Mol Cancer Ther. 2023 Jul 13:MCT-22-0486. doi: 10.1158/1535-7163.MCT-22-0486. Online ahead of print.

ABSTRACT

As a result of tumor heterogeneity and solid cancers harboring multiple molecular defects, precision medicine platforms in oncology are most effective when both genetic and pharmacological determinants of a tumor are evaluated. Expandable patient-derived xenograft (PDX) mouse tumor and corresponding PDX culture (PDXC) models recapitulate many of the biological and genetic characteristics of the original patient tumor, allowing for a comprehensive pharmacogenomic analysis. Here, the somatic mutations of 23 matched patient tumor and PDX samples encompassing four cancers were first evaluated using next generation sequencing (NGS). 19 antitumor agents were evaluated across 78 patient-derived tumor cultures using clinically relevant drug exposures. A binarization threshold sensitivity classification determined in culture (PDXC) was used to identify tumors that best respond to drug in vivo (PDX). Utilizing this sensitivity classification, logic models of DNA mutations were developed for 19 antitumor agents to predict drug response. We determined that the concordance of somatic mutations across patient and corresponding PDX samples increased as variant allele frequency (VAF) increased. Notable individual PDXC responses to specific drugs, as well as lineage-specific drug responses where identified. Robust responses identified in PDXC were recapitulated in vivo in PDX-bearing mice and logic modeling determined somatic gene mutation(s) defining response to specific antitumor agents. In conclusion, combining NGS of primary patient tumors, high-throughput drug screen (HTDS) using clinically relevant doses, and logic modeling, can provide a platform for understanding response to therapeutic drugs targeting cancer.

PMID:37440705 | DOI:10.1158/1535-7163.MCT-22-0486

Nan Fang Yi Ke Da Xue Xue Bao. 2023 Jun 20;43(6):1047-1050. doi: 10.12122/j.issn.1673-4254.2023.06.23.

ABSTRACT

OBJECTIVE: To evaluate the value of pharmacogenetic testing for improving the efficacy and safety of treatment with cyclosporine, tacrolimus, and cyclophosphamide (CTX) for PLA2R-related membranous nephropathy and for determing individualized and precise treatment plans for the patients.

METHODS: A total of 63 patients with PLA2R-related membranous nephropathy hospitalized in the Department of Nephrology at our hospital from January, 2019 to October, 2021 were enrolled in this study. Thirty-three of the patients underwent pharmacogenetic testing before taking the immunosuppressive drugs selected based on the results of genetic screening for sensitive targets, and the other 30 patients were empirically given immunosuppressive drugs according to the guidelines (control group). The clinical efficacy and adverse effects of the immunosuppressive drugs were analyzed for all the patients. The two groups of patients were compared for demographic and biochemical parameters including 24-h urine protein, serum albumin, renal function, and serum anti-phospholipase A2 receptor antibody both before and at 3 months after the beginning of the treatment.

RESULTS: Among the 33 patients undergoing pharmacogenetic testing, 51.5% showed a GG genotype for cyclosporine, and 61.6% had an AG genotype for tacrolimus; for CTX, 51.5% of the patients showed a homozygous deletion and 63.6% had an AA genotype. After treatment for 3 months, serum anti-phospholipase A2 receptor antibody, 24-h urine protein, and serum albumin levels were significantly improved in pharmacogenetic testing group as compared with the control group (P < 0.05).

CONCLUSION: Individualized and precise administration of immunosuppressive drugs based on pharmacogenetic testing better controls proteinuria and serum antiphospholipase A2 receptor antibodies and increases serum albumin level in patients with PLA2R-related membranous nephropathy.

PMID:37439180 | DOI:10.12122/j.issn.1673-4254.2023.06.23

Br J Clin Pharmacol. 2023 Jul 12. doi: 10.1111/bcp.15849. Online ahead of print.

ABSTRACT

AIM: To investigate the effect of aging, sex, and CYP genotypes on the exposure of quetiapine (QUE) and the pharmacologically active metabolite N-desalkylquetiapine (NDQ).

METHODS: Patients with serum concentrations of QUE and NDQ were included retrospectively from a therapeutic drug monitoring service. The outcome measures were concentration:dose (C:D) ratios of QUE and NDQ, and NDQ-to-QUE metabolic ratio (MPR). Linear mixed model analyses were used to evaluate the effects of age, sex, and subsequently, CYP2D6/3A genotypes.

RESULTS: The average age of the included population (n=8,118 patients) was 44 years (13.5% ≥65y). The C:D ratio of QUE and NDQ gradually increased in patients aged >50y compared to those aged 18-30y, with 28% and 29% increase, respectively, for patients aged >70y (p<0.001). Compared to males, females had 15% lower QUE C:D ratio and 10% higher C:D ratio of NDQ (both p<0.001). The MPR was 30% higher in females than in males (p<0.001). For females ≥65y, the NDQ C:D ratio was 36% higher compared to males <65y (p<0.001). A significantly higher NDQ C:D ratio was observed for CYP2D6 intermediate- (IMs: +7%, p=0.012) and poor- (PMs: +17%, p=0.001) compared to normal metabolizers (NMs). No effects of CYP3A4*22 and CYP3A5*1 allele variants were observed.

CONCLUSION: This study shows an increase of the QUE and NDQ exposures during aging. Old age, female sex and CYP2D6 allele variants encoding reduced activity are factors associated with high NDQ exposure. Therefore, females ≥65y carrying CYP2D6 allele variants encoding reduced activity have the highest risk of dose-dependent side effects of NDQ during QUE treatment.

PMID:37438870 | DOI:10.1111/bcp.15849

ACS Appl Mater Interfaces. 2023 Jul 12. doi: 10.1021/acsami.3c04285. Online ahead of print.

ABSTRACT

The conventional detection methods cannot satisfy the need for early and rapid detection of monkeypox virus (MPXV) infection. This is due to complicated pretreatment, time consumption, and complex operation of the diagnostic tests. Based on surface-enhanced Raman spectroscopy (SERS), this study attempted to capture the characteristic fingerprints of the MPXV genome and multiple antigenic proteins without the need to design specific probes. The minimum detection limit of this method is 100 copies/mL, with good reproducibility and signal-to-noise ratio. Therefore, the relationship between characteristic peak intensity and the protein and nucleic acid concentration can be used to construct a concentration-dependent spectral line with a good linear relationship. Additionally, principal component analysis (PCA) could identify the SERS spectra of four different MPXV proteins in serum. Therefore, this rapid detection method in the current outbreak of monkeypox control and the future response to possible new outbreaks has broad application prospects.

PMID:37436060 | DOI:10.1021/acsami.3c04285

Pharmacogenomics. 2023 Jul 12. doi: 10.2217/pgs-2023-0018. Online ahead of print.

ABSTRACT

Aim: To evaluate the prevalence of medications with actionable pharmacogenomic (PGx) safety and efficacy recommendations in patients receiving care from the Veterans Health Administration. Materials & methods: Outpatient prescription data from 2011 to 2021 and any documented adverse drug reactions (ADRs) were reviewed for those who received PGx testing at one Veterans Administration location between November 2019 and October 2021. Results: Among the reviewed prescriptions, 381 (32.8%) were associated with an actionable recommendation based on the Clinical Pharmacogenetics Implementation Consortium (CPIC) prescribing guidelines, with 205 (17.7%) for efficacy concerns and 176 (15.2%) for safety concerns. Among those with a documented ADR for a PGx-impacted medication, 39.1% had PGx results that aligned with CPIC recommendations. Conclusion: Medications with actionable PGx recommendations for safety and efficacy concerns are received with similar frequency, and most patients who have undergone PGx testing at the Phoenix Veterans Administration have received medications that may be impacted by PGx testing.

PMID:37435738 | DOI:10.2217/pgs-2023-0018

Pharmacogenomics. 2023 Jul 12. doi: 10.2217/pgs-2023-0016. Online ahead of print.

ABSTRACT

Meaningful clinical decision support (CDS) recommendations are vital for implementation of pharmacogenomics (PGx) into routine clinical care. PGx CDS alerts include interruptive and noninterruptive alerts. The objective of this study was to evaluate provider ordering behavior after noninterruptive alerts are displayed. A retrospective manual chart review was conducted from the time of noninterruptive alert implementation to the time of data analysis to determine congruence with CDS recommendations. The congruence rate for noninterruptive alerts was 89.8% across all drug-gene interactions. The drug-gene interaction with the most alerts for analysis included metoclopramide (n = 138). The high rate of medication order congruence after noninterruptive alerts were deployed suggests this modality may be appropriate for PGx CDS as a method for best practice adherence.

PMID:37435734 | DOI:10.2217/pgs-2023-0016

Pharmacogenomics. 2023 Jul 12. doi: 10.2217/pgs-2023-0089. Online ahead of print.

ABSTRACT

Aim: A prospective observational study was conducted to evaluate the feasibility of implementing clinical guidelines for warfarin dosing in black Zimbabwean patients. Methods: CYP2C9*5, CYP2C9*6, CYP2C9*8 and CYP2C9*11 and VKORC1 c. 1639 G>A variations were observed in 62 study patients. Results & Conclusion: Overall, 39/62 (62.90%) participants did not receive a warfarin starting dose as would have been recommended by Clinical Pharmacogenetics Implementation Consortium guidelines. US FDA and Dutch Pharmacogenetics Working Group guidelines are based on CYP2C9*2 and CYP2C9*3 only, hence, unlikely useful in this cohort, where such variants were not detected. Clinical Pharmacogenetics Implementation Consortium guidelines, on the other hand, have a specific recommendation on the African-specific variants CYP2C9*5, CYP2C9*6 and CYP2C9*11, and are hence suitable for implementation in Zimbabwe and would help optimize warfarin doses in patients in the study cohort.

PMID:37435666 | DOI:10.2217/pgs-2023-0089

Front Immunol. 2023 Jun 26;14:1199422. doi: 10.3389/fimmu.2023.1199422. eCollection 2023.

ABSTRACT

Chronic Graft-versus-Host Disease is a life-threatening inflammatory condition that affects many patients after allogeneic hematopoietic stem cell transplantation. Although we have made substantial progress in understanding disease pathogenesis and the role of specific immune cell subsets, treatment options are still limited. To date, we lack a global understanding of the interplay between the different cellular players involved, in the affected tissues and at different stages of disease development and progression. In this review we summarize our current knowledge on pathogenic and protective mechanisms elicited by the major involved immune subsets, being T cells, B cells, NK cells and antigen presenting cells, as well as the microbiome, with a special focus on intercellular communication of these cell types via extracellular vesicles as up-and-coming fields in chronic Graft-versus-Host Disease research. Lastly, we discuss the importance of understanding systemic and local aberrant cell communication during disease for defining better biomarkers and therapeutic targets, eventually enabling the design of personalized treatment schemes.

PMID:37435079 | PMC:PMC10332803 | DOI:10.3389/fimmu.2023.1199422

Mol Psychiatry. 2023 Jul 11. doi: 10.1038/s41380-023-02149-1. Online ahead of print.

ABSTRACT

Lithium is regarded as the first-line treatment for bipolar disorder (BD), a severe and disabling mental health disorder that affects about 1% of the population worldwide. Nevertheless, lithium is not consistently effective, with only 30% of patients showing a favorable response to treatment. To provide personalized treatment options for bipolar patients, it is essential to identify prediction biomarkers such as polygenic scores. In this study, we developed a polygenic score for lithium treatment response (Li+PGS) in patients with BD. To gain further insights into lithium's possible molecular mechanism of action, we performed a genome-wide gene-based analysis. Using polygenic score modeling, via methods incorporating Bayesian regression and continuous shrinkage priors, Li+PGS was developed in the International Consortium of Lithium Genetics cohort (ConLi+Gen: N = 2367) and replicated in the combined PsyCourse (N = 89) and BipoLife (N = 102) studies. The associations of Li+PGS and lithium treatment response - defined in a continuous ALDA scale and a categorical outcome (good response vs. poor response) were tested using regression models, each adjusted for the covariates: age, sex, and the first four genetic principal components. Statistical significance was determined at P < 0.05. Li+PGS was positively associated with lithium treatment response in the ConLi+Gen cohort, in both the categorical (P = 9.8 × 10-12, R2 = 1.9%) and continuous (P = 6.4 × 10-9, R2 = 2.6%) outcomes. Compared to bipolar patients in the 1st decile of the risk distribution, individuals in the 10th decile had 3.47-fold (95%CI: 2.22-5.47) higher odds of responding favorably to lithium. The results were replicated in the independent cohorts for the categorical treatment outcome (P = 3.9 × 10-4, R2 = 0.9%), but not for the continuous outcome (P = 0.13). Gene-based analyses revealed 36 candidate genes that are enriched in biological pathways controlled by glutamate and acetylcholine. Li+PGS may be useful in the development of pharmacogenomic testing strategies by enabling a classification of bipolar patients according to their response to treatment.

PMID:37433967 | DOI:10.1038/s41380-023-02149-1

Stat Methods Med Res. 2023 Jul 11:9622802231181704. doi: 10.1177/09622802231181704. Online ahead of print.

ABSTRACT

Parallel design and crossover design are two of the most frequently used designs for studying drug-gene interactions. Due to the concerns of statistical power and ethics, it is often more prudent to use the crossover design while allowing the patients to have choices of not switching the treatment if the first stage treatment is effective. This complicates the calculation of the required sample size to achieve pre-specified statistical power. We propose a method to determine the required sample size with a closed-form formula. The proposed approach is applied to determine the sample size of an adaptive crossover trial in studying gene-drug interaction in treating atrial fibrillation, the most common cardiac arrhythmia in clinical practice. Our simulation study confirms the power achieved by the sample size determined using the proposed approach. Issues related to the adaptive crossover trial are also discussed and practical guidelines are provided.

PMID:37431594 | DOI:10.1177/09622802231181704

Bioimpacts. 2023;13(3):181-182. doi: 10.34172/bi.2023.27686. Epub 2023 May 1.

NO ABSTRACT

PMID:37431482 | PMC:PMC10329749 | DOI:10.34172/bi.2023.27686

Pharm Res. 2023 Jul 10. doi: 10.1007/s11095-023-03558-1. Online ahead of print.

ABSTRACT

INTRODUCTION: Polymorphisms in the Thiopurine S-Methyltransferase (TPMT) gene are associated with decreased TPMT activity, but little is known about their impact on TPMT protein expression in the liver. This project is to conduct a genome-wide association study (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with altered TPMT protein expression in human livers and to determine if demographics affect hepatic TPMT protein expression.

METHODS: Human liver samples (n = 287) were genotyped using a whole genome genotyping panel and quantified for TPMT protein expression using a Data-Independent Acquisition proteomics approach.

RESULTS AND DISCUSSION: Thirty-one SNPs were found to be associated with differential expression of TPMT protein in the human livers. Subsequent analysis, conditioning on rs1142345, a SNP associated with the TPMT*3A and TPMT*3C alleles, showed no additional independent signals. Mean TPMT expression is significantly higher in wildtype donors compared to those carrying the known TPMT alleles, including TPMT*3A, TPMT*3C, and TPMT*24 (0.107 ± 0.028 vs. 0.052 ± 0.014 pmol/mg total protein, P = 2.2 × 10-16). After removing samples carrying the known TPMT variants, European ancestry donors exhibited significantly higher expression than African ancestry donors (0.109 ± 0.026 vs. 0.090 ± 0.041 pmol/mg total protein, P = 0.020).

CONCLUSION: The GWAS identified 31 SNPs associated with TPMT protein expression in human livers. Hepatic TPMT protein expression was significantly lower in subjects carrying the TPMT*3A, TPMT*3C, and TPMT*24 alleles compared to non-carriers. European ancestry was associated with significantly higher hepatic TPMT protein expression than African ancestry, independent of known TPMT variants.

PMID:37430149 | DOI:10.1007/s11095-023-03558-1

Per Med. 2023 Jul 10. doi: 10.2217/pme-2022-0117. Online ahead of print.

ABSTRACT

Aim: Interindividual and interethnic differences in drug efficacy drive the development and progress of pharmacogenomics and precision medicine. This study was performed to enrich the pharmacogenomic information for the Lisu population from China. Methods: Fifty-four very important pharmacogene variants were selected from PharmGKB and genotyped in 199 Lisu individuals. The genotype distribution data of 26 populations were downloaded from the 1000 Genomes Project and analyzed with the χ2 test. Results: Among the 26 populations in the 1000 Genomes Project, African Caribbeans in Barbados; Esan in Nigeria; Gambian in Western Divisions, The Gambia; Luhya in Webuye, Kenya; Yoruba in Ibadan; Finnish in Finland; Toscani in Italy and Sri Lankan Tamil in the UK were the top eight nationalities with the most significant differences in genotype distribution from the Lisu population. The loci of CYP3A5 rs776746, KCNH2 rs1805123, ACE rs4291, SLC19A1 rs1051298 and CYP2D6 rs1065852 were significantly different in the Lisu. Conclusion: The results showed that there were substantial differences in SNPs of very important pharmacogene variants, which can provide a theoretical basis for individualized drug use for the Lisu.

PMID:37427690 | DOI:10.2217/pme-2022-0117

Pharmacogenomics. 2023 Jul 10. doi: 10.2217/pgs-2023-0100. Online ahead of print.

NO ABSTRACT

PMID:37427432 | DOI:10.2217/pgs-2023-0100

Front Oncol. 2023 Jun 22;13:1239304. doi: 10.3389/fonc.2023.1239304. eCollection 2023.

NO ABSTRACT

PMID:37427122 | PMC:PMC10325716 | DOI:10.3389/fonc.2023.1239304

Pharmgenomics Pers Med. 2023 Jul 3;16:693-706. doi: 10.2147/PGPM.S415259. eCollection 2023.

ABSTRACT

PURPOSE: Pharmacogenetics (PGx) is an emerging aspect of personalized medicine with the potential to increase efficacy and safety of pharmacotherapy. However, PGx testing is still not routinely integrated into clinical practice. We conducted an observational case series study where PGx information from a commercially available panel test covering 30 genes was integrated into medication reviews. The aim of the study was to identify the drugs that are most frequently object of drug-gene-interactions (DGI) in the study population.

PATIENTS AND METHODS: In out-patient and in-patient settings, we recruited 142 patients experiencing adverse drug reaction (ADR) and/or therapy failure (TF). Collected anonymized data from the individual patient was harmonized and transferred to a structured database.

RESULTS: The majority of the patients had a main diagnosis of a mental or behavioral disorder (ICD-10: F, 61%), of musculoskeletal system and connective tissue diseases (ICD-10: M, 21%), and of the circulatory system (ICD-10: I, 11%). The number of prescribed medicines reached a median of 7 per person, resulting in a majority of patients with polypharmacy (≥5 prescribed medicines, 65%). In total, 559 suspected DGI were identified in 142 patients. After genetic testing, an association with at least one genetic variation was confirmed for 324 suspected DGI (58%) caused by 64 different drugs and 21 different genes in 141 patients. After 6 months, PGx-based medication adjustments were recorded for 62% of the study population, whereby differences were identified in subgroups.

CONCLUSION: The data analysis from this study provides valuable insights for the main focus of further research in the context of PGx. The results indicate that most of the selected patients in our sample represent suitable target groups for PGx panel testing in clinical practice, notably those taking drugs for mental or behavioral disorder, circulatory diseases, immunological diseases, pain-related diseases, and patients experiencing polypharmacy.

PMID:37426898 | PMC:PMC10327911 | DOI:10.2147/PGPM.S415259

Front Pharmacol. 2023 Jun 22;14:1195778. doi: 10.3389/fphar.2023.1195778. eCollection 2023.

ABSTRACT

Complex regions in the human genome such as repeat motifs, pseudogenes and structural (SVs) and copy number variations (CNVs) present ongoing challenges to accurate genetic analysis, particularly for short-read Next-Generation-Sequencing (NGS) technologies. One such region is the highly polymorphic CYP2D loci, containing CYP2D6, a clinically relevant pharmacogene contributing to the metabolism of >20% of common drugs, and two highly similar pseudogenes, CYP2D7 and CYP2D8. Multiple complex SVs, including CYP2D6/CYP2D7-derived hybrid genes are known to occur in different configurations and frequencies across populations and are difficult to detect and characterize accurately. This can lead to incorrect enzyme activity assignment and impact drug dosing recommendations, often disproportionally affecting underrepresented populations. To improve CYP2D6 genotyping accuracy, we developed a PCR-free CRISPR-Cas9 based enrichment method for targeted long-read sequencing that fully characterizes the entire CYP2D6-CYP2D7-CYP2D8 loci. Clinically relevant sample types, including blood, saliva, and liver tissue were sequenced, generating high coverage sets of continuous single molecule reads spanning the entire targeted region of up to 52 kb, regardless of SV present (n = 9). This allowed for fully phased dissection of the entire loci structure, including breakpoints, to accurately resolve complex CYP2D6 diplotypes with a single assay. Additionally, we identified three novel CYP2D6 suballeles, and fully characterized 17 CYP2D7 and 18 CYP2D8 unique haplotypes. This method for CYP2D6 genotyping has the potential to significantly improve accurate clinical phenotyping to inform drug therapy and can be adapted to overcome testing limitations of other clinically challenging genomic regions.

PMID:37426826 | PMC:PMC10324673 | DOI:10.3389/fphar.2023.1195778

JHEP Rep. 2023 Mar 22;5(7):100742. doi: 10.1016/j.jhepr.2023.100742. eCollection 2023 Jul.

ABSTRACT

BACKGROUND & AIMS: Incidence rates of liver cancer in most populations are two to three times higher among men than women. The higher rates among men have led to the suggestion that androgens are related to increased risk whereas oestrogens are related to decreased risk. This hypothesis was investigated in the present study via a nested case-control analysis of pre-diagnostic sex steroid hormone levels among men in five US cohorts.

METHODS: Concentrations of sex steroid hormones and sex hormone-binding globulin were quantitated using gas chromatography-mass spectrometry and a competitive electrochemiluminescence immunoassay, respectively. Multivariable conditional logistic regression was used to calculate odds ratios (ORs) and 95% CIs for associations between hormones and liver cancer among 275 men who subsequently developed liver cancer and 768 comparison men.

RESULTS: Higher concentrations of total testosterone (OR per one-unit increase in log2 = 1.77, 95% CI = 1.38-2.29), dihydrotestosterone (OR = 1.76, 95% CI = 1.21-2.57), oestrone (OR = 1.74, 95% CI = 1.08-2.79), total oestradiol (OR = 1.58, 95% CI=1.22-20.05), and sex hormone-binding globulin (OR = 1.63, 95% CI = 1.27-2.11) were associated with increased risk. Higher concentrations of dehydroepiandrosterone (DHEA), however, were associated with a 53% decreased risk (OR = 0.47, 95% CI = 0.33-0.68).

CONCLUSIONS: Higher concentrations of both androgens (testosterone, dihydrotestosterone) and their aromatised oestrogenic metabolites (oestrone, oestradiol) were observed among men who subsequently developed liver cancer compared with men who did not. As DHEA is an adrenal precursor of both androgens and oestrogens, these results may suggest that a lower capacity to convert DHEA to androgens, and their subsequent conversion to oestrogens, confers a lower risk of liver cancer, whereas a greater capacity to convert DHEA confers a greater risk.

IMPACT AND IMPLICATIONS: This study does not fully support the current hormone hypothesis as both androgen and oestrogen levels were associated with increased risk of liver cancer among men. The study also found that higher DHEA levels were associated with lower risk, thus suggesting the hypothesis that greater capacity to convert DHEA could be associated with increased liver cancer risk among men.

PMID:37425211 | PMC:PMC10326694 | DOI:10.1016/j.jhepr.2023.100742

Front Cardiovasc Med. 2023 Jun 23;10:1161029. doi: 10.3389/fcvm.2023.1161029. eCollection 2023.

ABSTRACT

In the era of Precision Medicine the approach to disease diagnosis, treatment, and prevention is being transformed across medical specialties, including Cardiology, and increasingly involves genomics approaches. The American Heart Association endorses genetic counseling as an essential component in the successful delivery of cardiovascular genetics care. However, with the dramatic increase in the number of available cardiogenetic tests, the demand, and the test result complexity, there is a need not only for a greater number of genetic counselors but more importantly, for highly specialized cardiovascular genetic counselors. Consequently, there is a pressing need for advanced cardiovascular genetic counseling training, along with innovative online services, telemedicine, and patient-facing digital tools, as the most effective way forward. The speed of implementation of these reforms will be of essence in the translation of scientific advancements into measurable benefits for patients with heritable cardiovascular disease and their families.

PMID:37424912 | PMC:PMC10325680 | DOI:10.3389/fcvm.2023.1161029

Front Genet. 2023 Jun 23;14:1213457. doi: 10.3389/fgene.2023.1213457. eCollection 2023.

ABSTRACT

Nanopore sequencing has been examined as a method for rapid and high-resolution human leukocyte antigen (HLA) typing in recent years. We aimed to apply ultrarapid nanopore-based HLA typing for HLA class I alleles associated with drug hypersensitivity, including HLA-A*31:01, HLA-B*15:02, and HLA-C*08:01. Most studies have used the Oxford Nanopore Ligation Sequencing kit for HLA typing, which requires several enzymatic reactions and remains relatively expensive, even when the samples are multiplexed. Here, we used the Oxford Nanopore Rapid Barcoding kit, which is transposase-based, with library preparation taking less than 1 h of hands-on time and requiring minimal reagents. Twenty DNA samples were genotyped for HLA-A, -B, and -C; 11 samples were from individuals of different ethnicity and nine were from Thai individuals. Two primer sets, a commercial set and a published set, were used to amplify the HLA-A, -B, and -C genes. HLA-typing tools that used different algorithms were applied and compared. We found that without using several third-party reagents, the transposase-based method reduced the hands-on time from approximately 9 h to 4 h, making this a viable approach for obtaining same-day results from 2 to 24 samples. However, an imbalance in the PCR amplification of different haplotypes could affect the accuracy of typing results. This work demonstrates the ability of transposase-based sequencing to report 3-field HLA alleles and its potential for race- and population-independent testing at considerably decreased time and cost.

PMID:37424729 | PMC:PMC10326273 | DOI:10.3389/fgene.2023.1213457