyaev SR, Taschner PE. Pathogenicity Interpretation in the Age of Precision Medicine: The 2015 Annual Scientific Meeting of the Human Genome Variation Society. Hum Mutat 2016; 37:406-11. [PMID: 26791113 DOI: 10.1002/humu.22958] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 01/10/2016] [Indexed: 11/05/2022]
Affiliation(s)
- William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California
| | | | | | | | - Rachel Karchin
- Departments of Biomedical Engineering/Oncology and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Peter E Taschner
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Generade Centre of Expertise Genomics and University of Applied Sciences, Leiden, The Netherlands
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27
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Kalman LV, Agúndez JA, Appell ML, Black JL, Bell GC, Boukouvala S, Bruckner C, Bruford E, Bruckner C, Caudle K, Coulthard S, Daly AK, Del Tredici AL, den Dunnen JT, Drozda K, Everts R, Flockhart D, Freimuth R, Gaedigk A, Hachad H, Hartshorne T, Ingelman-Sundberg M, Klein TE, Lauschke VM, Maglott DR, McLeod HL, McMillin GA, Meyer UA, Müller DJ, Nickerson DA, Oetting WS, Pacanowski M, Pratt VM, Relling MV, Roberts A, Rubinstein WS, Sangkuhl K, Schwab M, Scott SA, Sim SC, Thirumaran RK, Toji LH, Tyndale R, van Schaik RHN, Whirl-Carrillo M, Yeo KTJ, Zanger UM. Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting. Clin Pharmacol Ther 2016; 99:172-85. [PMID: 26479518 PMCID: PMC4724253 DOI: 10.1002/cpt.280] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 12/21/2022]
Abstract
This article provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward.
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Affiliation(s)
- Lisa V. Kalman
- Centers for Disease, Control and Prevention, 1600 Clifton Rd, MSG23, Atlanta GA 30333, 404 498-2707, 404 498-2231
| | - José A.G. Agúndez
- Dept. Pharmacology, University of Extremadura, Avda de la, Universidad s/n., 10071 Cáceres, SPAIN, +34924289458, +34927257000
| | - Malin Lindqvist Appell
- Department of Medical and Health sciences, Faculty of Medicine and Health Sciences, Linköping University, Division of Drug Research, Linköping University, SE-581 83, LINKÖPING, +4613286880
| | | | - Gillian C. Bell
- Moffitt Cancer Center, 12902 Magnolia Dr Tampa, FL 33612, 813-745-6525, 813-745-3882
| | - Sotiria Boukouvala
- Democritus University of Thrace, Department of Molecular Biology and Genetics, Building 10, University Campus, Alexandroupolis 68100, Greece, +30-25510-30613, +30-25510-30632
| | - Carsten Bruckner
- Affymetrix, 3420 Central Expy, Santa Clara, CA 95051, USA, 1-408-731-5879
| | - Elspeth Bruford
- HUGO Gene, Nomenclature, Committee (HGNC), EMBL-EBI, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK, +44-1223-494468, +44-1223-492624
| | - Carsten Bruckner
- Affymetrix, 3420 Central Expy, Santa Clara, CA 95051, USA, 1-408-731-5879
| | - Kelly Caudle
- St. Jude Children’s Research Hospital, 262 Danny Thomas Place, MS 313 Memphis, TN 38105, 901-595-3125, 901-595-3994
| | - Sally Coulthard
- Newcastle University, Institute for Cellular Medicine, William Leech Building, Newcastle Medical School, Framlington Place, Newcastle University NE2 4HH UK, +44 1912080723, +44 1912085232
| | - Ann K. Daly
- Newcastle University, Institute of Cellular Medicine, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK, None, 44-191-208-7031
| | - Andria L. Del Tredici
- Millennium Health, LLC, 16981 Via Tazon, San Diego, CA 92127, none, (858) 451-3535 x1682
| | - Johan T den Dunnen
- Leiden University Medical Center, Human Genetics and Clinical Genetics, PO Box 9600, 2300RC Leiden, Nederland, none, +31-71-5269501
| | - Katarzyna Drozda
- Food and Drug Administration, 10903 New Hampshire Ave. Silver Spring, MD 20993, 240 402-0422
| | - Robin Everts
- Agena Bioscience, 3565 General Atomics Court, San Diego, CA 92121, None, +1 858-882-2655
| | - David Flockhart
- Indiana University, 950 W. Walnut St., room 402, Indianaplis, IN 46202, 317-274-2810
| | - Robert Freimuth
- Mayo Clinic, 200 First Street SW Rochester, MN 55905, 507-284-0753
| | - Andrea Gaedigk
- Division of Clinical Pharmacology & Therapeutic Innovation, Children’s Mercy Kansas City and School of Medicine, University of Missouri-Kansas City, 2401 Gillham Road, Kansas City, MO 64108, 816-234-1958, 816-234-3941
| | - Houda Hachad
- Translational Software, 12410 SE 32 Street Suite 150, Bellevue, WA 98005, 206-777-4132
| | - Toinette Hartshorne
- Genetic Analysis, Thermo Fisher Scientific, 180 Oyster Point Blvd. South San Francisco, CA 94080, 650-244-1669, 650-246-4080
| | - Magnus Ingelman-Sundberg
- Karolinska Institutet, Department of Physiology and Pharmacology, Nanna Svartz väg 2, 17177 Stockholm, SwedenSE, +468337327, +46852487735+
| | - Teri E. Klein
- Department of Genetics, Stanford University, 443 Via Ortega Avenue, Stanford, CA 94305, 650-725-3863, 650-736-0156
| | - Volker M. Lauschke
- Karolinska Institutet, Department of Physiology and Pharmacology, Nanna Svartz väg 2, 17177 Stockholm, Sweden, +46 8-337327, +46 8-5248-7711
| | - Donna R. Maglott
- National Institutes of Health / National Library of Medicine / National Center for Biotechnology Information, 45 Center Drive, Bethesda, MD 20894, 301 435-4895
| | - Howard L. McLeod
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa FL 33612, 813-745-3347
| | - Gwendolyn A. McMillin
- University of Utah and ARUP Laboratories, 500 Chipeta Way, Salt Lake City UT 84108, 801-584-5207, 801-583-2787
| | - Urs A. Meyer
- University of Basel, Biozentrum, Klingelbergstrasse 50/70, CH 4056, Basel, Switzerland, +41612672208, +41 61 267 2220
| | - Daniel J. Müller
- Dept. of Psychiatry, University of Toronto, CAMH, 250 College ST., R132, 416 979 4666, 416 535 8501 (x. 36851)
| | - Deborah A. Nickerson
- University of Washington, Department of Genome Sciences, Box 355065, Seattle, WA, 98195-5065, 206-221-6498, 206-685-7387
| | - William S. Oetting
- Experimental and Clinical Pharmacology, University of Minnesota, 7-115 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, 612-624-6645, 612-624-1139
| | - Michael Pacanowski
- U.S. Food and Drug Administration, 10903 New Hampshire Ave., WO Building 51, Rm 2132, HFD870, Silver Spring, MD 20993, 301-847-8720, 301-796-3919
| | - Victoria M. Pratt
- Indiana University School of Medicine, 975 W. Walnut St., IB-130, Indianapolis IN 46202, 317-274-2293, 317-274-8322
| | - Mary V. Relling
- Chair, Pharmaceutical Dept., St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Room I-5112 Memphis, TN 38105, ph 901 595 2348, fax 901 595 8869
| | - Ali Roberts
- Aegis Science Corporation, 515 Great Circle Road, Nashville, TN 37228, 615-255-3030, 615-477-9429
| | - Wendy S. Rubinstein
- National Institutes of Health / National Library of Medicine / National Center for Biotechnology Information, 45 Center Drive, Bethesda, MD 20894, 301.480.4023, 301.435.5991
| | - Katrin Sangkuhl
- Stanford University, 443 Via Ortega, Room 213, MC4245, Stanford CA 94305, 650-725-3863, 650-725-0659
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch- Institute of Clinical Pharmacology, Stuttgart and Department of Clinical Pharmacology, University Hospital, Tuebingen, Germany, Auerbachstrasse 112, 70378 Stuttgart, +49 711 859295, +49 711 8101 3700
| | - Stuart A. Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1487, 212-241-0139, 212-241-3780
| | - Sarah C Sim
- Karolinska Institutet, Department of Physiology and Pharmacology, Nanna Svartz Väg 2, 171 77 Stockholm, Sweden, +468337327, +46852487735
| | - Ranjit K Thirumaran
- Genelex Corporation, 3101 Western Ave., Suite 100, Seattle, WA 98121., 206 219-4000, 206 826-1926
| | - Lorraine H. Toji
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden, NJ 08103, 856 757-9719
| | - Rachel Tyndale
- CAMH and Departments of Psychiatry, Pharmacology and Toxicology, University of Toronto, Rm 4326, Department of Pharmacology, 1 King’s College Circle, Toronto, Canada, M5S 1A8., 416 978-6395, 416 978-6374
| | - Ron HN van Schaik
- 1Dept Clinical Chemistry, Erasmus MC Rotterdam; 2IFCC Task Force Pharmacogenetics, Room Na-415; Wytemaweg 80, 3015CN Rotterdam, The Netherlands, +31-10-7033119
| | - Michelle Whirl-Carrillo
- Department of Genetics, Stanford University, 443 Via Ortega, Rm 213 Stanford, CA 94305, 650-725-3863, 650-725-0659
| | - Kiang-Teck J Yeo
- Department of Pathology, The University of Chicago, 5841 S Maryland Ave, MC 0004, TW010, Chicago, IL 60637, 773-702-6268, 773-702-1318
| | - Ulrich M. Zanger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstrasse 112, Stuttgart, 70376, Germany, +49-711-859295, +49-711-81013704
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28
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Sanghavi K, Brundage RC, Miller MB, Schladt DP, Israni AK, Guan W, Oetting WS, Mannon RB, Remmel RP, Matas AJ, Jacobson PA. Genotype-guided tacrolimus dosing in African-American kidney transplant recipients. Pharmacogenomics J 2015; 17:61-68. [PMID: 26667830 PMCID: PMC4909584 DOI: 10.1038/tpj.2015.87] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 10/07/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022]
Abstract
Tacrolimus is dependent on CYP3A5 enzyme for metabolism. Expression of the CYP3A5 enzyme is controlled by several alleles including CYP3A5*1, CYP3A5*3, CYP3A5*6 and CYP3A5*7. African Americans (AAs) have on average higher tacrolimus dose requirements than Caucasians; however, some have requirements similar to Caucasians. Studies in AAs have primarily evaluated the CYP3A5*3 variant; however, there are other common nonfunctional variants in AAs (CYP3A5*6 and CYP3A5*7) that do not occur in Caucasians. These variants are associated with lower dose requirements and may explain why some AAs are metabolically similar to Caucasians. We created a tacrolimus clearance model in 354 AAs using a development and validation cohort. Time after transplant, steroid and antiviral use, age and CYP3A5*1, *3, *6 and *7 alleles were significant toward clearance. This study is the first to develop an AA-specific genotype-guided tacrolimus dosing model to personalize therapy.
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Affiliation(s)
- K Sanghavi
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - R C Brundage
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - M B Miller
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - D P Schladt
- Department of Nephrology and Chronic Disease Research Group, Minneapolis Medical Research Foundation, Hennepin County Medical Center, Minneapolis, MN, USA
| | - A K Israni
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - W Guan
- Department of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - W S Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - R B Mannon
- Department of Nephrology, University of Alabama, Birmingham, AL, USA
| | - R P Remmel
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - A J Matas
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - P A Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
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29
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Pulk RA, Schladt DS, Oetting WS, Guan W, Israni AK, Matas AJ, Remmel RP, Jacobson PA. Multigene predictors of tacrolimus exposure in kidney transplant recipients. Pharmacogenomics 2015; 16:841-54. [PMID: 26067485 DOI: 10.2217/pgs.15.42] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
AIM Determine the effect of the genetic variants beyond CYP3A5*3 on tacrolimus disposition. PATIENTS & METHODS We studied genetic correlates of tacrolimus trough concentrations with POR*28, CYP3A4*22 and ABCC2 haplotypes in a large, ethnically diverse kidney transplant cohort (n = 2008). RESULTS Subjects carrying one or more CYP3A5*1 alleles had lower tacrolimus trough concentrations (p = 9.2 × 10(-75)). The presence of one or two POR*28 alleles was associated with a 4.63% reduction in tacrolimus trough concentrations after adjusting for CYP3A5*1 and clinical factors (p = 0.037). In subset analyses, POR*28 was significant only in CYP3A5*3/*3 carriers (p = 0.03). The CYP3A4*22 variant and the ABBC2 haplotypes were not associated. CONCLUSION This study confirmed that CYP3A5*1 was associated with lower tacrolimus trough concentrations. POR*28 was associated with decreased tacrolimus trough concentrations although the effect was small possibly through enhanced CYP3A4 enzyme activity. CYP3A4*22 and ABCC2 haplotypes did not influence tacrolimus trough concentrations. Original submitted 19 December 2014; Revision submitted 2 April 2015.
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Affiliation(s)
- Rebecca A Pulk
- Department of Experimental & Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - David S Schladt
- Department of Nephrology & Chronic Disease Research Group, Minneapolis Medical Research Foundation, Hennepin County Medical Center, MN, USA
| | - William S Oetting
- Department of Experimental & Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, MN, USA
| | - Ajay K Israni
- Department of Nephrology & Chronic Disease Research Group, Minneapolis Medical Research Foundation, Hennepin County Medical Center, MN, USA
| | - Arthur J Matas
- Division of Transplantation, Department of Surgery, University of Minnesota, MN, USA
| | - Rory P Remmel
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, MN, USA
| | - Pamala A Jacobson
- Department of Experimental & Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
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Dorr C, Wu B, Guan W, Muthusamy A, Sanghavi K, Schladt DP, Maltzman JS, Scherer SE, Brott MJ, Matas AJ, Jacobson PA, Oetting WS, Israni AK. Differentially expressed gene transcripts using RNA sequencing from the blood of immunosuppressed kidney allograft recipients. PLoS One 2015; 10:e0125045. [PMID: 25946140 PMCID: PMC4422721 DOI: 10.1371/journal.pone.0125045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/09/2015] [Indexed: 02/05/2023] Open
Abstract
We performed RNA sequencing (RNAseq) on peripheral blood mononuclear cells (PBMCs) to identify differentially expressed gene transcripts (DEGs) after kidney transplantation and after the start of immunosuppressive drugs. RNAseq is superior to microarray to determine DEGs because it’s not limited to available probes, has increased sensitivity, and detects alternative and previously unknown transcripts. DEGs were determined in 32 adult kidney recipients, without clinical acute rejection (AR), treated with antibody induction, calcineurin inhibitor, mycophenolate, with and without steroids. Blood was obtained pre-transplant (baseline), week 1, months 3 and 6 post-transplant. PBMCs were isolated, RNA extracted and gene expression measured using RNAseq. Principal components (PCs) were computed using a surrogate variable approach. DEGs post-transplant were identified by controlling false discovery rate (FDR) at < 0.01 with at least a 2 fold change in expression from pre-transplant. The top 5 DEGs with higher levels of transcripts in blood at week 1 were TOMM40L, TMEM205, OLFM4, MMP8, and OSBPL9 compared to baseline. The top 5 DEGs with lower levels at week 1 post-transplant were IL7R, KLRC3, CD3E, CD3D, and KLRC2 (Striking Image) compared to baseline. The top pathways from genes with lower levels at 1 week post-transplant compared to baseline, were T cell receptor signaling and iCOS-iCOSL signaling while the top pathways from genes with higher levels than baseline were axonal guidance signaling and LXR/RXR activation. Gene expression signatures at month 3 were similar to week 1. DEGs at 6 months post-transplant create a different gene signature than week 1 or month 3 post-transplant. RNAseq analysis identified more DEGs with lower than higher levels in blood compared to baseline at week 1 and month 3. The number of DEGs decreased with time post-transplant. Further investigations to determine the specific lymphocyte(s) responsible for differential gene expression may be important in selecting and personalizing immune suppressant drugs and may lead to targeted therapies.
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Affiliation(s)
- Casey Dorr
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America
- Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Baolin Wu
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Weihua Guan
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Amutha Muthusamy
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America
| | - Kinjal Sanghavi
- College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - David P. Schladt
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America
| | - Jonathan S. Maltzman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Steven E. Scherer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Dallas, Texas, United States of America
| | - Marcia J. Brott
- College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Arthur J. Matas
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Pamala A. Jacobson
- College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - William S. Oetting
- College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ajay K. Israni
- Minneapolis Medical Research Foundation, Minneapolis, Minnesota, United States of America
- Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Epidemiology and Community Health, University of Minnesota School of Medicine, Minneapolis, Minnesota, United States of America
- * E-mail:
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Oetting WS. The Ultimate Guide to DMD Variants. Hum Mutat 2015. [DOI: 10.1002/humu.22780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Oetting WS, Greenblatt MS, Brookes AJ, Karchin R, Mooney SD. Germline & Somatic Mosaicism: The 2014 Annual Scientific Meeting of the Human Genome Variation Society. Hum Mutat 2015; 36:390-3. [DOI: 10.1002/humu.22757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 01/10/2015] [Indexed: 11/09/2022]
Affiliation(s)
- William S. Oetting
- Department of Experimental and Clinical Pharmacology; University of Minnesota; Minneapolis Minnesota
| | | | | | - Rachel Karchin
- Departments of Biomedical Engineering/Oncology and Institute for Computational Medicine; Johns Hopkins University; Baltimore Maryland
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Stanley CM, Sunyaev SR, Greenblatt MS, Oetting WS. Clinically relevant variants - identifying, collecting, interpreting, and disseminating: the 2013 annual scientific meeting of the Human Genome Variation Society. Hum Mutat 2015; 35:505-10. [PMID: 24470180 DOI: 10.1002/humu.22516] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 01/22/2014] [Indexed: 11/09/2022]
Abstract
The dramatic advances in genetic sequencing technologies used in research laboratories are now entering the clinic, and applications of whole-genome and whole-exome sequencing to disease diagnosis, predisposition, and treatment will soon be commonplace. However, the standards and methods for identifying clinically relevant variants are currently being debated and defined. Multiple agencies worldwide have recognized that we have reached an exciting and critical transition point into the clinic, and many important issues are being discussed that impact how genetic variation data in the clinic will be interpreted and used. The 2013 annual scientific meeting of the Human Genome Variation Society (HGVS) had as its main theme the discovery, interpretation, and dissemination of clinically relevant DNA variants. The meeting featured the continuously developing technology of databasing genetic variation and computational tools for allelic variant discovery. Attention was given to curating and integrating these data with clinical findings, including approaches to distinguish between functional alleles underlying clinical phenotypes and benign sequence variants and making data sources interoperable and functional for clinical diagnostic utility, citing examples in specific diseases.
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Wu J, Lin R, Huang J, Guan W, Oetting WS, Sriramarao P, Blumenthal MN. Functional Fcgamma receptor polymorphisms are associated with human allergy. PLoS One 2014; 9:e89196. [PMID: 24586589 PMCID: PMC3931680 DOI: 10.1371/journal.pone.0089196] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 01/16/2014] [Indexed: 01/13/2023] Open
Abstract
Objective IgG Fc receptors (FcγRs) play important roles in immune responses. It is not clear whether FcγR receptors play a role in human asthma and allergy. The aim of current study was to investigate whether functional single nucleotide polymorphisms (SNPs) of FcγR genes (FCGR) are associated with human asthma and allergy. Methods Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-187Ile>Thr, rs1050501), FCGR2C (FcγRIIC-13Gln>Stop, rs10917661), FCGR3A (FcγRIIIA-158Val>Phe, rs396991), and FCGR3B variants (FcγRIIIB NA1 and NA2) were genotyped in an asthma family cohort including 370 atopy positive, 239 atopy negative, and 169 asthma positive subjects. The genotype and phenotype data (asthma, bronchial hyper-responsiveness, and atopy) of subjects were analyzed using family-based association tests (FBAT) and logistic regression adjusted for age and sex. Result The FcγRIIA-131His>Arg SNP is significantly associated with atopy in a family-based association test (P = 0.00287) and in a logistic regression analysis (P = 0.0269, OR 0.732, 95% CI: 0.555–0.965). The FcγRIIA-131His (or rs1801274-A) allele capable of binding human IgG2 has a protective role against atopy. In addition, the rare FcγRIIB-187Thr (or rs1050501-C) allele defective for the receptor-mediated inhibitory signals is a risk factor for atopy (P = 0.0031, OR 1.758, 95% CI: 1.209–2.556) and IgE production (P<0.001). However, variants of activating FcγRIIIA (rs396991), and FcγRIIIB (NA1 and NA2), and FcγRIIC (rs10917661) are not associated with asthma, BHR, and atopy (P>0.05). Conclusions FcγRIIA and FcγRIIB functional polymorphisms may have a role in the pathogenesis of allergy.
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Affiliation(s)
- Jianming Wu
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
| | - Rui Lin
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Jinhai Huang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Weihua Guan
- Department of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - P. Sriramarao
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Malcolm N. Blumenthal
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
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35
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Irons DE, Iacono WG, Oetting WS, Kirkpatrick RM, Vrieze SI, Miller MB, McGue M. Gamma-aminobutyric acid system genes--no evidence for a role in alcohol use and abuse in a community-based sample. Alcohol Clin Exp Res 2014; 38:938-47. [PMID: 24460875 DOI: 10.1111/acer.12352] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 11/13/2013] [Indexed: 12/17/2022]
Abstract
BACKGROUND While twin and adoption studies point to substantial genetic influence upon alcohol use, dependence, and other alcohol-related phenotypes, few of the genes underlying variation in these phenotypes have been identified. Markers in genes related to GABAergic activity-a system integral to many of alcohol's biological effects-have been implicated in alcohol use and alcohol-related psychopathology in linkage and association studies. METHODS Using multiple methods, we conducted a comprehensive examination of the effects of markers in γ-aminobutyric acid (GABA) system genes in a community-based sample of 7,224 individuals assessed in early and middle adulthood. In addition to testing the effect of individual single nucleotide polymorphism (SNP) markers on alcohol-related phenotypes, we computed a polygenic score reflecting the aggregated effects of multiple GABA system SNPs. We also estimated the variance in alcohol-related phenotypes attributable to all GABA system markers considered simultaneously and conducted gene-based association tests. RESULTS No method produced results indicative of an effect of GABA system variants on measures of alcohol use or misuse. CONCLUSIONS These results reflect alcohol-related behaviors in a population-representative sample, many of whom are still in adolescence, and in which the incidence of heavy drinking and alcohol-related symptomatology are relatively low. Contrasted with existing studies of the association between alcohol use and GABA system genes, our results suggest that the relationship may be limited to particular contexts, such as when accompanied by polysubstance abuse or a familial history of alcoholism.
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Affiliation(s)
- Daniel E Irons
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota
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36
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Oetting WS, Robinson PN, Greenblatt MS, Cotton RG, Beck T, Carey JC, Doelken SC, Girdea M, Groza T, Hamilton CM, Hamosh A, Kerner B, MacArthur JAL, Maglott DR, Mons B, Rehm HL, Schofield PN, Searle BA, Smedley D, Smith CL, Bernstein IT, Zankl A, Zhao EY. Getting ready for the Human Phenome Project: the 2012 forum of the Human Variome Project. Hum Mutat 2013; 34:661-6. [PMID: 23401191 DOI: 10.1002/humu.22293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 02/05/2013] [Indexed: 11/05/2022]
Abstract
A forum of the Human Variome Project (HVP) was held as a satellite to the 2012 Annual Meeting of the American Society of Human Genetics in San Francisco, California. The theme of this meeting was "Getting Ready for the Human Phenome Project." Understanding the genetic contribution to both rare single-gene "Mendelian" disorders and more complex common diseases will require integration of research efforts among many fields and better defined phenotypes. The HVP is dedicated to bringing together researchers and research populations throughout the world to provide the resources to investigate the impact of genetic variation on disease. To this end, there needs to be a greater sharing of phenotype and genotype data. For this to occur, many databases that currently exist will need to become interoperable to allow for the combining of cohorts with similar phenotypes to increase statistical power for studies attempting to identify novel disease genes or causative genetic variants. Improved systems and tools that enhance the collection of phenotype data from clinicians are urgently needed. This meeting begins the HVP's effort toward this important goal.
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Affiliation(s)
- William S Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA.
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Ellard S, Patrinos GP, Oetting WS. Clinical Applications of Next-Generation Sequencing: The 2013 Human Genome Variation Society Scientific Meeting. Hum Mutat 2013; 34:1583-7. [DOI: 10.1002/humu.22400] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/12/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Sian Ellard
- University of Exeter Medical School; Exeter United Kingdom
| | - George P. Patrinos
- Department of Pharmacy; School of Health Sciences; University of Patras; Patras Greece
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology; University of Minnesota; Minneapolis Minnesota
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38
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McGue M, Zhang Y, Miller MB, Basu S, Vrieze S, Hicks B, Malone S, Oetting WS, Iacono WG. A genome-wide association study of behavioral disinhibition. Behav Genet 2013; 43:363-73. [PMID: 23942779 PMCID: PMC3886341 DOI: 10.1007/s10519-013-9606-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
Abstract
We report results from a genome wide association study (GWAS) of five quantitative indicators of behavioral disinhibition: nicotine, alcohol consumption, alcohol dependence, illicit drugs, and non-substance related behavioral disinhibition. The sample, consisting of 7,188 Caucasian individuals clustered in 2,300 nuclear families, was genotyped on over 520,000 SNP markers from Illumina's Human 660W-Quad Array. Analysis of individual SNP associations revealed only one marker-component phenotype association, between rs1868152 and illicit drugs, with a p value below the standard genome-wide threshold of 5 × 10(-8). Because we had analyzed five separate phenotypes, we do not consider this single association to be significant. However, we report 13 SNPs that were associated at p < 10(-5) for one phenotype and p < 10(-3) for at least two other phenotypes, which are potential candidates for future investigations of variants associated with general behavioral disinhibition. Biometric analysis of the twin and family data yielded estimates of additive heritability for the component phenotypes ranging from 49 to 70%, GCTA estimates of heritability for the same phenotypes ranged from 8 to 37%. Consequently, even though the common variants genotyped on the GWAS array appear in aggregate to account for a sizable proportion of heritable effects in multiple indicators of behavioral disinhibition, our data suggest that most of the additive heritability remains "missing".
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Affiliation(s)
- Matt McGue
- Minnesota Center for Twin and Family Research, Department of Psychology, University of Minnesota, Elliott Hall, Minneapolis, MN 55455, USA.
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Israni AK, Riad SM, Leduc R, Oetting WS, Guan W, Schladt D, Matas AJ, Jacobson PA. Tacrolimus trough levels after month 3 as a predictor of acute rejection following kidney transplantation: a lesson learned from DeKAF Genomics. Transpl Int 2013; 26:982-9. [PMID: 23879408 DOI: 10.1111/tri.12155] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 03/29/2013] [Accepted: 07/01/2013] [Indexed: 02/06/2023]
Abstract
Most calcineurin inhibitor (CNI)-based protocols reduce blood trough goals approximately 2-3 months post-transplant in clinically stable kidney transplant recipients. The CNI target trough level to prevent rejection, after reduction, is unknown. Using a multivariate Cox proportional hazards model, we determined the association of time-varying tacrolimus (TAC) trough levels with acute rejection (AR) occurring in the first 6 months post-transplant, but specifically we assessed this association after 3 months. A total of 1930 patients received TAC-based immunosuppression prior to AR in a prospective study. Of the 151 (7.8%) who developed AR, 47 developed AR after 3 months post-transplant. In an adjusted time-varying multivariate model, each 1 ng/ml decrease in TAC trough levels was associated with a 7.2% increased risk of AR [hazards ratio (HR) = 1.07, 95% confidence interval (CI) (1.01, 1.14) P = 0.03] in the first 6 months. There was an additional 23% increased risk of AR with each 1 ng/ml decrease in the TAC trough levels in months 3-6 [HR = 1.23, 95% CI (1.06, 1.43) P = 0.008]. In conclusion, lower TAC trough levels were significantly associated with increased risk of AR in the first 6 months post-transplant with additional risk of AR between months 3 and 6 post-transplant. The timing and practice of TAC dose reduction should be personalized based on the individual's risk factors.
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Affiliation(s)
- Ajay K Israni
- Nephrology Division, Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, MN, USA; Department of Epidemiology & Community Health, University of Minnesota, Minneapolis, MN, USA
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Oetting WS, Jacobson PA, Israni AK. Transplant rejection and risk: in search of the genetic dark matter. J Gastrointestin Liver Dis 2013; 22:125-126. [PMID: 23799208 PMCID: PMC4105001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
| | | | - Ajay K. Israni
- Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, MN, USA
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Passey C, Birnbaum AK, Brundage RC, Schladt DP, Oetting WS, Leduc RE, Israni AK, Guan W, Matas AJ, Jacobson PA. Validation of tacrolimus equation to predict troughs using genetic and clinical factors. Pharmacogenomics 2013; 13:1141-7. [PMID: 22909204 DOI: 10.2217/pgs.12.98] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Tacrolimus is an immunosuppressant used in transplantation. This article reports the validation of the authors' recently developed genetics-based tacrolimus equation that predicts troughs. METHODS Validation was performed in an independent cohort of 795 kidney transplant recipients receiving tacrolimus. The performance of the equation to predict initial troughs was assessed by calculating the bias and precision of the equation. For all troughs in the first 6 months post-transplant, a comparison was made between the troughs predicted using the equation versus those predicted using a basic apparent clearance model with no covariates. RESULTS For initial troughs, the equation had a low bias (0.2 ng/ml) and high precision (1.8 ng/ml). For all troughs, the equation predicted troughs significantly better than the basic apparent clearance model. CONCLUSION The tacrolimus equation had good bias and precision in predicting initial troughs and performed better than a basic apparent clearance model for all the troughs.
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Affiliation(s)
- Chaitali Passey
- Department of Experimental & Clinical Pharmacology, 717 Delaware Street, University of Minnesota, Minneapolis, MN 55455, USA
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Israni AK, Leduc R, Jacobson PA, Wildebush W, Guan W, Schladt D, Matas AJ, Oetting WS. Inflammation in the setting of chronic allograft dysfunction post-kidney transplant: phenotype and genotype. Clin Transplant 2013; 27:348-58. [PMID: 23350966 DOI: 10.1111/ctr.12074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2012] [Indexed: 01/05/2023]
Abstract
BACKGROUND Chronic allograft dysfunction (CGD) is a common outcome in kidney transplants, but its pathogenesis is unclear. We investigated the CGD phenotype and single-nucleotide polymorphisms (SNPs) associated with CGD. METHOD This prospective study enrolled 2336 transplants from seven transplant centers in North America. CGD was defined as a >25% rise in serum creatinine relative to a three-month post-transplant baseline, requiring a kidney biopsy. We genotyped 2724 SNPs in the initial 979 transplants, which form the test cohort. RESULTS CGD occurred 11.2 times per 100 person-years at a median of 509 ± 387 days from the three-month baseline. CGD was independently associated with death-censored, allograft failure, in an adjusted analysis [HR=20.6 (11.8-35.8, p < 0.001)]. Among 366 transplant recipients with CGD, 91% had inflammation on biopsy scores. 94 (26%) had inflammatory changes consistent with a diagnosis of concomitant acute rejection. SNPs in FM06 and FM03, potential drug metabolism genes, were associated with CGD, after accounting for multiple testing. CONCLUSION CGD phenotype with concomitant inflammation is associated with increased risk of allograft failure. SNPs associated with CGD in novel drug metabolism and transport genes, will be validated in subsequent transplants.
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Affiliation(s)
- Ajay K Israni
- Nephrology Division, Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, MN 55415-1829, USA.
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Koutlas IG, Forsman CL, Kyrkanides S, Oetting WS, Petryk A. Autosomal dominant mesomandibular fibro-osseous dysplasia: a self-resolving inherited fibro-osseous lesion of the jaws. Front Physiol 2012; 3:458. [PMID: 23230423 PMCID: PMC3515761 DOI: 10.3389/fphys.2012.00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/19/2012] [Indexed: 11/16/2022] Open
Abstract
A hereditary congenital condition characterized by a fibro-osseous lesion sharing some features with fibrous dysplasia and affecting the middle aspect of the mandible is presented. The condition was initially described as congenital monostotic fibrous dysplasia in two siblings, a male and a female. However, there is sufficient evidence that the disorder is autosomal dominant since it has been encountered in two of four children, both males, of the female propositus and one child, a boy, of the male propositus. All patients presented at birth or right after birth with enlargement of the middle part of the mandible. Radiographs from affected individuals have shown mesomandibular enlargement with irregular trabeculation akin of “ground-glass” appearance. Histologically, samples from all patients revealed woven bone proliferation in a cellular fibroblastic stroma. Interestingly, the originally described siblings, now in their 30s, have no evidence of jaw lesions either radiographically or clinically, thus indicating that the condition is self-limiting or self-resolving. An autosomal dominant mode of inheritance with apparent male predilection is favored. The molecular basis of this condition is currently unknown. However, the location of the lesions in the middle aspect of the mandible suggests dysregulation of Bone Morphogenetic Protein (BMP) signaling since BMPs regulate mandibular morphogenesis in utero, particularly in the medial region as well as postnatal bone remodeling. Immunohistochemical evaluation for a BMP-binding protein Twisted Gastrulation (TWSG1) revealed mosaic pattern of staining, with some cells, including osteoclasts, strongly stained and others exhibiting faint or no staining, thus supporting active regulation of BMP signaling within the lesion. Future investigations will determine if dysregulation of BMP signaling plays a causative role or rather reflects secondary activation of repair mechanisms and/or bone remodeling.
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Affiliation(s)
- Ioannis G Koutlas
- Division of Oral and Maxillofacial Pathology, School of Dentistry, University of Minnesota Minneapolis, MN, USA
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Oetting WS, Guan W, Schladt DP, Leduc RE, Jacobson PA, Matas AJ, Chinnakotla S, Schröppel B, Murphy BT, Israni AK. Donor polymorphisms of toll-like receptor 4 associated with graft failure in liver transplant recipients. Liver Transpl 2012; 18:1399-405. [PMID: 22987288 PMCID: PMC3518641 DOI: 10.1002/lt.23549] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/22/2012] [Indexed: 12/14/2022]
Abstract
There have been many reports showing significant associations between recipient genetic variants and allograft outcomes, including acute rejection and graft failure, but less is known about the contribution of the donor genotype. We analyzed 37 single-nucleotide polymorphisms (SNPs) within the toll-like receptor 4 (TLR4) gene from deceased donor liver allografts transplanted into 738 recipients to determine their effects on liver graft failure (LGF). Two SNPs exhibited a significant association with LGF after adjustments for donor race and recipient race and corrections for multiple test comparisons: rs11536865 [hazard ratio (HR) = 2.5, P = 0.0003] and rs5030717 (HR = 1.67, P = 0.0008). An additional SNP, rs913930, exhibited a significant association in Caucasian donors (HR = 1.62, P = 0.0006), and 2 SNPs exhibited a suggestive association in African American donors: rs11536865 (HR = 2.45, P = 0.002) and rs5030717 (HR = 2.32, P = 0.002). Additionally, the liver donor risk index (HR = 2.56, 95% confidence interval = 1.54-4.26, P = 0.0003) and the recipient hepatitis C virus (HCV) status (HR = 1.53, 95% confidence interval = 1.04-2.24, P = 0.032) increased the risk of all-cause LGF in a Cox proportional hazards model adjusted for recipient race. Donor polymorphisms in TLR4 could be important factors in modulating TLR4 activity and, therefore, affect the risk of graft loss. Additionally, there is a suggestion of an interaction between polymorphisms within TLR4 and the HCV status.
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Affiliation(s)
- William S. Oetting
- College of Pharmacy, University of Minnesota, Minneapolis, MN,Institute of Human Genetics, University of Minnesota, Minneapolis, MN
| | - Weihua Guan
- Division of Biostatistics, University of Minnesota, Minneapolis, MN
| | - David P. Schladt
- Division of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Robert E. Leduc
- Division of Biostatistics, University of Minnesota, Minneapolis, MN
| | | | - Arthur J. Matas
- Department of Surgery, University of Minnesota, Minneapolis, MN
| | | | | | | | - Ajay K. Israni
- Department of Medicine, Hennepin County Medical Center, University of Minnesota, Minneapolis, MN
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Jacobson PA, Schladt D, Oetting WS, Leduc R, Guan W, Matas AJ, Israni A. Lower calcineurin inhibitor doses in older compared to younger kidney transplant recipients yield similar troughs. Am J Transplant 2012; 12:3326-36. [PMID: 22947444 PMCID: PMC3513646 DOI: 10.1111/j.1600-6143.2012.04232.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The number of older adults undergoing kidney transplantation has increased, yet little is known about calcineurin inhibitor (CNI) metabolism in this group. We studied CNI troughs and doses to determine if there were age-related differences in metabolism and dose requirements. We studied 348 young (18-34 years), 1831 middle (35-64 years) and 374 older (65-84 years) adult kidney transplant recipients enrolled in a seven-center prospective study. Troughs were obtained from each patient 2×/week in weeks 1-8 and 2×/month in months 3-6. A multivariable linear-mixed model examined the effect of age on log dose and weight normalized troughs. Older recipients had higher normalized tacrolimus troughs than middle or young age adults despite receiving doses a median of 1-2 mg/day lower. Age and CYP3A5*1 genotype had the largest effect on tacrolimus troughs. Older recipients also had higher normalized cyclosporine troughs than middle or young adults despite receiving median doses 100 mg/day lower. After normalization for dose and weight, CNI troughs were more than 50% higher in older adults than young adults. These data support age-related changes in CNI metabolism. Further studies are needed to determine optimal dosing of CNIs in the elderly.
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Affiliation(s)
- Pamala A. Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, 7-151 Weaver Densford Hall, 308 Harvard St SE, Minneapolis, MN 55455
| | - David Schladt
- Division of Biostatistics, University of Minnesota, 2221 University Ave SE, Suite 200, Minneapolis, MN 55414
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology and Institute of Human Genetics, University of Minnesota, 14-255 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455
| | - Robert Leduc
- Division of Biostatistics, University of Minnesota, 2221 University Ave SE, Suite 200, Minneapolis, MN 55414
| | - Weihau Guan
- Division of Biostatistics, University of Minnesota, 14-255 Moos Tower, 515 Delaware Street, S.E. Minneapolis, MN 55455
| | - Arthur J. Matas
- Division of Transplantation, Department of Surgery, University of Minnesota, 11-200 PWB, 516 Delaware St SE, Minneapolis, MN 55455
| | - Ajay Israni
- Department of Medicine, Nephrology Division, Hennepin County Medical Center, 5th Floor HFA Shapiro Building, 701 Park Avenue, Minneapolis, MN 55415
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Irons DE, Iacono WG, Oetting WS, McGue M. Developmental trajectory and environmental moderation of the effect of ALDH2 polymorphism on alcohol use. Alcohol Clin Exp Res 2012; 36:1882-91. [PMID: 22563891 DOI: 10.1111/j.1530-0277.2012.01809.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 02/14/2012] [Indexed: 12/13/2022]
Abstract
BACKGROUND In the aldehyde dehydrogenase 2 (ALDH2) gene, the ALDH2*2 allele, prevalent in East Asian populations, encodes an enzyme with severely reduced activity, thereby disrupting the normal metabolism of alcohol. Possession of the ALDH2*2 allele has been repeatedly shown to be associated with lower risk for alcohol dependence and reduced alcohol use. However, relatively few studies have considered whether the magnitude of the effect of ALDH2 polymorphism upon drinking is related to developmental stage or varies by environmental context. METHODS In a longitudinally assessed sample of 356 adopted adolescents and young adults of East Asian descent, we examined the progression over time of the relationship between ALDH2 genotype and multiple measures of drinking behavior. We also sought to determine whether the environmental influences of nonbiological parent and elder sibling alcohol use and misuse, as well as deviant peer behavior, moderated the effect of ALDH2 genotype upon alcohol use. RESULTS Across all measures of alcohol use, the association between ALDH2*2 allele possession and reduced drinking went from negligible to moderate between mid-adolescence and early adulthood. A combined index of adoptive parent alcohol use and misuse consistently moderated the protective effect of the ALDH2*2 allele across the measures of quantity and frequency of alcohol use, and symptomology, such that high parental alcohol use and misuse reduced the protective effect of the ALDH2*2 allele, while low parental alcohol use and misuse enhanced the effect of the allele. Neither a combined index of elder sibling alcohol use and misuse, nor deviant peer behavior was consistently related to the effect of ALDH2 genotype. CONCLUSIONS The protective effect of the ALDH2*2 allele increases over the course of adolescence and young adulthood and is modified by the environmental influence of parental alcohol use and misuse. As such, ALDH2 provides a model system for exploring the nature of gene-environment interplay across development.
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Affiliation(s)
- Daniel E Irons
- Department of Psychology, University of Minnesota, 75 East River Road, Minneapolis, MN 55455, USA.
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Jacobson PA, Schladt D, Israni A, Oetting WS, Lin YC, Leduc R, Guan W, Lamba V, Matas AJ. Genetic and clinical determinants of early, acute calcineurin inhibitor-related nephrotoxicity: results from a kidney transplant consortium. Transplantation 2012; 93:624-31. [PMID: 22334041 DOI: 10.1097/tp.0b013e3182461288] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Calcineurin inhibitor (CNI)-related acute nephrotoxicity is a common complication of transplantation. Clinical factors and elevated CNI levels are associated with nephrotoxicity; however, they do not fully explain the risk. Genetic factors may also predispose individuals to nephrotoxicity. METHODS We enrolled 945 kidney recipients into a multicenter, prospective study. DNA was genotyped for 2724 single-nucleotide polymorphisms (SNPs) using a customized chip. Cox models, unadjusted and adjusted for clinical factors, examined the association between SNPs and time to early CNI-related acute nephrotoxicity in the first 6 months posttransplant. RESULTS Cyclosporine was associated with a 1.49 hazard (95% confidence interval, 1.04-2.14) of acute nephrotoxicity relative to tacrolimus. Acute nephrotoxicity occurred in 22.6% of cyclosporine and 19.8% of tacrolimus recipients. The median (interquartile range) daily dose and trough concentration at time of nephrotoxicity were 400 mg (400-500 mg) and 228 ng/mL (190-272 ng/mL) in the cyclosporine group, and 6 mg (4-8 mg) and 12.6 ng/mL (10.2-15.9 ng/mL) in the tacrolimus group, respectively. In single-SNP adjusted analysis, nine SNPs in the XPC, CYP2C9, PAX4, MTRR, and GAN genes were associated with cyclosporine nephrotoxicity. In a multi-SNP analysis, SNPs from the same genes remained significant after adjusting for the clinical factors, showing that the SNPs are jointly and independently predictive of cyclosporine nephrotoxicity. No SNPs were associated with tacrolimus nephrotoxicity. CONCLUSION We identified SNPs that were potentially associated with early, acute cyclosporine-related nephrotoxicity. Identifying risk SNPs before transplantation provides an opportunity for personalization of immunosuppression by identifying those who may benefit from CNI-avoidance or minimization, or assist in selecting CNI type. These SNPs require independent validation.
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Affiliation(s)
- Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA.
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Passey C, Birnbaum AK, Brundage RC, Oetting WS, Israni AK, Jacobson PA. Dosing equation for tacrolimus using genetic variants and clinical factors. Br J Clin Pharmacol 2012; 72:948-57. [PMID: 21671989 DOI: 10.1111/j.1365-2125.2011.04039.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
AIM To develop a dosing equation for tacrolimus, using genetic and clinical factors from a large cohort of kidney transplant recipients. Clinical factors and six genetic variants were screened for importance towards tacrolimus clearance (CL/F). METHODS Clinical data, tacrolimus troughs and corresponding doses were collected from 681 kidney transplant recipients in a multicentre observational study in the USA and Canada for the first 6 months post transplant. The patients were genotyped for 2,724 single nucleotide polymorphisms using a customized Affymetrix SNP chip. Clinical factors and the most important SNPs (rs776746, rs12114000, rs3734354, rs4926, rs3135506 and rs2608555) were analysed for their influence on tacrolimus CL/F. RESULTS The CYP3A5*1 genotype, days post transplant, age, transplant at a steroid sparing centre and calcium channel blocker (CCB) use significantly influenced tacrolimus CL/F. The final model describing CL/F (l h(-1)) was: 38.4 ×[(0.86, if days 6-10) or (0.71, if days 11-180)]×[(1.69, if CYP3A5*1/*3 genotype) or (2.00, if CYP3A5*1/*1 genotype)]× (0.70, if receiving a transplant at a steroid sparing centre) × ([age in years/50](-0.4)) × (0.94, if CCB is present). The dose to achieve the desired trough is then prospectively determined using the individuals CL/F estimate. CONCLUSIONS The CYP3A5*1 genotype and four clinical factors were important for tacrolimus CL/F. An individualized dose is easily determined from the predicted CL/F. This study is important towards individualization of dosing in the clinical setting and may increase the number of patients achieving the target concentration. This equation requires validation in an independent cohort of kidney transplant recipients.
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Affiliation(s)
- Chaitali Passey
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
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Oetting WS. Exome and genome analysis as a tool for disease identification and treatment: the 2011 Human Genome Variation Society scientific meeting. Hum Mutat 2012; 33:586-90. [PMID: 22213110 DOI: 10.1002/humu.22018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 12/14/2011] [Indexed: 11/10/2022]
Abstract
The 2011 annual scientific meeting of the Human Genome Variation Society (HGVS) was held on the 11th of October, in Montreal, Canada. The theme of this meeting was "Exome and Genome Analysis as a Tool for Disease Identification and Treatment." In the last few years, there has been a substantial increase in the use of next-generation sequencing in identifying variants associated with both single-gene disorders and complex diseases. The advent of exome sequencing with the subsequent transition to whole genome sequencing will require methods to identify candidate causal variants both in coding and regulatory regions. As this technology slowly moves into the clinical diagnostic laboratory, the need to accurately predict the functional consequences of variants becomes more critical for the both the diagnosis and treatment of disease. This year's annual meeting focused on these issues.
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Affiliation(s)
- William S Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, USA.
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Oetting WS, Schladt DP, Leduc RE, Jacobson PA, Guan W, Matas AJ, Israni A. Validation of single nucleotide polymorphisms associated with acute rejection in kidney transplant recipients using a large multi-center cohort. Transpl Int 2011; 24:1231-8. [PMID: 21955043 DOI: 10.1111/j.1432-2277.2011.01359.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There have been numerous reports proposing a statistically significant association between a genetic variant, usually in the form of a single nucleotide polymorphism (SNP), and acute rejection (AR). Unfortunately, there are additional publications reporting a lack of association with AR when a different cohort of recipients was analyzed for the same SNP. The objective of this report was to attempt replication of these published finding in our own kidney allograft recipient cohort. We analyzed 23 genetic variants, previously reported to have a significant association with AR, using a cohort of 969 clinically well-defined kidney transplant recipients. Only one SNP, rs6025 (Leiden mutation), within the coagulation factor V gene, showed a significant association with a P-value of 0.011 in a race-adjusted analysis and a P-value of 0.0003 in multiple variable analysis. An additional SNP, rs11706052 in IMPDH2, gave a modest P-value of 0.044 using multiple variable analysis, which is not significant when multiple testing is taken into consideration. Our results suggest that careful validation of previously reported associations with AR is necessary, and different strategies other than candidate gene studies can help to identify causative genetic variants associated with AR.
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Affiliation(s)
- William S Oetting
- College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA.
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