Sissades Tongsima

• PhD in Computer Science and Engineering
• Principal Investigator/ Director at National Science and Technology Development Agency

Aim Type 2 diabetes is a heterogeneous disease with strong genetic components. We showed earlier that newly diagnosed type 2 diabetes in Thai patients could be categorized into four clusters. This study aimed to determine the evidence of hereditary factors in these type 2 diabetes clusters. Methods A total of 487 subjects who were diagnosed with t...

The 16S rRNA gene is crucial for bacterial identification, but primer biases and intergenomic variation can compromise its effectiveness, especially in complex ecosystems like the human gut microbiome. This study systematically evaluates 57 commonly used 16S rRNA primer sets through in silico PCR simulations against the SILVA database. We identifie...

The authors wish to make a change to the author names (adding a new author—Teerada Daroontum) on this paper [...]

Thailand has a high burden of tuberculosis, with control efforts hindered by drug-resistant Mycobacterium tuberculosis (Mtb). The increasing use of whole-genome sequencing (WGS) of Mtb offers valuable insights for clinical management and public health surveillance. WGS can be used to profile drug resistance, identify circulating sub-lineages, and t...

Type 2 diabetes (T2D) is a heterogeneous disease that can be distinguished at newly diagnosis by variations in clinical presentation, disease trajectory, therapeutic response, and risk of complications. Its global prevalence is increasing, particularly among Asian populations such as Thais, due to unique genetic and environmental factors. Thai pati...

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...

Background To prevent the development of cholangiocarcinoma, an effective screening opisthorchiasis viverrini and/or differential diagnosis of and the cholangiocarcinoma is crucial needed. The level and quality of cfDNA in plasma are being investigated for their potential role as biomarkers in cholangiocarcinoma. Methods The study enrolled 43 heal...

Recent research highlights the significant impact of the gut microbiota on health and disease. Thalassemia, a hereditary blood disorder, requires regular blood transfusions, leading to an accumulation of iron in the body. Such changes could potentially alter the intestinal microbiota, thereby increasing the susceptibility of thalassemic patients to...

Aims This study aims to compare the trends in the quality of hospital care for WHO’s three disease groups pre-, during, and post-COVID-19 pandemic peak in Thailand. Methods The study utilized existing hospital admission data from the Thai Health Information Portal (THIP) database, covering the period from 2017 to 2022. We categorized WHO’s three d...

The World Health Organization has set a target to eliminate viral hepatitis as a public threat by 2030. In pursuit of this goal, Thailand initiated a hepatitis C virus (HCV) microelimination project targeting Phetchabun province, a well-recognized high-burden HCV endemic area. However, the historical transmission dynamics of HCV in Phetchabun, and...

Background Next-generation sequencing of Mycobacterium tuberculosis , the infectious agent causing tuberculosis, is improving the understanding of genomic diversity of circulating lineages and strain-types, and informing knowledge of drug resistance mutations. An increasingly popular approach to characterizing M. tuberculosis genomes (size: 4.4 Mbp...

Ramon syndrome (MIM 266270) is an extremely rare genetic syndrome, characterized by gingival fibromatosis, cherubism-like lesions, epilepsy, intellectual disability, hypertrichosis, short stature, juvenile rheumatoid arthritis, and ocular abnormalities. Hereditary or non-syndromic gingival fibromatosis (HGF) is also rare and considered to represent...

Polygenic Risk Scores (PRS) are now playing an important role in predicting overall risk of breast cancer risk by means of adding contribution factors across independent genetic variants influencing the disease. However, PRS models may work better in some ethnic populations compared to others, thus requiring populaion specific validation. This stud...

Introduction CYP2C19 plays a major role in the metabolism of various drugs. The most common genetic variants were the CYP2C19*2 and *3 alleles (rs4244285 and rs4986893, non-functional variants). In previous studies, we found that genetic polymorphisms in CYP2C19 variants influenced the active metabolites of clopidogrel and caused major adverse card...

Congenital insensitivity to pain is a rare human condition in which affected individuals do not experience pain throughout their lives. This study aimed to identify the molecular etiology of congenital insensitivity to pain in two Thai patients. Clinical, radiographic, histopathologic, immunohistochemical, and molecular studies were performed. Pati...

KCTD1 plays crucial roles in regulating both the SHH and WNT/β-catenin signaling pathways, which are essential for tooth development. The objective of this study was to investigate if genetic variants in KCTD1 might also be associated with isolated dental anomalies. We clinically and radiographically investigated 362 patients affected with isolated...

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...

BACKGROUND The prevalence of metabolic-associated fatty liver disease (MAFLD) is a growing public health issue in people living with human immunodeficiency virus (PLWH). However, the pathophysiology of MAFLD is still unknown, and the role of genetic variables is only now becoming evident. AIM To evaluate the associations of gene-polymorphism-relat...

Background In order to generate a normal set of teeth, fine‐tuning of Wnt/β‐catenin signaling is required, in which WNT ligands bind to their inhibitors or WNT inhibitors bind to their co‐receptors. Lrp4 regulates the number of teeth and their morphology by modulating Wnt/β‐catenin signaling as a Wnt/β‐catenin activator or inhibitor, depending on i...

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...

Karst caves are distinctive ecosystems that have limited nutrients, darkness, low to moderate temperatures, and high moisture levels, which allow for a diverse range of fungal communities to thrive. Despite their significance, little is understood about the fungi found in karst caves in Thailand. In 2019, we studied the cultured mycobiota from five...

Variant imputation, a common practice in genome-wide association studies, relies on reference panels to infer unobserved genotypes. Multiple public reference panels are currently available with variations in size, sequencing depth, and represented populations. Currently, limited data exist regarding the performance of public reference panels when u...

Background: Supernumerary teeth refer to extra teeth that exceed the usual number of dentitions. A mesiodens is a particular form of supernumerary tooth, which is located in the premaxilla region. The objective of the study was to investigate the genetic etiology of extra tooth phenotypes, including mesiodens and isolated supernumerary teeth. Metho...

Simple Summary A mesiodens is an extra tooth located in the midline of the upper jaw. To investigate the genetic cause of mesiodens, clinical and radiographic examination were performed on 23 family members of a two-generation Hmong family. Whole exome or Sanger sequencing were performed in 22 family members. We found an extremely rare mutation (c....

Background: Enamel knots and Hertwig epithelial root sheath (HERS) regulate the growth and folding of the dental epithelium, which subsequently determines the final form of tooth crown and roots. We would like to investigate the genetic etiology of seven patients affected with unique clinical manifestations, including multiple supernumerary cusps,...

Objectives: To identify the molecular etiology of distinct dental anomalies found in eight Thai patients and explore the mutational effects on cellular functions. Material and methods: Clinical and radiographic examinations were performed on eight patients. Whole exome sequencing, mutant protein modelling, qPCR, Western blot analysis, Scratch as...

Each family member had a SALL4 variant. This is the first report of quadricuspid aortic valve and a genetic variant. The variation in phenotype caused by SALL4 mutations questions the division of SALL4‐related phenotypes in three different entities. image

The activation of Wnt/β-catenin signalling is a prerequisite for odontogenesis. APC, a member of the AXIN-CK1-GSK3β-APC β-catenin destruction complex, functions to modulate Wnt/β-catenin signalling to establish regular teeth number and positions. APC loss-of-function mutations are associated with the over-activation of WNT/β-catenin signalling and...

Simple Summary Low density lipoprotein receptor-related protein 4 (LRP4; MIM 604270) modulates WNT/β-catenin signaling, through its binding of WNT ligands, and to co-receptors LRP5/6, and WNT inhibitors DKK1, SOSTDC1, and SOST. LRP4 binds to SOSTDC1 and WNT proteins establishing a negative feedback loop between Wnt/β-catenin, Bmp, and Shh signaling...

One of the most important steps in post-translational modifications of collagen type I chains is the hydroxylation of carbon-3 of proline residues by prolyl-3-hydroxylase-1 (P3H1). Genetic variants in P3H1 have been reported to cause autosomal recessive osteogenesis imperfecta (OI) type VIII. Clinical and radiographic examinations, whole-exome sequ...

Background: Generalized pustular psoriasis (GPP; MIM 614204) is a rare and severe pustular autoinflammatory skin disease in which acute generalized erythema and scaling develop with numerous sterile pustules. GPP shares skin manifestations, especially pustular skin reaction, with adult-onset immunodeficiency (AOID) with anti-interferon-γ autoantibo...

A mutation in DKK1 gene leads to inhibitory DKK1 function, over‐activation of WNT/β‐catenin signaling, disruptive development of dental epithelium, and subsequent mesiodens formation. image

Introduction: Inactivating mutations of the calcium-sensing receptor (CASR) gene result in neonatal severe hyperparathyroidism (NSHPT). Total parathyroidectomy is an effective way to control life-threatening hypercalcemia in NSHPT but leads to permanent hypoparathyroidism. An alternative surgical option is subtotal parathyroidectomy. However, few...

SNP-based information is used in several existing clustering methods to detect shared genetic ancestry or to identify population substructure. Here, we present a methodology, called IPCAPS for unsupervised population analysis using iterative pruning. Our method, which can capture fine-level structure in populations, supports ordinal data, and thus...

Background: Generalized pustular psoriasis (GPP; MIM 614204) is a rare multisystemic autoinflammatory disease, characterized by episodes of acute generalized erythema and scaling developed with the spread of numerous sterile pustules. Adult-onset immunodeficiency syndrome (AOID) with anti-interferon-γ autoantibodies is an immunodeficiency disorder...

Objective: To investigate dental anomalies and the molecular etiology of a patient with Ellis–van Creveld syndrome and two patients with Bardet–Biedl syndrome, two examples of ciliopathies. Patients and Methods: Clinical examination, radiographic evaluation, whole exome sequencing, and Sanger direct sequencing were performed. Results: Patient 1 had...

Cryptococcal meningoencephalitis caused by Cryptococcus neoformans infection is the most common cause of death in HIV/AIDS patients. Macrophages are pivotal for the regulation of immune responses to cryptococcal infection by either playing protective function or facilitating fungal dissemination. However, the mechanisms underlying macrophage respon...

Sugarcane accounts for a large portion of the worlds sugar production. Modern commercial cultivars are complex hybrids of S. officinarum , S. spontaneum , and several other Saccharum species, resulting in an auto-allopolyploid with 8–12 copies of each chromosome. The current genome assembly gold standard is to generate a long read assembly followed...

Background Canonical and non-canonical WNT signaling are important for odontogenesis. WNT ligand secretion mediator (WLS; MIM611514) is required to transport lipid-modified WNT proteins from the Golgi to the cell membrane, where canonical and non-canonical WNT proteins are released into the extracellular milieu. Biallelic pathogenic variants in WLS...

The Plasmodium falciparum human malaria parasite genome is incompletely annotated and does not accurately represent the transcriptomic diversity of this species. To address this need, we performed long-read transcriptomic sequencing. 5′ capped mRNA was enriched from samples of total and nuclear-fractionated RNA from intra-erythrocytic stages and co...

The core promoter plays an essential role in regulating transcription initiation by controlling the interaction between transcriptional factors and sequence motifs in the core promoter. Although mutation in core promoter sequences is expected to cause abnormal gene expression leading to pathogenic consequences, limited supporting evidence showed th...

Objective: To report the clinical and radiographic findings and molecular etiology of the first monozygotic twins affected with Pfeiffer syndrome. Methods: Clinical and radiographic examination and whole exome sequencing were performed on two monozygotic twins with Pfeiffer syndrome. Results: An acceptor splice site mutation in FGFR2 (c.940-2A>G) w...

WNT/β‐catenin and BMP signaling pathways play important roles in the process of tooth development. Dysregulation of WNT/β‐catenin and BMP signaling is implicated in a number of human malformations, including dental anomalies. Whole exome and Sanger sequencing identified seven patients with LRP5 mutations (p.Asn1121Asp, p.Asp856Asn, p.Val1433Met, an...

Objective The objective of this study was to investigate molecular etiologies of oral exostoses and dental anomalies in 14 patients from eight families. Methods Oral and radiographic examinations were performed on every patient. Whole exome and Sanger sequencing were performed on DNA of the patients, the unaffected parents and unaffected siblings....

Objective WNT/β-catenin signaling is initiated by binding of a WNT protein to a Frizzled (FZD) receptor and a co-receptor, low-density lipoprotein (LDL) receptor-related protein 5 or 6 (LRP5/6). The objective of this study was to find the genetic variants responsible for dental anomalies found in 4 families. Methods Clinical and radiographic exami...

Mutations in LTBP3 are associated with Dental Anomalies and Short Stature syndrome (DASS; MIM 601216), which is characterized by hypoplastic type amelogenesis imperfecta, hypodontia, underdeveloped maxilla, short stature, brachyolmia, aneurysm and dissection of the thoracic aorta. Here we report a novel (p.Arg545ProfsTer22) and a recurrent (c.3107‐...

Whole-genome sequence (WGS) analysis provides the best resolution for reconstructing bacterial phylogeny. However, the resulting tree could vary according to parameters used in the WGS pipeline, making it difficult to compare results across multiple studies. This study compares effects on phylogenies when applying different parameter stringencies....

Background Mutations in SLC4A4 have been reported to be associated with proximal renal tubular acidosis (RTA), short stature, band keratopathy, cataract, glaucoma, and hypoplastic-type amelogenesis imperfecta. In this study, the authors describe the clinical manifestations, and investigate the molecular etiology, in a patient with RTA. Case Descri...

Asymptomatic hepatitis C virus (HCV) infection without treatment is associated with chronic liver diseases including hepatocellular carcinoma. A major obstacle to hepatitis C diagnosis leading to antiviral treatment in some developing countries is the complicated HCV testing required before treatment. To simplify an HCV test-to-treat strategy, whic...

Methicillin-resistant Staphylococcus aureus (MRSA) is a significant causative agent of hospital-acquired infections. We characterized MRSA isolated from August 2012 to July 2015 from Thammasat University Hospital. Genotypic characterization of MRSA SCCmec type II and III isolates were scrutinized by whole genome sequencing (WGS). The WGS data revea...

Thalassemia/HbE disease has a wide spectrum of clinical phenotypes ranging from asymptomatic to dependent on regular blood transfusions. Ability to predict disease severity is helpful for clinical management and treatment decision making. A thalassemia severity score has been developed from Mediterranean β-thalassemia patients. However, different e...

The increasing availability of next generation sequencing (NGS) for personal genomics could promote pharmacogenomics (PGx) discovery and application. However, current tools for analysis and interpretation of pharmacogenomic variants from NGS data are inadequate, as none offer comprehensive analytic functions in a simple, web-based platform. In addi...

To maximize the potential of genomics in medicine, it is essential to establish databases of genomic variants for ethno‐geographic groups that can be used for filtering and prioritizing candidate pathogenic variants. Populations with non‐European ancestry are poorly represented among current genomic variant databases. Here, we report the first high...

Background The genome of the human malaria parasite Plasmodium falciparum is poorly annotated, in particular, the 5′ capped ends of its mRNA transcripts. New approaches are needed to fully catalog P. falciparum transcripts for understanding gene function and regulation in this organism. Methods We developed a transcriptomic method based on next-ge...

The extent to which viral genomic RNAs interact with host factors and contribute to host response and disease pathogenesis is not well known. Here, we report that the human RNA helicase DDX6 specifically binds to the viral most conserved RNA hairpin in the A3 element in the dengue 3´-UTR, with nanomolar affinities. DDX6 CLIP confirmed the interacti...

Adult‐onset immunodeficiency syndrome (AOID) with anti‐interferon (IFN)‐γ autoantibodies is characterized by an AIDS‐like illness with disruptive IFN‐γ signaling. Patients generally present with recurrent and disseminated opportunistic infections along with neutrophilic dermatoses. Generalized pustular psoriasis (GPP; Online Mendelian Inheritance i...

FREM2 is a member of the FREM2–FRAS1–FREM1 protein complex which contributes to epithelial–mesenchymal coupling. We report a Thai woman with cryptophthalmos, dental anomalies, and oral vestibule defect. A compound heterozygous mutation (c.6499C>T; p.Arg2167Trp and c.641_642del; p.Glu214GlyfsTer135) in the FREM2 gene was identified. The frameshift v...

β-Thalassemia/HbE disease has a wide spectrum of clinical phenotypes ranging from asymptomatic to dependent on regular blood transfusions. Ability to predict disease severity is helpful for clinical management and treatment decision making. A thalassemia severity score has been developed from Mediterranean β-thalassemia patients. However, different...

Abstract Forest biomass estimation at large scale is challenging and generally entails large uncertainty in tropical regions. With their wall‐to‐wall coverage ability, passive remote sensing signals are frequently used to extrapolate field estimates of forest aboveground biomass (AGB). However, studies often use limited reference data and/or flawed...

The southeast Andaman Sea 52-m off the west coast of Phang Nga province, Thailand, is located in the Indian Ocean, representing a hotspot for marine biodiversity of the world. This study utilized metagenomics combined 16S rRNA gene (V3–V4) sequencing, and firstly revealed the microbiota and their metabolism potentials of this site at an epipelagic...

Objective Our objective was to investigate the molecular etiology of osteogenesis imperfecta type VIII and dental anomalies in four siblings of a Karen tribe family. Materials and Methods Four patients and the unaffected parents were studied by clinical and radiographic examination. In situ hybridization of P3h1 during early murine tooth developme...

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...

Objective: Juberg-Hayward syndrome (JHS; MIM 216100) is a rare autosomal recessive malformation syndrome, characterized by cleft lip/palate, microcephaly, ptosis, hypoplasia or aplasia of thumbs, short stature, dislocation of radial head, and fusion of humerus and radius leading to elbow restriction. A homozygous mutation in ESCO2 has recently bee...

Viruses manipulate the life cycle in host cells via the use of viral properties and host machineries. Development of antiviral peptides against dengue virus (DENV) infection has previously been concentrated on blocking the actions of viral structural proteins and enzymes in virus entry and viral RNA processing in host cells. In this study, we propo...

Background Diabetes mellitus (DM) is a common complication found in β-thalassemia patients. The mechanism of DM in β-thalassemia patients is still unclear, but it could be from an iron overload and increase of some cytokines, such as interleukin1-β (IL-1β) and tumor necrosis factor-α (TNF-α). The objective of this study was to study the effect of i...

Background: The number of porcine Single Nucleotide Polymorphisms (SNPs) used in genetic association studies is very large, suitable for statistical testing. However, in breed classification problem, one needs to have a much smaller porcine-classifying SNPs (PCSNPs) set that could accurately classify pigs into different breeds. This study attempte...

Chronic hepatitis C virus (HCV) infection can lead to liver cirrhosis and hepatocellular carcinoma. To eliminate HCV infection in an endemic area, an epidemiological baseline of the current HCV infection in the population is required. We therefore aimed to evaluate the HCV burden in the Thai Province of Phetchabun, which has the highest HCV infecti...

Treacher Collins syndrome (TCS: OMIM 154500) is an autosomal dominant craniofacial disorder belonging to the heterogeneous group of mandibulofacial dysostoses. Objective To investigate four Treacher Collins syndrome patients of the Sgaw Karen family living in Thailand. Method Clinical examination, hearing tests, lateral cephalometric analyses, Co...

Malaria is a life-threatening disease causing by an infection of the protozoan parasite Plasmodium. Plasmodium falciparum is the deadliest and most common human infected parasites hosted by anopheles mosquito vector. To cure a malaria infected patient and prevent further spreading, malaria diagnosis using microscopy to visualize Giemsa-stained para...

Background: Juberg-Hayward syndrome (JHS; MIM 216100) is a rare autosomal recessive malformation syndrome, characterized by cleft lip/palate, microcephaly, ptosis, short stature, hypoplasia or aplasia of thumbs, and dislocation of radial head and fusion of humerus and radius leading to elbow restriction. Objective: To report for the first time t...

ipADMIXTURE is an R package to infer clusters and their phylogeny based on Q matrices of genetic admixture analysis. It is the first software of its kind to infer not just only clusters, but also the hierarchy of sub-populations w.r.t. the minimum number of ancestors that split any pair of clusters apart. Since inputs of the package, Q matrices, ca...

DNA sequence similarity search has been used by scientists to facilitate biological research. Over the years, more sequences are added to databases, making them constantly larger. Existing sequence search techniques usually focus on the improvement of sequence search algorithms to make the search faster, ignoring the possibility of reducing unrelat...

Human leukocyte antigen (HLA) class I and II are known to have association with severe cutaneous adverse reactions (SCARs) when exposing to certain drug treatment. Due to genetic differences at population level, drug hypersensitivity reactions are varied, and thus common pharmacogenetics markers for one country might be different from another count...

An abnormal activation of human epidermal growth factor receptor (HER) 2 has been found to associate with several types of human cancer, and thus the protein is a prominent target for cancer therapy. Although several small chemical molecules targeting the tyrosine kinase (TK) of HER family have been identified, the development of a new class of inh...

Ancestry-informative markers (AIMs) can be used to infer the ancestry of an individual to minimize the inaccuracy of self-reported ethnicity in biomedical research. In this study, we describe three methods for selecting AIM SNPs for the Malay population (Malay AIM panel) using different approaches based on pairwise FST, informativeness for assignme...