1
|
Moyer AM, Gandhi MJ. Human Leukocyte Antigen (HLA) Testing in Pharmacogenomics. Methods Mol Biol 2022; 2547:21-45. [PMID: 36068459 DOI: 10.1007/978-1-0716-2573-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The genetic region on the short arm of chromosome 6 where the human leukocyte antigen (HLA) genes are located is the major histocompatibility complex. The genes in this region are highly polymorphic, and some loci have a high degree of homology with other genes and pseudogenes. Histocompatibility testing has traditionally been performed in the setting of transplantation and involves determining which specific alleles are present. Several HLA alleles have been associated with disease risk or increased risk of adverse drug reaction (ADR) when treated with certain medications. Testing for these applications differs from traditional histocompatibility in that the desired result is simply presence or absence of the allele of interest, rather than determining which allele is present. At present, the majority of HLA typing is done by molecular methods using commercially available kits. A subset of pharmacogenomics laboratories has developed their own methods, and in some cases, query single nucleotide variants associated with certain HLA alleles rather than directly testing for the allele. In this chapter, a brief introduction to the HLA system is provided, followed by an overview of a variety of testing technologies including those specifically used in pharmacogenomics, and the chapter concludes with details regarding specific HLA alleles associated with ADR.
Collapse
Affiliation(s)
- Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - Manish J Gandhi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
2
|
Buchner A, Hu X, Aitchison KJ. Validation of Single Nucleotide Variant Assays for Human Leukocyte Antigen Haplotypes HLA-B*15:02 and HLA-A*31:01 Across Diverse Ancestral Backgrounds. Front Pharmacol 2021; 12:713178. [PMID: 34381365 PMCID: PMC8350439 DOI: 10.3389/fphar.2021.713178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
The human leukocyte antigen haplotypes HLA-B*15:02 and HLA-A*31:01 have been linked to life-threatening adverse drug reactions to the anticonvulsants carbamazepine and oxcarbazepine. Identification of these haplotypes via pharmacogenetic techniques facilitates implementation of precision medicine to prevent such reactions. Using reference samples from diverse ancestral origins, we investigated the test analytical validity (i.e., ability to detect whether or not the haplotypes were present or absent) of TaqMan assays for single nucleotide variants previously identified as potentially being able to "tag" these haplotypes. A TaqMan custom assay for rs10484555 and an inventoried assay for rs17179220 and were able to identify with 100% sensitivity and 100% specificity HLA-B*15:02 and HLA-A*31:01 respectively. A custom assay for rs144012689 that takes into account a neighboring single nucleotide variant with manual calling was also able to identify HLA-B*15:02 with 100% sensitivity and 100% specificity. A custom assay for rs106235 identified HLA-A*31:01 with 100% sensitivity and 95% specificity. The slight reduction in specificity for the latter was owing to another haplotype (HLA-A*33:03) also being detected. While any positive call using the rs106235 assay could therefore be further investigated, as the presence of the HLA-A*31:01 haplotype confers adverse drug reaction risk, the absence of false negatives (indexed by sensitivity) is more important than false positives. In summary, we present validated TaqMan assay methodology for efficient detection of HLA haplotypes HLA-B*15:02 and HLA-A*31:01. Our data are relevant for other genotyping technologies that identify, or have the potential to identify, these haplotypes using single nucleotide variants.
Collapse
Affiliation(s)
- Amanda Buchner
- Department of Psychiatry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
| | - Xiuying Hu
- Department of Psychiatry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Katherine J Aitchison
- Department of Psychiatry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada.,Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
3
|
van Nguyen D, Chu HC, Vidal C, Fulton RB, Nguyen NN, Quynh Do NT, Tran TL, Nguyen TN, Thu Nguyen HT, Chu HH, Thanh Thuc HT, Minh Le HT, van Nunen S, Anderson J, Fernando SL. Genetic susceptibilities and prediction modeling of carbamazepine and allopurinol-induced severe cutaneous adverse reactions in Vietnamese. Pharmacogenomics 2020; 22:1-12. [PMID: 33356553 DOI: 10.2217/pgs-2019-0146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aims: To determine genetic susceptibility markers for carbamazepine (CBZ) and allopurinol-induced severe cutaneous adverse reactions (SCARs) in Vietnamese. Methods: A case-control study was performed involving 122 patients with CBZ or allopurinol-induced SCARs and 120 drug tolerant controls. Results: HLA-B*58:01 was strongly associated with allopurinol-induced SCARs and strongly correlated with SNP rs9263726. HLA-B*15:02 was associated with CBZ-induced Stevens-Johnson syndrome/toxic epidermal necrolysis but not with drug-induced hypersensitivity syndrome/drug rash with eosinophilia and systemic symptoms. No association was found between HLA-A*31:01 and CBZ-induced SCARs. HLA-B*58:01 and rs3909184 allele A with renal insufficiency were shown to increase the risk of allopurinol-induced SCARs. Conclusion: HLA-B*58:01 and HLA-B*15:02 confer susceptibility to allopurinol-induced SCARs and CBZ-induced SJS/TEN in Vietnamese. SNP rs9263726 can be used as a surrogate marker in identifying HLA-B*58:01.
Collapse
Affiliation(s)
- Dinh van Nguyen
- Vinmec Healthcare System, Hanoi, 100000, Vietnam.,College of Health Science, VinUniversity, Hanoi, 100000, Vietnam.,Sydney Medical School - Northern, The University of Sydney, Sydney, 2065, Australia.,ImmunoRheumatology Laboratory, NSW Health Pathology-North, Royal North Shore Hospital, Sydney, 2065, Australia
| | - Hieu Chi Chu
- Center of Allergology & Clinical Immunology, Bach Mai Hospital, Hanoi, 115000, Vietnam
| | - Christopher Vidal
- Sydney Medical School - Northern, The University of Sydney, Sydney, 2065, Australia
| | - Richard B Fulton
- ImmunoRheumatology Laboratory, NSW Health Pathology-North, Royal North Shore Hospital, Sydney, 2065, Australia
| | - Nguyet Nhu Nguyen
- Center of Allergology & Clinical Immunology, Bach Mai Hospital, Hanoi, 115000, Vietnam
| | - Nga Thi Quynh Do
- Department of Immunology & Molecular Biology, National Institute of Hygiene & Epidemiology, Hanoi, 100000, Vietnam
| | | | | | - Ha Thi Thu Nguyen
- Department of Allergy & Clinical Immunology, Hanoi Medical University, Hanoi, 100000, Vietnam
| | - Hanh Hong Chu
- Department of Allergy, Immunology & Rheumatology, National Hospital of Pediatrics, Hanoi, 100000, Vietnam
| | - Huyen Thi Thanh Thuc
- Department of Allergy, Immunology & Rheumatology, National Hospital of Pediatrics, Hanoi, 100000, Vietnam
| | - Huong Thi Minh Le
- Department of Allergy, Immunology & Rheumatology, National Hospital of Pediatrics, Hanoi, 100000, Vietnam
| | - Sheryl van Nunen
- Sydney Medical School - Northern, The University of Sydney, Sydney, 2065, Australia.,Department of Clinical immunology & Allergy, Royal North Shore Hospital, Sydney, 2065, Australia
| | - Janet Anderson
- ImmunoRheumatology Laboratory, NSW Health Pathology-North, Royal North Shore Hospital, Sydney, 2065, Australia
| | - Suran L Fernando
- Sydney Medical School - Northern, The University of Sydney, Sydney, 2065, Australia.,ImmunoRheumatology Laboratory, NSW Health Pathology-North, Royal North Shore Hospital, Sydney, 2065, Australia.,Department of Clinical immunology & Allergy, Royal North Shore Hospital, Sydney, 2065, Australia
| |
Collapse
|
4
|
Nguyen DV, Vidal C, Chu HC, van Nunen S. Developing pharmacogenetic screening methods for an emergent country: Vietnam. World Allergy Organ J 2019; 12:100037. [PMID: 31198488 PMCID: PMC6558218 DOI: 10.1016/j.waojou.2019.100037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/24/2019] [Accepted: 05/01/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The finding of strong associations between certain human leukocyte antigen (HLA) genotypes and the development of severe cutaneous adverse drug reactions (SCARs), [for example, HLA-B*57:01 and abacavir (ABC), HLA-B*15:02 and carbamazepine (CBZ) and HLA-B*58:01 and allopurinol], has led to HLA screening being used to prevent SCARs. Screening has been shown to be of great benefit in a number of studies. Clinical translation from bench to bedside, however, depends upon the development of simple, rapid and cost-effective assays to detect these risk alleles. In highly populated developing countries such as Vietnam, where there is a high prevalence of HLA-B*15:02 and HLA-B*58:01 correlating with a high incidence of CBZ- and allopurinol-induced SCARs, the crucial factor in the implementation of comprehensive screening programs to detect these major risk HLA alleles is the availability of suitable assays. BODY We have summarized the role and economic benefits of HLA screening, reviewed published HLA screening methods used currently in pharmacogenetic screening and examined the advantages and disadvantages of assays developed specifically for use in screening for risk alleles in the prevention of HLA-associated SCARs in Vietnam. CONCLUSION The optimal approach we propose may serve as a template for the development of screening programs in other emergent countries.
Collapse
Affiliation(s)
- Dinh Van Nguyen
- Respiratory, Allergy and Clinical Immunology, Vinmec International Hospital, Times City and Vin University, Hanoi, Viet Nam
- Northern Clinical School, The University of Sydney, Sydney, Australia
- Department of Allergy and Clinical Immunology, Hanoi Medical University, Hanoi, Viet Nam
| | - Christopher Vidal
- Northern Clinical School, The University of Sydney, Sydney, Australia
| | - Hieu Chi Chu
- Center of Allergology and Clinical Immunology, Bach Mai Hospital, Hanoi, Viet Nam
| | - Sheryl van Nunen
- Northern Clinical School, The University of Sydney, Sydney, Australia
- Department of Clinical Immunology and Allergy, Royal North Shore Hospital, Sydney, Australia
| |
Collapse
|
5
|
Fang H, Xu X, Kaur K, Dedek M, Zhu GD, Riley BJ, Espin FG, Del Tredici AL, Moreno TA. A Screening Test for HLA-B∗15:02 in a Large United States Patient Cohort Identifies Broader Risk of Carbamazepine-Induced Adverse Events. Front Pharmacol 2019; 10:149. [PMID: 30971914 PMCID: PMC6443844 DOI: 10.3389/fphar.2019.00149] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 02/08/2019] [Indexed: 11/13/2022] Open
Abstract
Purpose: HLA-B∗15:02 is strongly associated with life-threatening severe skin hypersensitivity reactions in patients treated with carbamazepine (CBZ) and structurally related medications. FDA-approved labeling recommends HLA-B∗15:02 screening before CBZ therapy in patients of Asian ancestry. In this study, we aimed to (a) identify a direct method for screening HLA-B∗15:02, and (b) evaluate prevalence in a large cohort of United States patients. Methods: Candidate genetic markers were identified by mining public data. Association was tested in 28,897 individuals by comparing SNP results with high-resolution HLA typing. Retrospective analysis of de-identified SNP and ethnicity data from 130,460 individuals was performed to evaluate the ethnic distribution of HLA-B∗15:02 in the United States. Results: 28,897 United States individuals showed 100% concordance between HLA-B∗15:02 and the minor allele of rs144012689 (100% sensitivity/99.97% specificity). Retrospective analysis of 160 positive individuals (66 with physician-reported ethnicity) notably included 28 Asians (42%), 15 African Americans (22%), 11 Caucasians (17%), 2 Hispanics (3%), and 10 "Other" (15%). Conclusion: Screening United States patients for HLA-B∗15:02 without ethnicity-based preselection identifies more than twice the number of carriers at risk of CBZ-related adverse events than screening patients of Asian ancestry alone. Risk assessment based on ethnicity assumptions may not identify a large portion of at-risk patients in the ethnically diverse United States population.
Collapse
Affiliation(s)
- Hua Fang
- Millennium Health, San Diego, CA, United States
| | - Xiequn Xu
- Millennium Health, San Diego, CA, United States
| | | | | | | | - Bae J Riley
- Millennium Health, San Diego, CA, United States
| | | | | | | |
Collapse
|