[Show abstract][Hide abstract] ABSTRACT: Purpose: To identify disease-causing mutations and describe genotype-phenotype correlations in Thai patients with nonsyndromic retinitis pigmentosa (RP). Methods: 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. Results: Seventeen variants (13 novel and four known) in 13 genes were identified in 11 patients. These variants include 10 missense substitutions, two nonsense mutations, three deletions, one insertion, and one 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. Conclusions: This is the first report of mutations in Thai RP patients. These findings are useful for genotype-phenotype comparisons among different ethnic groups.
[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.
[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.
IEEE Engineering in Medicine and Biology Magazine 05/2013; 28(4):25-31. · 2.73 Impact Factor
[Show abstract][Hide abstract] 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. Methods: Comprehensive molecular, hematology and hemoglobin analyses of the α and β globin genes were performed in 141 healthy individuals identified as β thalassemia carriers. Results: 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. Conclusions: 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.
Clinical Chemistry and Laboratory Medicine 03/2013; · 2.96 Impact Factor
[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: 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.
European journal of medical genetics 07/2012; 55(11):599-604. · 1.57 Impact Factor
[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).
American Journal of Medical Genetics Part A 06/2012; 158A(7):1750-3. · 2.30 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We characterized the chromosomal aberration in family with intellectual disability, including two affected children and their affected mother. Initial standard karyotypes of the three individuals showed an apparently balanced translocation of chromosomes 8 and 20. Using molecular cytogenetic techniques, we observed complex structural chromosomal aberration comprising of reciprocal translocation between chromosomes 8 and 20 with pericentric inversion (8p11.12q22.3) and insertion of chromosome 4 segments into both der(8) and der(20). In particular, the insertion of chromosome 4 was complex. Two segments (4q13.2-q13.3 and 4q21.21-q22.1) were inserted into the der(8)t(8;20) breakpoint and one segment (4q13.3-q21.21) into the der(20)t(8;20) breakpoint. Both children inherited two normal chromosomes 4 from their parents and the der(8) and der(20) from the mother, resulting in partial trisomy of 4q13.2-q22.1. Interestingly, the mother, in addition to the same complex insertions and inversion, was founded to have a deletion of 4q13.2-q22.1 in one of her chromosomes 4, yielding no genetic imbalance but with potential disruption of intellectual dysfunction-related gene(s) at the breakpoints as the cause of her intellectual impairment. This family is the third case report of an insertional translocation mechanism causing partial trisomy 4q syndrome. Our study demonstrates that an insertion of an extra chromosomal segment, not primarily involving in translocation breakpoints, which results in partial trisomy, can be an unapparent cause of the abnormal phenotypes.
American Journal of Medical Genetics Part A 03/2012; 158A(4):901-8. · 2.30 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This article presents the classification of blood characteristics by a C4.5 decision tree, a naïve Bayes classifier and a multilayer perceptron for thalassaemia screening. The aim is to classify eighteen classes of thalassaemia abnormality, which have a high prevalence in Thailand, and one control class by inspecting data characterised by a complete blood count (CBC) and haemoglobin typing. Two indices namely a haemoglobin concentration (HB) and a mean corpuscular volume (MCV) are the chosen CBC attributes. On the other hand, known types of haemoglobin from six ranges of retention time identified via high performance liquid chromatography (HPLC) are the chosen haemoglobin typing attributes. The stratified 10-fold cross-validation results indicate that the best classification performance with average accuracy of 93.23% (standard deviation=1.67%) and 92.60% (standard deviation=1.75%) is achieved when the naïve Bayes classifier and the multilayer perceptron are respectively applied to samples which have been pre-processed by attribute discretisation. The results also suggest that the HB attribute is redundant. Moreover, the achieved classification performance is significantly higher than that obtained using only haemoglobin typing attributes as classifier inputs. Subsequently, the naïve Bayes classifier and the multilayer perceptron are applied to an additional data set in a clinical trial which respectively results in accuracy of 99.39% and 99.71%. These results suggest that a combination of CBC and haemoglobin typing analysis with a naïve Bayes classifier or a multilayer perceptron is highly suitable for automatic thalassaemia screening.
Biomedical Signal Processing and Control 03/2012; · 1.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A protocol for the identification of Ancestry Informative Markers (AIMs) from genome-wide Single Nucleotide Polymorphism (SNP) data is proposed. The protocol consists of three main steps: identification of potential positive selection regions via F(ST) extremity measurement, SNP screening via two-stage attribute selection and classification model construction using a Naïve Bayes classifier. The two-stage attribute selection is composed of a newly developed round robin Symmetrical Uncertainty (SU) ranking technique and a wrapper embedded with a Naïve Bayes classifier. The protocol has been applied to the HapMap Phase II data. Two AIM panels, which consist of 10 and 16 SNPs that lead to complete classification between CEU, CHB, JPT and YRI populations, are identified. Moreover, the panels are at least four times smaller than those reported in previous studies. The results suggest that the protocol could be useful in a scenario involving a larger number of populations.
International Journal of Data Mining and Bioinformatics 01/2012; 6(6):651-74. · 0.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To develop CYP2D6 genotyping scheme for accurate allele calling and reliable estimation of functional allele dosage in Thais.
We analyzed CYP2D6 copy numbers by pentaplex PCR coupled with semi-quantitative denaturing high performance liquid chromatography (DHPLC)-based technique. Ten common SNPs were genotyped from CYP2D6 gene product using single base extension (SBE) followed by DHPLC analysis. This detection scheme was compared with real-time PCR and conventional PCR-RFLP for cost-effectiveness.
The distribution of CYP2D6 gene copy numbers in our population ranged from zero (0.69%), one (7.99%), two (60.07%), three (28.13%) and four (3.13%). The most commonly detected SNPs were related to CYP2D6*10 haplotype. CYP2D6*36 in tandem with CYP2D6*10B is the major rearrangement type in Thais (18.75%).
Multiplex PCR coupled with DHPLC-based strategy is convenient and reliable method for CYP2D6 genotyping offering sufficient allele coverage for Asians. Both cost and analytical time saving were shown and the method could potentially be modified to accommodate CYP2D6 genotyping in other ethnics.
[Show abstract][Hide abstract] ABSTRACT: Orientia tsutsugamushi is the causal agent of scrub typhus, a public health problem in the Asia-Pacific region and a life-threatening disease. O. tsutsugamushi is an obligate intracellular bacterium that mainly infects endothelial cells. We demonstrated here that O. tsutsugamushi also replicated in monocytes isolated from healthy donors. In addition, O. tsutsugamushi altered the expression of more than 4,500 genes, as demonstrated by microarray analysis. The expression of type I interferon, interferon-stimulated genes and genes associated with the M1 polarization of macrophages was significantly upregulated. O. tsutsugamushi also induced the expression of apoptosis-related genes and promoted cell death in a small percentage of monocytes. Live organisms were indispensable to the type I interferon response and apoptosis and enhanced the expression of M1-associated cytokines. These data were related to the transcriptional changes detected in mononuclear cells isolated from patients with scrub typhus. Here, the microarray analyses revealed the upregulation of 613 genes, which included interferon-related genes, and some features of M1 polarization were observed in these patients, similar to what was observed in O. tsutsugamushi-stimulated monocytes in vitro. This is the first report demonstrating that monocytes are clearly polarized in vitro and ex vivo following exposure to O. tsutsugamushi. These results would improve our understanding of the pathogenesis of scrub typhus, during which interferon-mediated activation of monocytes and their subsequent polarization into an M1 phenotype appear critical. This study may give us a clue of new tools for the diagnosis of patients with scrub typhus.
[Show abstract][Hide abstract] ABSTRACT: The low-density lipoprotein receptor (LDL-R) has been proposed to function as a receptor for the hepatitis C virus (HCV) entry. Polymorphism of LDL-R gene may influence the clearance of virus and response to treatment. This study was conducted to evaluate the association of LDL-R gene polymorphism and the response to antiviral treatment in patients with chronic HCV infection.
A total of 112 naïve patients with HCV genotype 3 were enrolled in the study. All patients were treated with a combination of pegylated interferon and ribavirin for 24 weeks. Polymerase chain reaction combined with restriction fragment length polymorphism was used to detect the polymorphism at the LDL-R gene intron 11 loci, including intron1, intron 3.1, intron 3.2, intron 4, intron 6, exon 8, intron 11, intron 13, intron 14 and 3'UTR-2 SNPs in intron 16 region. Comparisons of genotype and allele frequency between responders and nonresponders were analyzed.
Patients had a mean age of 54 years and 43% were male. Mean HCVRNA viral load and alanine aminotransferase level were 6.3 log, IU/mL and 100 IU/L, respectively. Sustained virological response, relapse and no response were documented in 68.7%, 17.9% and 13.4%, respectively. Baseline characteristics including age, sex, body weight, aminotransferase levels and HCV RNA viral load were similar between responders and nonresponders. No statistical difference was found for either genotype distribution or allele frequency among responders and nonresponders.
This study did not provide the evidence for a role of LDL-R polymorphism the response to antiviral treatment in patients with HCV genotype 3. This indicates that a genetic component via the LDL-R may not control HCV treatment outcome in HCV genotype 3
Journal of the Medical Association of Thailand = Chotmaihet thangphaet 02/2011; 94 Suppl 1:S147-53.
[Show abstract][Hide abstract] ABSTRACT: Alternatives to the available stavudine-containing paediatric fixed-dose combination (FDC) tablets are rapidly needed due to concerns regarding the cumulative toxicity of long-term stavudine exposure. We report the bioavailability and short-term safety of a novel paediatric FDC tablet of zidovudine (ZDV)/lamivudine (3TC)/nevirapine (NVP; 30/15/28 mg) in HIV-infected children.
In this Phase I/II open-label pharmacokinetic study, 42 children weighing 6-30 kg treated with NVP-based HAART for ≥4 weeks were randomized to receive the FDC tablets (GPO-VIR Z30) or the liquid formulations. Dosing was weight-based. Intensive 12-h blood sampling was performed after 2 weeks; subjects then crossed-over to the alternate formulation at equal doses and sampling repeated 2 weeks later. Pharmacokinetic parameters were determined by non-compartmental analysis. Buccal-swab samples were collected for cytochrome P450 (CYP)2B6 polymorphism analysis.
With the FDC tablet, the geometric mean (90% CI) area under the curve (AUC) for ZDV, 3TC and NVP was 1.58 (1.49-1.68), 7.78 (7.38-8.19) and 68.88 (62.13-76.36) μg•h/ml, respectively. Rules for NVP therapeutic inadequacy were defined a priori, and despite lower NVP exposure with the tablet (P<0.001), the levels remained therapeutically adequate. ZDV AUC was similar between formulations. 3TC exposure was significantly higher with the tablet but comparable to historical data in adults and children taking branded tablets. While receiving the tablet, NVP AUC in children with CYP2B 516 GG (45%), GT (45%) and TT (10%) genotypes were 67.0, 74.5 and 106.4 μg•h/ml, respectively (P=0.04).
Disparities in drug exposure between formulations were observed; however, the FDC tablet delivered therapeutically adequate exposures of each drug and could well play an important role in simplifying antiretroviral treatment for children.
[Show abstract][Hide abstract] ABSTRACT: To identify the causative paired box 6 (PAX6) mutation in a family with autosomal dominant aniridia.
A family with autosomal dominant aniridia with three affected individuals in two generations was investigated for the causative PAX6 mutation by single strand conformation polymorphism (SSCP) followed by sequencing of genomic DNA from peripheral blood.
A novel PAX6 mutation in the donor splice site of intron 12 was identified in all three affected individuals from the family. The automated splice site analysis web interface indicated a disturbance of splicing and it was predicted that this mutation could lead to an elimination of the normal stop codon and an abnormal 3' elongation of the mRNA.
We report a novel PAX6 mutation in autosomal dominant aniridia that presumably affects splicing. The presence of chorioretinal degeneration in one of the affected individual raises the possibility that run-on mutations are associated with chorioretinal involvement in aniridia.
[Show abstract][Hide abstract] ABSTRACT: The spreading of thalassemia, the most common genetic disease in tropical areas, is increasing due to a migration thus the prevention and control program (PCP) of Thalassemia has been established. To better promote the yet unsuccessful PCP for thalassemia, ontology called PCPThalOnto is developed. The proposed ontology represents domain knowledge while a list of executable production rule is generated to represent operational knowledge. The PCPThalOnto consists of 1) class component to represent concepts of strategies, methodologies, techniques and activities of the PCP and 2) relation component to link between those classes or class and its instance. In the production rules, conditions for individual case determination are employed to execute a proper action. The well-constructed knowledge representation of PCP for thalassemia is developed as an electronic knowledge base for future applications to efficiently disseminate the underlying knowledge to people bridging the gap that deter the success of PCP.
7th International Conference on Natural Language Processing and Knowledge Engineering, NLPKE 2011, Tokushima, Japan, November 27-29, 2011; 01/2011
[Show abstract][Hide abstract] ABSTRACT: Cartilage-hair hypoplasia (CHH) is a rare autosomal-recessive disorder characterized by short-limbed dwarfism, sparse hair, and immune deficiency. It is caused by mutations in the RMRP gene, which encodes the RNA component of the mitochondrial RNA-processing ribonuclease (RNase MRP). Several mutations have been identified in its promoter region or transcribed sequence. However, homozygous mutations in the promoter region have been only reported in a patient with primary immunodeficiency without other features of CHH. We report on a Thai girl who first presented with chronic diarrhea, recurrent pneumonia, and severe failure to thrive, without apparently disproportionate dwarfism. The diagnosis of CHH was made after the severe wasting was corrected, and disproportionate growth became noticeable. The patient had the typical features of CHH, including sparse hair and metaphyseal abnormalities. The immunologic profiles were consistent with combined immune deficiency. Mutation analysis identified a novel homozygous mutation, g.-19_-25 dupACTACTC, in the promoter region of the RMRP gene. Identification of the mutation enabled us to provide a prenatal diagnosis in the subsequent pregnancy. This patient is the first CHH case with the characteristic features due to the homozygous mutation in the promoter region of the RMRP gene. The finding of severe immunodeficiency supports that promoter mutations markedly disrupt mRNA cleavage function, which causes cell-cycle impairment.
Journal of applied genetics 12/2010; 51(4):523-8. · 1.90 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: WD is an autosomal recessive disorder of copper transport resulting in excessive copper deposition in the liver and brain. It is caused by defects of ATP7B encoding a copper transporting P-type ATPase. To identify the mutations in ATP7B in Thai patients with WD, DHPLC analysis was applied to detect mutations and polymorphisms of the entire ATP7B gene in 19 Thai patients with WD. Mutations in ATP7B were identified in 14 of 19 patients: 2 homozygotes, 8 compound heterozygotes and 4 heterozygotes. Eighteen mutations distributed throughout the entire coding region of ATP7B gene including 11 missense, 3 nonsense, 1 splice-site, 1 deletion and 2 insertions. Of 18 different mutations identified, 6 were found to be novel. Twelve single nucleotide polymorphisms (SNPs) were also identified and two SNPs have not yet previously been reported. Segregation analysis using DHPLC analysis showed mutation transmission patterns within each family of Thai patients with WD. Mutations in ATP7B in Thai patients with WD are worth adding into the public database for genetic epidemiology and population genetics.
European journal of medical genetics 10/2010; 54(2):103-7. · 1.57 Impact Factor