[Show abstract][Hide abstract] ABSTRACT: Dyskeratosis congenita (DKC) is a rare inherited disease that is characterized by abnormal skin pigmentation, nail dystrophy and mucosal leukoplakia. DKC is caused by an abnormality in a component of the telomerase and shelterin complexes. TINF2 encodes a protein in the shelterin complex and TERC encodes a component of the telomerase complex. Mutations of both genes have been associated with DKC. This study examined mutations in TINF2 and TERC by direct DNA sequencing in a Thai patient with DKC. We identified a novel mutation (c.845G>T) that is located in exon 6 of TINF2 and changes an arginine to leucine (Arg282Leu). This identified mutation could be applied for molecular genetic diagnosis and genetic counseling of patients with DKC.
Full-text · Article · Sep 2015 · Case Reports in Dermatology
[Show abstract][Hide abstract] ABSTRACT: Genetic variants of the POMC and PCSK1 genes cause severe obesity among patients in the early stages of childhood. This family-based study analyzed the links between single nucleotide polymorphisms (SNPs) in either the POMC or PCSK1 genes and obesity, as well as obesity-related traits among obese Thai children and their families. The variants rs1042571 and rs6713532 in the POMC gene in a sample of 83 obese children and their family members were investigated using polymerase chain reaction (PCR)-restriction fragment length polymorphism. In addition, the SNPs rs6232, rs155971, rs3762986, rs3811942, and rs371897784 of PCSK1 were analyzed in all samples using PCR and gene sequencing methods. Participants with the homozygous variant genotype in rs155971 had significantly elevated cholesterol and low-density lipoprotein cholesterol (LDL-C) levels (P = 0.011, OR = 1.025, 95%CI = 1.006-1.045; and P = 0.006, OR = 1.030, 95%CI = 1.009-1.053, respectively) after adjustment for age, gender, and body mass index (BMI). In addition, patients with the heterozygous variant genotype in rs371897784 of PCSK1 had a 1.249- fold higher risk (95%CI = 1.081-1.444, P = 0.027) of increased waist circumference than patients with the normal genotype, after adjustment for age, gender, and BMI. However, this analysis did not find any correlation between obesity and SNPs in PCSK1 and POMC. Therefore, these common variants in PCSK1 and POMC were not the major cause of obesity in the Thai subjects sampled. However, variants in PCSK1 did affect cholesterol level, LDL-C level, and waist circumference.
No preview · Article · Sep 2015 · Genetics and molecular research: GMR
[Show abstract][Hide abstract] ABSTRACT: To determine the prognostic significance of deficient mismatch repair (dMMR) and BRAF V600E in Thai sporadic colorectal cancer (CRC) patients.
We studied a total of 211 out of 405 specimens obtained from newly diagnosed CRC patients between October 1, 2006 and December 31, 2007 at Siriraj Hospital, Mahidol University. Formalin-fixed paraffin-embedded blocks of CRC tissue samples were analyzed for dMMR by detection of MMR protein expression loss by immunohistochemistry or microsatellite instability using polymerase chain reaction (PCR)-DHPLC. BRAF V600E mutational analysis was performed in DNA extracted from the same archival tissues by two-round allele-specific PCR and analyzed by high sensitivity DHPLC. Associations between patient characteristics, MMR and BRAF status with disease-free survival (DFS) and overall survival (OS) were determined by Kaplan-Meier survival plots and log-rank test together with Cox's proportional hazard regression.
dMMR and BRAF V600E mutations were identified in 31 of 208 (14.9%) and 23 of 211 (10.9%) tumors, respectively. dMMR was more commonly found in patients with primary colon tumors rather than rectal cancer (20.4% vs 7.6%, P =0.01), but there was no difference in MMR status between the right-sided and left-sided colon tumors (20.8% vs 34.6%, P = 0.24). dMMR was associated with early-stage rather than metastatic disease (17.3% vs 0%, P = 0.015). No clinicopathological features such primary site or tumor differentiation were associated with the BRAF mutation. Six of 31 (19.3%) samples with dMMR carried the BRAF mutation, while 17 of 177 (9.6%) with proficient MMR (pMMR) harbored the mutation (P = 0.11). Notably, patients with dMMR tumors had significantly superior DFS (HR = 0.30, 95%CI: 0.15-0.77; P = 0.01) and OS (HR = 0.29, 95%CI: 0.10-0.84; P = 0.02) compared with patients with pMMR tumors. By contrast, the BRAF V600E mutation had no prognostic impact on DFS and OS.
The prevalence of dMMR and BRAF V600E in Thai sporadic CRC patients was 15% and 11%, respectively. The dMMR phenotype was associated with a favorable outcome.
Full-text · Article · Jan 2015 · World Journal of Gastroenterology
[Show abstract][Hide abstract] ABSTRACT: Single nucleotide polymorphisms (SNPs) in PCSK1, namely, rs6234, rs6235, and rs271939 have been linked to obesity in European population; and rs3811951 has also been connected to type 2 diabetes and obesity parameters in Chinese population. In this family-based case-control study, we analyzed links between PCSK1 genetic variants and obesity in Thai children and their families. Eleven obese children with a percent weight for height > or = 140 who had family history of obesity and 69 family members were recruited. SNPs rs6234, rs6235, rs3811951, and rs271939 of PCSK1 were analyzed using PCR and gene sequencing methods. DNA of 200 normal weight subjects was used as control. Participants with variant genotypes in the rs6234-6235 pair are at significantly more risk of being obese [OR = 2.44 (1.35-4.43), p = 0.003], and also at increased risk of being severely obese (obese class III) [OR = 3.03 (1.20-7.66), p = 0.015]. Variant rs3811951 showed no association with being obese, but is significantly linked to an increased risk of being severely obese [OR = 3.59 (1.42-9.08) p = 0.005]. Moreover, high density lipoprotein (HDL)-C levels between normal and variant rs3811951 group differed considerably, with patients with variant genotype having a lower HDL-C level (p = 0.037). Thus, Thais carrying SNPs rs6234-5 are at increased risk of being obese, and the risk of severe obesity increases when carrying both rs6234-5 and rs3811951, but not with rs271939. Furthermore, patients with genetic variations at rs3811951 are at risk of having low HDL-C levels.
No preview · Article · Jun 2014 · The Southeast Asian journal of tropical medicine and public health
[Show abstract][Hide abstract] ABSTRACT: Purpose:
To identify disease-causing mutations and describe genotype-phenotype correlations in Thai patients with nonsyndromic retinitis pigmentosa (RP).
Whole exome sequencing was performed in 20 unrelated patients. Eighty-six genes associated with RP, Leber congenital amaurosis, and cone-rod dystrophy were analyzed for variant detection.
Seventeen variants (13 novel and 4 known) in 13 genes were identified in 11 patients. These variants include 10 missense substitutions, 2 nonsense mutations, 3 deletions, 1 insertion, and 1 splice site change. Nine patients with identified inheritance patterns carried a total of 10 potentially pathogenic mutations located in genes CRB1, C8orf37, EYS, PROM1, RP2, and USH2A. Three of the nine patients also demonstrated additional heterozygous variants in genes ABCA4, GUCY2D, RD3, ROM1, and TULP1. In addition, two patients carried variants of uncertain significance in genes FSCN2 and NR2E3. The RP phenotypes of our patients were consistent with previous reports.
This is the first report of mutations in Thai RP patients. These findings are useful for genotype-phenotype comparisons among different ethnic groups.
No preview · Article · Mar 2014 · Investigative ophthalmology & visual science
[Show abstract][Hide abstract] ABSTRACT: Distal myopathy with rimmed vacuoles (DMRV) is an autosomal recessive or sporadic early adult-onset myopathy caused by mutations in the UDP-N-acetylglucosamine 2-epimerase and N-acetylmannosamine kinase (GNE) gene. Characteristic pathologic features of DMRV are rimmed vacuoles on muscle biopsy and tubulofilamentous inclusion in ultrastructural study. Presence of inflammation in DMRV is unusual. We report a sporadic case of DMRV in a 40-year-old Thai man who presented with slowly progressive distal muscle weakness. Gene analysis revealed a compound heterozygous mutation of the GNE gene including a novel mutation c.1057A>G (p.K353E) and a known mutation c.2086G>A (p.V696M). The latter is the most common mutation in Thai DMRV patients. The muscle pathology was compatible with DMRV except for focal inflammation.
Full-text · Article · Mar 2014 · Case Reports in Neurology
[Show abstract][Hide abstract] ABSTRACT: This article presents the ability of an omnibus permutation test on ensembles of two-locus analyses (2LOmb) to detect pure epistasis in the presence of genetic heterogeneity. The performance of 2LOmb is evaluated in various simulation scenarios covering two independent causes of complex disease where each cause is governed by a purely epistatic interaction. Different scenarios are set up by varying the number of available single nucleotide polymorphisms (SNPs) in data, number of causative SNPs and ratio of case samples from two affected groups. The simulation results indicate that 2LOmb outperforms multifactor dimensionality reduction (MDR) and random forest (RF) techniques in terms of a low number of output SNPs and a high number of correctly-identified causative SNPs. Moreover, 2LOmb is capable of identifying the number of independent interactions in tractable computational time and can be used in genome-wide association studies. 2LOmb is subsequently applied to a type 1 diabetes mellitus (T1D) data set, which is collected from a UK population by the Wellcome Trust Case Control Consortium (WTCCC). After screening for SNPs that locate within or near genes and exhibit no marginal single-locus effects, the T1D data set is reduced to 95,991 SNPs from 12,146 genes. The 2LOmb search in the reduced T1D data set reveals that 12 SNPs, which can be divided into two independent sets, are associated with the disease. The first SNP set consists of three SNPs from MUC21 (mucin 21, cell surface associated), three SNPs from MUC22 (mucin 22), two SNPs from PSORS1C1 (psoriasis susceptibility 1 candidate 1) and one SNP from TCF19 (transcription factor 19). A four-locus interaction between these four genes is also detected. The second SNP set consists of three SNPs from ATAD1 (ATPase family, AAA domain containing 1). Overall, the findings indicate the detection of pure epistasis in the presence of genetic heterogeneity and provide an alternative explanation for the aetiology of T1D in the UK population.
[Show abstract][Hide abstract] ABSTRACT: This paper presents a non-parametric classification technique for identifying
a candidate bi-allelic genetic marker set that best describes disease
susceptibility in gene-gene interaction studies. The developed technique
functions by creating a mapping between inferred haplotypes and case/control
status. The technique cycles through all possible marker combination models
generated from the available marker set where the best interaction model is
determined from prediction accuracy and two auxiliary criteria including
low-to-high order haplotype propagation capability and model parsimony. Since
variable-length haplotypes are created during the best model identification,
the developed technique is referred to as a variable-length haplotype
construction for gene-gene interaction (VarHAP) technique. VarHAP has been
benchmarked against a multifactor dimensionality reduction (MDR) program and a
haplotype interaction technique embedded in a FAMHAP program in various
two-locus interaction problems. The results reveal that VarHAP is suitable for
all interaction situations with the presence of weak and strong linkage
disequilibrium among genetic markers.
Full-text · Article · May 2013 · IEEE Engineering in Medicine and Biology Magazine
[Show abstract][Hide abstract] ABSTRACT: Background:
Prevention and control of severe β thalassemia by carrier detection and identification of couples at risk in developed countries is one of the most successful stories in modern medicine. Similar programs in developing countries especially Southeast Asia, are more problematic because both α and β thalassemias are highly prevalent. In Thailand, there are limited data on whether we could determine, based on hematological phenotypes, the mutation severity and/or coinheritance of α thalassemia in β thalassemia traits.
Comprehensive molecular, hematology and hemoglobin analyses of the α and β globin genes were performed in 141 healthy individuals identified as β thalassemia carriers.
Seventeen different β globin mutations were successfully identified out of all cases analyzed. Although the majority of the mutations identified were the β⁰ or severe β⁺ thalassemia alleles, a high proportion of mild mutations (25%) was observed. Of these β thalassemia traits, 22.3% were found to co-inherit the α thalassemias. Milder hematological phenotypes were noted in β⁺ compared with β⁰ thalassemia traits when the α globin genes were intact. Although co-inheritance of α⁰ thalassemia might be suspected in cases with skewed profiles, due to the overlapping values, it remains difficult to apply these parameters for reliable carrier determination.
A combination of hemoglobin analysis and DNA testing seems to be the best way to confirm carrier status in a region with high frequency for both α and β thalassemias. Underdiagnoses of carrier status could hamper the effectiveness of a thalassemia prevention and control program.
No preview · Article · Mar 2013 · Clinical Chemistry and Laboratory Medicine
[Show abstract][Hide abstract] ABSTRACT: CCT chaperonin is a highly conserved molecular chaperone, which plays an important role in the folding of complex proteins in mammalian cells. CCT chaperonin interacts with huntingtin and results in decrease of aggregate formation followed by increase of cell survival. Using yeast-two-hybrid system, we screen for specific CCT chaperonin subunit, which can recognize and bind to androgen receptor. We show that subunit 6 of CCT chaperonin interacts with androgen receptor. Interestingly, CCT chaperonin shows higher binding affinity to polyglutamine expanded androgen receptor than that of the wild-type. We prove this interaction in mammalian cell models, which show co-localization of androgen receptor and subunit 6 of CCT in cellular cytosol. Therefore, not only huntingtin but also androgen receptor is a polyglutamine expanded protein, which is a substrate of CCT chaperonin. Our results suggest that CCT might play an essential role in modulation of folding of polyglutamine expanded proteins and could be another target for further therapeutic studies.
Full-text · Article · Jul 2012 · European journal of medical genetics
[Show abstract][Hide abstract] ABSTRACT: Our earlier genome-wide expression study revealed up-regulation of a tryptophan-catabolizing enzyme, indoleamine 2,3-dioxygenase (IDO1), in patients with scrub typhus. This gene has been previously reported to have anti-microbial activity in a variety of infectious diseases; therefore, we aimed to prove whether it is also involved in host defense against Orientia tsutsugamushi (OT) infection.
Using LC-MS, we observed an increased ratio of serum L-kynurenine to serum L-tryptophan in patients with scrub typhus, which suggests an active catalytic function of this enzyme upon the illness. To evaluate the effect of IDO1 activation on OT infection, a human macrophage-like cell line THP-1 was used as a study model. Although transcription of IDO1 was induced by OT infection, its functional activity was not significantly enhanced unless the cells were pretreated with IFN-γ, a potent inducer of IDO1. When the degree of infection was evaluated by quantitative real-time PCR, the relative number of OT 47 kDa gene per host genes, or infection index, was markedly reduced by IFN-γ treatment as compared to the untreated cultures at five days post-infection. Inhibition of IDO1 activity in IFN-γ treated cultures by 1-methyl-L-tryptophan, a competitive inhibitor of IDO1, resulted in partial restoration of infection index; while excessive supplementation of L-tryptophan in IFN-γ treated cultures raised the index to an even higher level than that of the untreated ones. Altogether, these data implied that IDO1 was partly involved in restriction of OT growth caused by IFN-γ through deprivation of tryptophan.
Activation of IDO1 appeared to be a defensive mechanism downstream of IFN-γ that limited intracellular expansion of OT via tryptophan depletion. Our work provided not only the first link of in vivo activation of IDO1 and IFN-γ-mediated protection against OT infection but also highlighted the promise of this multifaceted gene in scrub typhus research.
[Show abstract][Hide abstract] ABSTRACT: A Thai woman, who was affected with neurofibromatosis type 1, was followed up and re-evaluated at ages 45, 61, and 67 years. Her mother and her three brothers were also affected. The proposita was very severely affected. She was born blind with underdeveloped eyeglobes and had large plexiform neurofibromas on her face. Her eyelids were gigantic and tears drained from the orifice between them. Cutaneous neurofibromas were observed all over her body. A novel mutation c.4821delA was identified in NF1 gene, which predicted truncation of neurofibromin (p.Leu1607fs).
No preview · Article · Jul 2012 · American Journal of Medical Genetics Part A