
Prapat SuriyapholBioinformatics and Data Management for Research · Office for Research and Development, Mahidol University
Prapat Suriyaphol
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125
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Publications (125)
Inter-individual variability in drug responses is significantly influenced by genetic factors, underscoring the importance of population-specific pharmacogenomic studies to optimize clinical outcomes. In this study, we analyzed whole genome sequencing data from 949 unrelated Thai individuals and conducted an in-depth analysis of 3239 genes involved...
The Asian king vulture (AKV), a vital forest scavenger, is facing globally critical endangerment. This study aimed to construct a reference genome to unveil the mechanisms underlying its scavenger abilities and to assess the genetic relatedness of the captive population in Thailand. A reference genome of a female AKV was assembled from sequencing r...
Breast cancer stands as a formidable global health challenge for women. While neoantigens exhibit efficacy in activating T cells specific to cancer and instigating anti-tumor immune responses, the accuracy of neoantigen prediction remains suboptimal. In this study, we identified neoantigens from the patient-derived breast cancer cells, PC-B-142CA a...
Eld’s deer, a conserved wildlife species of Thailand, is facing inbreeding depression, particularly in the captive Siamese Eld’s deer (SED) subspecies. In this study, we constructed genomes of a male SED and a male Burmese Eld’s deer (BED), and used genome-wide single nucleotide polymorphisms to evaluate the genetic purity and the inbreeding status...
Currently licensed dengue vaccines do not induce long-term protection in children without prior dengue virus exposure. A better understanding of the mechanism by which the immune system prevents dengue virus infection is urgently needed to improve vaccine efficacy. In this study, the induction of protective antibody responses against dengue virus i...
The 2021 WHO Classification of Central Nervous System Tumors recommended evaluation of cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) deletion in addition to codeletion of 1p/19q to characterize IDH-mutant glio-mas. Here, we demonstrated the use of a nanopore-based copy-number variation sequencing (nCNV-seq) approach to simultaneously identify d...
Tumors frequently found in dogs include canine oral tumors, either cancerous or noncancerous. The bloodstream is an important route for tumor metastasis, particularly for late-stage oral melanoma (LOM) and late-stage oral squamous cell carcinoma (LOSCC). The present study aimed to investigate serum peptidome-based biomarkers of dogs with early-stag...
This study aimed to characterize the alteration of the fecal microbiome and antimicrobial resistance (AMR) determinants in 24 piglets at day 3 pre-weaning (D. − 3), weaning day (D.0), days 3 (D.3) and 8 post-weaning (D.8), using whole-genome shotgun sequencing. Distinct clusters of microbiomes and AMR determinants were observed at D.8 when Prevotel...
We present RNA sequencing data sets and their genome sequence assembly for dengue virus that was isolated from a patient with dengue hemorrhagic fever and serially propagated in Vero cells. RNA sequencing data obtained from the first, third, and fifth passages and their corresponding whole-genome sequences are provided in this work.
Detection and quantification of viruses in laboratory and clinical samples are standard assays in dengue virus (DENV) studies. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) is considered to be the standard for DENV detection and quantification due to its high sensitivity. However, qRT-PCR offers only quantification rela...
Background:
The error-prone replication of dengue virus (DENV) in host results in the highly diverse viral population. Together with the host factor, intra-host diversity may influence the disease severity. Therefore, it is worth investigating whether there is a correlation between intra-host genetic diversity and disease severity.
Objective:
To...
Tuberculosis disease (TB), caused by Mycobacterium tuberculosis, is a major public health issue in Thailand. The high prevalence of modern Beijing (Lineage 2.2.1) strains has been associated with multi- and extensively drug-resistant infections (MDR-, XDR-TB), complicating disease control. The impact of rarer proto-Beijing (L2.1) strains is less cl...
Dengue prototype strains are widely used for virological study. The strains presented here have been cultured under different laboratory environments, resulting in accumulating genetic variations. We present the genomes of four serotypes of the dengue prototype strain that were continuously maintained in the laboratory. These genomes contain bases...
The spirochete species Leptospira interrogans is the most common cause of leptospirosis, producing acute to chronic infections in most mammalian species. This pathogenic bacterium has an ability to evolve in many ways to occupy various environments and hosts. In this study, we performed chronology analysis to look for insight into the emergence of...
Drug-resistant tuberculosis (TB) is a major public health problem. There is little information regarding the genotypic-phenotypic association of anti-TB drugs, especially for second-line drugs. This study compared phenotypic drug susceptibility testing (DST) with predictions based on whole-genome sequencing (WGS) data for 266 Mycobacterium tubercul...
Background
Leptospirosis is an emerging infectious disease worldwide that can cause high morbidity and mortality rates in humans and animals. The causative spirochetes have reservoirs in mammalian hosts, but there has been limited analysis of the genomes of isolates recovered from animals. The aims of this study were to characterize genomic feature...
Tuberculous meningitis (TBM) is a severe form of tuberculosis with a high mortality rate. The factors associated with TBM pathogenesis are still unclear. Using comparative whole-genome sequence analysis we compared Mycobacterium tuberculosis (Mtb) isolates from cerebrospinal fluid of TBM cases (n = 73) with those from sputum of pulmonary tuberculos...
Pythium insidiosum is a human-pathogenic oomycete. Many patients infected with it lose organs or die. Toward the goal of developing improved treatment options, we want to understand how Py. insidiosum has evolved to become a successful human pathogen. Our approach here involved the use of comparative genomic and other analyses to identify genes wit...
LD (D’) values for the PLCE1 region in the Chinese population (CDX) from 1000 Genomes database.
BMIX identified significant SNPs are indicated by a box. All SNPs have at least 5% minimum allele frequency in the population analysed.
(DOCX)
Manhattan plots for the conventional association tests with PCA correction for population structure.
A–DSS test (p-values and D’ for SNPs surrounding the two spurious SNPs are highlighted). B—DF test. The red line indicates the significance threshold.
(DOCX)
PCA of the Thai samples.
Plot of PC1 versus PC2 in the Thai control and patient cohorts.
(DOCX)
Annotation of the significant SNPs in BMIX analysis for Vietnam DSS test, inferred by using the Variant Effect Predictor (VEP) tool from Ensemble.
(DOCX)
Annotation of the significant SNPs in BMIX analysis for Thai DSS test, inferred by using the Variant Effect Predictor (VEP) tool from Ensemble.
(DOCX)
Annotation of the significant SNPs in BMIX analysis for Thai DF test, inferred by using the Variant Effect Predictor (VEP) tool from Ensemble.
(DOCX)
Association p-values in the entire Thai cohort in six and two SNPs selected from the sets of BMIX-associated SNPs with DF and DSS phenotypes, respectively.
(DOCX)
Primers used for mutagenesis and DNA assembly protocols.
(DOCX)
LD (D’) values for the MICB region in the Chinese population (CDX) from 1000 Genomes database.
BMIX identified significant SNPs are indicated by a box. All SNPs have at least 5% minimum allele frequency in the population analysed.
(DOCX)
LD (D’) values for the CHST10 region in the Chinese population (CDX) from 1000 Genomes database.
BMIX identified significant SNPs are indicated by a box. All SNPs have at least 5% minimum allele frequency in the population analysed.
(DOCX)
LD (D’) values for the AHRR region in the Chinese population (CDX) from 1000 Genomes database.
BMIX identified significant SNPs are indicated by a box. All SNPs have at least 5% minimum allele frequency in the population analysed.
(DOCX)
Gene expression for CHST10 (A) and AHRR (B) in Thai dengue cohort along the course of disease from a transcriptome dataset for whole blood.[17] No significant differences in expression were observed.
(DOCX)
mRNA expression profiles for the eQTLs in PPP2R5E and AHRR genes (information from GTEx database).
The protective alleles are indicated in green while the causative alleles are in red.
(DOCX)
Significant SNPs in BMIX analysis for Thai DF test.
The base position refers to GRCh37 genome assembly.
(DOCX)
Detailed identification of motif sequences across DENV serotypes.
(DOCX)
ADMIXTURE plot for K = 3 for Thai and Vietnamese cohorts and the parental populations used in this work (CDX–Chinese Dai in Xishuangbanna; ITU–Indian Telugu from the UK (ITU); and MAL–Malaysian).
(DOCX)
Significant SNPs in BMIX analysis for Thai DSS vs control test.
The base position refers to GRCh37 genome assembly.
(DOCX)
Association and BMIX results for the 10 runs of pseudo datasets, permutating case and control labels.
(DOCX)
Global ancestry inferred through RFMix when using three parental ancestries (South, Northeast and Southeast Asian) for the three Thai hospital dengue cohorts.
Each vertical line represents an individual, and the three colours represent the proportion of the three parental populations in each genome (light orange for South Asian, dark orange for Sou...
LD (D’) values for the PLCB4 region in the Chinese population (CDX) from 1000 Genomes database.
BMIX identified significant SNPs are indicated by a box. All SNPs have at least 5% minimum allele frequency in the population analysed.
(DOCX)
Locus zoom of the chromosomal region around genes (A–PLCB4, B–PLCE1, C–CHST10, D–AHRR, E–GRIP1, F–PPP2R5E) with significant p-values obtained for DSS and DF tests. The Asian recombination map was used.
(DOCX)
LD (D’) values for the PPP2R5E region in the Chinese population (CDX) from 1000 Genomes database.
BMIX identified significant SNPs are indicated by a box. All SNPs have at least 5% minimum allele frequency in the population analysed.
(DOCX)
Significant SNPs in BMIX analysis for Vietnam DSS test.
The base position refers to GRCh37 genome assembly.
(DOCX)
Information on DENV serotype and primary/secondary in the Thai cohort.
(DOCX)
Background
Imputation involves the inference of untyped single nucleotide polymorphisms (SNPs) in genome-wide association studies. The haplotypic reference of choice for imputation in Southeast Asian populations is unclear. Moreover, the influence of SNP annotation on imputation results has not been examined. Methods
This study was divided into two...
Supplementary information from the paper.
In 2014, Leptospira interrogans strain CUDO8 was isolated from the urine of an asymptomatic dog in Thailand. Here we report the draft genome sequence of this pathogenic bacterium.
The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major...
Antibiotic resistance genes are rapidly spread between pathogens and the normal flora, with plasmids playing an important role in their circulation. This study aimed to investigate antibiotic resistance plasmids in the gut microbiome of hospitalised patients. Stool samples were collected from seven inpatients at Siriraj Hospital (Bangkok, Thailand)...
Multi-drug and extensively drug-resistant tuberculosis (MDR and XDR-TB) are problems that threaten public health worldwide. Only some genetic markers associated with drug-resistant TB are known. Whole-genome sequencing (WGS) is a promising tool for distinguishing between re-infection and persistent infection in isolates taken at different times fro...
Drug resistance associated mutations detected using bioinformatics tools.
(XLSX)
Development of high-throughput technologies, such as Next-generation sequencing, allows thousands of experiments to be performed simultaneously while reducing resource requirement. Consequently, a massive amount of experiment data is now rapidly generated. Nevertheless, the data are not readily usable or meaningful until they are further analysed a...
Purpose:
Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of inherited retinal degenerations characterized by progressive loss of photoreceptor cells and RPE functions. More than 70 causative genes are known to be responsible for RP. This study aimed to identify the causative gene in a patient from a consanguineous fam...
Pythium insidiosum is an oomycete that causes a life-threatening infectious disease called pythiosis in humans and animals living in tropical
and subtropical countries. Here, we report the first draft genome sequence of P. insidiosum. The genome of P. insidiosum is 53.2 Mb and contains 14,962 open reading frames.
Dengue is a mosquito-borne viral disease that afflicts millions of individuals worldwide every year. Infection by any of the four serotypes can result in a spectrum of disease severity. We investigated the impact of variants of interferon regulated innate immunity genes with a potent anti-viral effect, on the outcome of dengue infection. We compare...
We present the draft genome sequence of DS-16780, with a rare spoligo-international type (SIT) 523 (777777777777771) genotype,
which reveals an extensively drug-resistant Mycobacterium tuberculosis (XDR-TB) phenotype. The isolate is a representative of clonal XDR-TB from the western part of Thailand.
We present the draft genome sequence of DS-16780, with a rare spoligo-international type (SIT) 523 (777777777777771) genotype,
which reveals an extensively drug-resistant Mycobacterium tuberculosis (XDR-TB) phenotype. The isolate is a representative
of clonal XDR-TB from the western part of Thailand
Infections with the Beijing family of Mycobacterium tuberculosis occur worldwide and are endemic in Asian countries. We present the draft genome sequence of DS6701, a multidrug-resistant
M. tuberculosis Beijing strain of sequence type 10. The isolate is a representative of strains isolated from a multidrug-resistant tuberculosis
outbreak in Thailan...
Oomycetes form a unique group of microorganisms that share hyphal morphology with fungi. Most of pathogenic oomycetes infect plants, while some species are capable of infecting animals. Pythium insidiosum is the only oomycete that can infect both humans and animals, and causes a life-threatening infectious disease, called “pythiosis”. Controlling a...
20.1 Introduction
The study of filaggrin in dogs (canine fi laggrin) began by immunohistochemistry (IHC) staining in the stratum granulosum (S. granulosum) of circumanal glands, identifi ed by a monoclonal antihuman fi laggrin antibody (Ab) in 1998 [ 1 ]. Since then, there have been no publications on canine fi laggrin until the “boom” of fi laggr...
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 detecti...
Many potentially life-threatening infectious viruses are highly mutable in nature. Characterizing the fittest variants within a quasispecies from infected patients is expected to allow unprecedented opportunities to investigate the relationship between quasispecies diversity and disease epidemiology. The advent of next-generation sequencing technol...
Here we present an approach that advances the throughput of a genetic analysis of a positive-sense RNA virus by simplifying
virus construction. It enabled comprehensive dissection of a complex, multigene phenotype through rapid derivation of a large
number of chimeric viruses and construction of a mutant library directly from a virus pool. The vers...
Dengue virus is responsible for 50-100 million new infections annually worldwide. The virus uses error-prone RNA polymerase during genome replication in a host, resulting in the formation of closely related viruses known as quasispecies. The availability of next-generation sequencing technology provides opportunities to analyze viral quasispecies....
This paper proposes the translational research on developing the homemade pulse detector to predict the hemoglobin (usually need blood test) by using the non-invasive method. The system uses the peak of each pulse signal from homemade-single infrared LED to calculate the amount of hemoglobin compare with the commercial product.
Accessibility to iron chelators including deferoxamine and deferasirox remains obscured in many developing countries. To provide an alternative, the government pharmaceutical organization of Thailand (GPO) manufactured deferiprone which has similar bioequivalent to the standard product. Seventy-three pediatric patients with severe β thalassemias, a...