A comprehensive Thai pharmacogenomics database (TPGxD-1): Phenotype prediction and variants identification in 942 whole-genome sequencing data.

Computational methods analyze genomic data to identify genetic variants linked to drug responses, thereby guiding personalized medicine. This study analyzed 942 whole-genome sequences from the Electricity Generating Authority of Thailand (EGAT) cohort to establish a population-specific pharmacogenomic database (TPGxD-1) in the Thai population. Sentieon (version 201808.08) implemented the GATK best workflow practice for variant calling. We then annotated variant call format (VCF) files using Golden Helix VarSeq 2.5.0 and employed Stargazer v2.0.2 for star allele analysis. The analysis of 63 very important pharmacogenes (VIPGx) reveals 85,566 variants, including 13,532 novel discoveries. Notably, we identified 464 known PGx variants and 275 clinically relevant novel variants. The phenotypic prediction of 15 VIPGx demonstrated a varied metabolic profile for the Thai population. Genes like CYP2C9 (9%), CYP3A5 (45.2%), CYP2B6 (9.4%), NUDT15 (15%), CYP2D6 (47%) and CYP2C19 (43%) showed a high number of intermediate metabolizers; CYP3A5 (41%), and CYP2C19 (9.9%) showed more poor metabolizers. CYP1A2 (52.7%) and CYP2B6 (7.6%) were found to have a higher number of ultra-metabolizers. The functional prediction of the remaining 10 VIPGx genes reveals a high frequency of decreased functional alleles in SULT1A1 (12%), NAT2 (84%), and G6PD (12%). SLCO1B1 reports 20% poor functional alleles, while PTGIS (42%), SLCO1B1 (4%), and TPMT (5.96%) showed increased functional alleles. This study discovered new variants and alleles in the 63 VIPGx genes among the Thai population, offering insights into advancing clinical pharmacogenomics (PGx). However, further validation is needed using other computational and genotyping methods.

Association of genetic variation on X chromosome with systemic lupus erythematosus in both Thai and Chinese populations.

OBJECTIVES: X chromosome has been considered as a risk factor for SLE, which is a prototype of autoimmune diseases with a significant sex difference (female:male ratio is around 9:1). Our study aimed at exploring the association of genetic variants in X chromosome and investigating the influence of trisomy X in the development of SLE. METHODS: X chromosome-wide association studies were conducted using data from both Thai (835 patients with SLE and 2995 controls) and Chinese populations (1604 patients with SLE and 3324 controls). Association analyses were performed separately in females and males, followed by a meta-analysis of the sex-specific results. In addition, the dosage of X chromosome in females with SLE were also examined. RESULTS: Our analyses replicated the association of TMEM187-IRAK1-MECP2, TLR7, PRPS2 and GPR173 loci with SLE. We also identified two loci suggestively associated with SLE. In addition, making use of the difference in linkage disequilibrium between Thai and Chinese populations, a synonymous variant in TMEM187 was prioritised as a likely causal variant. This variant located in an active enhancer of immune-related cells, with the risk allele associated with decreased expression level of TMEM187. More importantly, we identified trisomy X (47,XXX) in 5 of 2231 (0.22%) females with SLE. The frequency is significantly higher than that found in the female controls (0.08%; two-sided exact binomial test P=0.002). CONCLUSION: Our study confirmed previous SLE associations in X chromosome, and identified two loci suggestively associated with SLE. More importantly, our study indicated a higher risk of SLE for females with trisomy X.

Infantile onset Sandhoff disease: clinical manifestation and a novel common mutation in Thai patients.

BACKGROUND: Sandhoff disease (SD) is an autosomal recessive lysosomal storage disorder, resulting in accumulation of GM2 ganglioside, particular in neuronal cells. The disorder is caused by deficiency of ß-hexosaminidase B (HEX-B), due to pathogenic variant of human HEXB gene. METHOD: This study describes clinical features, biochemical, and genetic defects among Thai patients with infantile SD during 2008-2019. RESULTS: Five unrelated Thai patients presenting with developmental regression, axial hypotonia, seizures, exaggerated startle response to noise, and macular cherry red spot were confirmed to have infantile SD based on deficient HEX enzyme activities and biallelic variants of the HEXB gene. In addition, an uncommon presenting feature, cardiac defect, was observed in one patient. All the patients died in their early childhood. Plasma total HEX and HEX-B activities were severely deficient. Sequencing analysis of HEXB gene identified two variants including c.1652G>A (p.Cys551Tyr) and a novel variant of c.761T>C (p.Leu254Ser), in 90 and 10% of the mutant alleles found, respectively. The results from in silico analysis using multiple bioinformatics tools were in agreement that the p.Cys551Tyr and the p.Leu254Ser are likely pathogenic variants. Molecular modelling suggested that the Cys551Tyr disrupt disulfide bond, leading to protein destabilization while the Leu254Ser resulted in change of secondary structure from helix to coil and disturbing conformation of the active site of the enzyme. Genome-wide SNP array analysis showed no significant relatedness between the five affected individuals. These two variants were not present in control individuals. The prevalence of infantile SD in Thai population is estimated 1 in 1,458,521 and carrier frequency at 1 in 604. CONCLUSION: The study suggests that SD likely represents the most common subtype of rare infantile GM2 gangliosidosis identified among Thai patients. We firstly described a potential common variant in HEXB in Thai patients with infantile onset SD. The data can aid a rapid molecular confirmation of infantile SD starting with the hotspot variant and the use of expanded carrier testing.

PROC Promoter Single Nucleotide Polymorphisms Associated With Low Protein C Activity But Not Increased Risk of Thromboembolism in Pediatric Population.

Protein C (PC) deficiency, caused by mutations of the PROC gene, is a common inherited risk factor of thromboembolism (TE) among Thai people. This study aimed to investigate the association of 3 single nucleotide polymorphisms (SNPs; -1654 C/T, -1641 A/G, -1461A/T) at the PROC promoter region with PC activity and the risk of developing TE. A total of 216 patient s with TE, diagnosed at aged 0 to 20 years, and 102 healthy adults were enrolled. The SNPs were identified by Sanger sequencing. Protein C activity was measured using an automated functional clotting assay. Linear and logistic regression analyses were used to determine the association of SNPs with PC activity and the risk of TE. Patients and controls with homozygous TAA (119.6% ± 26.1%) and CGT haplotypes (102.7% ± 22.6%) had significantly lower PC activity than those with a homozygous CAA haplotype (140.4% ± 44.9%); P = .027 and .016, respectively. However, none of these haplotypes increased the risk of TE. This study suggested that the 3 PROC promoter SNPs were shown to be associated with lower PC activity but did not increase the risk of TE.

Contribution of Four Polymorphisms in Renin-Angiotensin-Aldosterone-Related Genes to Hypertension in a Thai Population.

INTRODUCTION: The roles of genes in the renin-angiotensin-aldosterone system (RAAS) in hypertension, including angiotensin-converting enzyme (ACE), angiotensinogen (AGT), angiotensin II receptor type 1 (AGTR1), and aldosterone synthase (CYP11B2), have been widely studied across different ethnicities, but there has been no such investigation in Thai population. MATERIALS AND METHODS: Using 4,150 Thais recorded in the Electricity Generating Authority of Thailand (EGAT) study, we examined the association of rs1799752, rs699, rs5186, and rs1799998 located in or near ACE, AGT, AGTR1, and CYP11B2 genes in hypertension. We investigated their roles in hypertension using multivariate logistic regression and further examined their roles in blood pressure (BP) using quantile regression. Sex, age, and BMI were adjusted as potential confounders. RESULTS: We did not observe associations between hypertension and rs1799752 (P=0.422), rs699 (P=0.36), rs5186 (P=0.49), and rs1799998 (P=0.71). No evidence of association between these SNPs and BP was found across an entire distribution. A nonlinear relationship between age and BP was observed. CONCLUSION: In Thai population, our study showed no evidence of association between RAAS-related genes and hypertension. While our study is the first and largest study to investigate the role of RAAS-related genes in hypertension in Thai population, restricted statistical power due to limited sample size is a limitation.

Precision medicine in Thailand.

Extraordinary advances in high throughput next generation sequencing (NGS) technology and bioinformatics are the main thrust that transforms the current state of healthcare into the era of precision medicine where clinical practice takes individual variability into account. Here, we summarize the current status of the infrastructure we have and the adoption of precision medicine in Thailand in four spheres: rare diseases, oncology, pharmacogenomics, and noncommunicable diseases. Moreover, we provide our perspectives to the future of precision medicine in Thailand, especially the manpower and ethical, legal, and social issues. We believe that with decreasing costs of NGS, increasing ability to interpret the genomic data, a greater number of actionable and available treatments, implementation of precision medicine at the public health level is not a matter of if but when.

Examination of previously identified associations within the Genetic Analysis Workshop 19 data.

We investigate the possible replication of "known" associated single-nucleotide polymorphisms (SNPs) with blood pressure and expression phenotypes. Previous studies have provided a list of 95 SNPs thought to be associated with blood pressure phenotypes, of which 44 were present in the Genetic Analysis Workshop 19 (GAW19) family-imputed genome-wide association studies (GWAS) data and 4 in the GAW19 unrelateds sequence data. Using only the real (not simulated) GAW19 data, we show through the use of statistical tests that account for family relatedness, using FaST-LMM (Factored Spectrally Transformed Linear Mixed Model), that none of our candidate SNPs yields a significant p value. Furthermore, a study of epistasis, aiming to detect statistical interactions between loci with respect to their association with transcription levels has provided a list of 30 associated interacting SNP pairs, of which 13 are present in the GAW19 family GWAS and expression data. We show for this set of results, using the program GEMMA (genome-wide efficient mixed-model analysis) to account for family relatedness, that there is evidence of replication within the real GAW19 data. Two individual SNP pairs reach significance, and the set of remaining results give a combined p value of 0.017 that at least 1 of these remaining SNP pairs interacts to influence an expression phenotype.

Accounting for relatedness in family-based association studies: application to Genetic Analysis Workshop 18 data.

In the last few years, a bewildering variety of methods/software packages that use linear mixed models to account for sample relatedness on the basis of genome-wide genomic information have been proposed. We compared these approaches as implemented in the programs EMMAX, FaST-LMM, Gemma, and GenABEL (FASTA/GRAMMAR-Gamma) on the Genetic Analysis Workshop 18 data. All methods performed quite similarly and were successful in reducing the genomic control inflation factor to reasonable levels, particularly when the mean values of the observations were used, although more variation was observed when data from each time point were used individually. From a practical point of view, we conclude that it makes little difference to the results which method/software package is used, and the user can make the choice of package on the basis of personal taste or computational speed/convenience.

Comparison of methods to account for relatedness in genome-wide association studies with family-based data.

Approaches based on linear mixed models (LMMs) have recently gained popularity for modelling population substructure and relatedness in genome-wide association studies. In the last few years, a bewildering variety of different LMM methods/software packages have been developed, but it is not always clear how (or indeed whether) any newly-proposed method differs from previously-proposed implementations. Here we compare the performance of several LMM approaches (and software implementations, including EMMAX, GenABEL, FaST-LMM, Mendel, GEMMA and MMM) via their application to a genome-wide association study of visceral leishmaniasis in 348 Brazilian families comprising 3626 individuals (1972 genotyped). The implementations differ in precise details of methodology implemented and through various user-chosen options such as the method and number of SNPs used to estimate the kinship (relatedness) matrix. We investigate sensitivity to these choices and the success (or otherwise) of the approaches in controlling the overall genome-wide error-rate for both real and simulated phenotypes. We compare the LMM results to those obtained using traditional family-based association tests (based on transmission of alleles within pedigrees) and to alternative approaches implemented in the software packages MQLS, ROADTRIPS and MASTOR. We find strong concordance between the results from different LMM approaches, and all are successful in controlling the genome-wide error rate (except for some approaches when applied naively to longitudinal data with many repeated measures). We also find high correlation between LMMs and alternative approaches (apart from transmission-based approaches when applied to SNPs with small or non-existent effects). We conclude that LMM approaches perform well in comparison to competing approaches. Given their strong concordance, in most applications, the choice of precise LMM implementation cannot be based on power/type I error considerations but must instead be based on considerations such as speed and ease-of-use.

Noonan syndrome, metabolic syndrome and stroke-in-the-young: coincidence, causal or contribution?

A 34-year-old Thai woman developed acute left hemiparesis with dysarthria from subcortical infarction of the right MCA territory eighteen months after being diagnosed with Noonan syndrome, diabetes mellitus, dyslipidaemia, and hypertension. Further investigations suggested atherosclerosis as a cause. Modifying her risk factors was difficult, partly because of limited adherence. Three years later, she had another attack of ischaemic stroke in the same area. Unlike the three previously reported cases, the causation of strokes in this patient appeared to be a more 'complex' interaction between genetic defect and environment including possible subtle arterial abnormalities, metabolic risk factors, and mental insufficiency.

Congestive heart failure with rhabdomyolysis and acute renal failure in a manifesting female carrier of Duchenne muscular dystrophy with duplication of dystrophin gene.

We report a 69-year-old woman who presented with dyspnea, orthopnea, and acute renal failure. She also had proximal muscle weakness suggestive of muscle disease. Her symptoms were alleviated by induced dieresis, although there was high-serum creatine kinase. Investigations for any possible etiologies of rhabdomyolysis were all negative. An X-linked recessive muscle disease was highly suspicious in view of the fact that both of her sons had suffered from muscle disease and died of respiratory failure at the ages of 22 and 29, respectively. Her muscle biopsy showed mosaic pattern with dystrophin antibody against amino-terminal, carboxy-terminal, and rod domain. Her DNA study revealed heterozygous duplication at exon 1 to 6 of the dystrophin gene as well. Therefore, she is a manifesting carrier of dystrophinopathy who was first diagnosed in late adulthood with congestive heart failure, acute episode of spontaneous rhabdomyolysis, and acute renal failure.

Frequencies of spinocerebellar ataxia subtypes in Thailand: window to the population history?

Spinocerebellar ataxias (SCAs) are a heterogeneous group of disorders with almost 30 subtypes. The prevalence and relative frequency of each subtype vary among different populations. In this article, we report the relative frequency of six SCA subtypes in the Thai population and attempt to explain the observed pattern when compared with other populations in this region. We searched for SCA type 1, SCA2, SCA3, SCA6, SCA7 and dentatorubral-pallidoluysian atrophy mutations using GeneScan analysis in 340 patients from 182 families, in which at least one person had a clinical diagnosis of SCA. We analyzed the relative frequencies of SCA subtypes on a family basis, and compared these with the data in the Chinese and Indian populations. SCA3 was found in 19.2% of the patients (Agresti-Coull 95% confidence interval: 14.1-25.6%), SCA1 in 11.5% (7.6-17.1%) and SCA2 in 10.4% (6.7-15.8%). SCA6 was found in three families, with a relative frequency of 1.6% (0.3-5.0%). Compared with the related populations, the Thai SCA3 frequency was less than that of the Chinese, whereas it was higher than that in most of the Indian studies. The reverse is true for the SCA1/SCA2 frequency. A similar study in Singapore, where there was a clear history of population admixture, also showed the frequencies between those of the Chinese and the Indian populations. Although SCA3 was the most common identifiable SCA subtype in Thailand, SCA1 and SCA2 were also relatively common. Our results also supported some degree of admixture with the Indians in the Thai population and justify further study in the area.

Association of estrogen receptor-alpha single-nucleotide polymorphism (codon 594 G-->A) and Thai patients affected by knee osteoarthritis.

BACKGROUND: Estrogen receptor-alpha single-nucleotide polymorphism (ER-alpha SNP) has previously shown its susceptibility to knee osteoarthritis (OA) but this association cannot be applied to ethnic groups with different genetic backgrounds. OBJECTIVE: To characterize the genetic association between ER-alpha SNP and knee OA in the Thai. MATERIAL AND METHOD: A case-control study was conducted at Ramathibodi Hospital from August 2007 to May 2008. Altogether, 104 cases affected by knee OA and 104 controls were included in this study. SNP rs2228480 (codon 594 G!A) on the ER-alpha gene was genotyped by a PCR-RFLP-based technique. Genotype frequencies were analyzed by logistic regression. RESULTS: ER-alpha SNP was normally distributed through the Hardy-Weinberg Equilibrium (HWE). The risk of knee OA was genetically associated to AG an AA genotypes compàred with homozygous wild-type GG (OR: 1.02, 95% CI: 0.60-1.80 for AG; OR: 1.27, 95% CI: 0.30-4.90 for AA). CONCLUSION: Our study showed that these genetic alterations might be associated with knee osteoarthritis in the Thai population. Further investigation on other informative SNPs on the ER-alpha gene should be performed to create a reliable haplotype that might provide a stronger link between genetic profiles and clinical picture.

Sensitivity and frequencies of dystrophin gene mutations in Thai DMD/BMD patients as detected by multiplex PCR.

BACKGROUND: Duchenne muscular dystrophy (DMD), a lethal X-linked disease affecting 1 in 3500 male births, and its more benign variant, Becker muscular dystrophy (BMD), are caused by mutations in the dystrophin gene. Because of its large size, analysing the whole gene is impractical. Methods have been developed to detect the commonest mutations i.e. the deletions of the exons. Although these tests are highly specific, their sensitivity is inherently limited by the prevalence of deletions, which differs among different populations. METHODS: We reviewed our database for the detection of Dystrophin gene mutation by means of 31-exon multiplex PCR in Thai males, diagnosed clinically and biochemically with DMD or BMD from July 1994 to November 2006. One index patient was chosen from each family for statistical analysis. The overall sensitivity of the test, the number of fragment deleted, and the deletion frequency of each fragment were calculated, along with their 95% confidence intervals (C.I.). RESULTS: We found deletions in 99 out of the 202 index patients (49%; Bayesian 95% C.I.=42%-56%). 51% of these had deletion in only one of the 31 exons tested, while the patient with the most extensive deletions had 14 exons deleted. The mean number of deleted exons were 2.84 (BC(a) bootstrap 95% C.I.=2.37-3.48), or 5.02 (3.81-6.85) if all the untested exons adjacent to the confirmed deleted exons were assumed to be deleted. The region spanning exons 44-52 was the most frequently deleted. These were similar to those reported in the Japanese. CONCLUSION: The multiplex PCR detected deletions only in about half of the Thai patients. The diseases therefore should not be excluded solely on the negative result if DMD/BMD is strongly suspected.