Sissades Tongsima

National Science and Technology Development Agency | NSTDA · National Biobank of Thailand

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...

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...

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...

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...

Global Mycobacterium tuberculosis population comprises 7 major lineages. The Beijing strains, particularly the ones classified as Modern groups, have been found worldwide, frequently associated with drug resistance, younger ages, outbreaks and appear to be expanding. Here, we report analysis of whole genome sequences of 1170 M. tuberculosis isolate...

Background: Bioactive peptides derived from food are important sources for alternative medicine and possess therapeutic activity. Several biochemical methods have been achieved to isolate bioactive peptides from food, which are tedious and time consuming. In silico methods are an alternative process to reduce cost and time with respect to bioactiv...

A panel of large number of common Single Nucleotide Polymorphisms (SNPs) distributed across an entire porcine genome has been widely used to represent genetic variability of pig. With the advent of SNP-array technology, a genome-wide genetic profile of a specimen can be easily observed. Among the large number of such variations, there exist a much...

Background Resolving population genetic structure is challenging, especially when dealing with closely related or geographically confined populations. Although Principal Component Analysis (PCA)-based methods and genomic variation with single nucleotide polymorphisms (SNPs) are widely used to describe shared genetic ancestry, improvements can be ma...

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...

Snake venom metalloproteinases (SVMPs) are the key enzymes in Russell's viper (RV) venom which target all important components of haemostasis, such as clotting factors, platelets, endothelial cells and basement membrane. The structural diversity of SVMPs contributes to the broad spectrum of biological activities. The aim of the study was to investi...

Mandibular prognathism is characterized by a prognathic or prominent mandible. The objective of this study was to find the gene responsible for mandibular prognathism. Whole exome sequencing analysis of a Thai family (family 1) identified the ADAMTSL1 c.176C>A variant as the potential defect. We cross‐checked our exome data of 215 people for rare v...

Single-nucleotide polymorphisms (SNPs) are important genetic variables that are very popular in Genome-wide association study at the present time. They are often used in studies related to genetic disorders. A distinctive trait of SNPs is that there are a lot of them since they are variables originated from various positions in a DNA sequence. Unfo...

Reef sites of Ko Samae San (S), Khao Ma Cho (K) and Ko Tao Mo (T) in the upper Gulf of Thailand have abundant corals and represent a hotspot of marine biodiversity. Coral reefs serve as major networks of food and energy, where bacteria, microbial eukaryotes (fungi) and small eukaryotes play significant roles as primary producers that convert inorga...

Background Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for sugarcane were generated using second-generation sequencing platforms, which provide short r...

Peptides derived from food proteins are promising bioactive source for inhibiting Angiotensin-I converting enzyme (ACE) activity. Bioactive peptides (BP) have received much attention, particularly from the pharmaceutical industry. As they not only own potent properties but also possess less side-effects than synthetic drugs. In this work, an 8000 p...

Virus-host interactions play important roles in virus infection and host cellular response. Several viruses, including dengue virus (DENV), usurp host chaperones to support their amplification and survival in the host cell. We investigated the interaction of nonstructural protein 1 (NS1) of DENV with three endoplasmic reticulum-resident chaperones...

Tuberculosis presents a global health challenge. Mycobacterium tuberculosis is divided into several lineages, each with a different geographical distribution. M. tuberculosis lineage 1 (L1) is common in the high-burden areas in East Africa and Southeast Asia. Although the founder effect contributes significantly to the phylogeographic profile, co-e...

We report a Thai father (patient 1) and his daughter (patient 2) affected with osteogenesis imperfecta type IV and dentinogenesis imperfecta. Both were heterozygous for the c.1451G>A (p.Gly484Glu) mutation in COL1A2. The father, a Thai boxer, had very mild osteogenesis imperfecta with no history of low-trauma bone fractures. Scanning electron micro...

Snake venom metalloproteinases (SVMPs) are the key enzymes in Russell's viper (RV) venom which target all important components of haemostasis, such as clotting factors, platelets, endothelial cells and basement membrane. The structural diversity of SVMPs contributes to the broad spectrum of biological activities. The aim of the study was to investi...

Single Nucleotide Polymorphism (SNP) is a variability of DNA sequence that connects to a unique trait of an organism. A good SNP selection can provide a good porcine breed that grows fast with high yield. SNP selection can be done by a computerized feature selection method and classification technique. At present, an effective classification model...

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 for unsupervised clustering using iterative pruning to capture fine-scale structure called IPCAPS. Our method supports ordinal data which can be applied directly to SNP data to...

Background Skin microbiome varies from person to person due to a combination of various factors, including age, biogeography, sex, cosmetics and genetics. Many skin disorders appear to be related to the resident microflora, yet databases of facial skin microbiome of many biogeographies, including Thai, are limited. Methods Metagenomics derived B-R...

Variance analysis by Boxplot of the 16S rDNA MiSeq data between 2 middle.hea foreheads subgroups, 2 teenage.acn cheeks subgroups, 2 teenage.acn foreheads subgroups, and 2 teenage.hea foreheads subgroups, respectively

Estimate GLOTU richness by rarefaction curves of cheek datasets

Primers in the B-RISA and 16S rDNA PCR amplifications Italic represents barcode sequence.

Estimate GLOTU richness by rarefaction curves of forehead datasets

Diversity and relative abundances of bacterial community compositions (as GLOTU) of the first (A) and second (B) subsampling datasets (Left) dendrogram computed with Morisita-Horn dissimilarity indices: teenage (red), middle-aged (green) and elderly (navy). Bacterial genera of <0.05% of relative abundance are not displayed.

Non-metric multidimensional scaling based on Morisita-Horn dissimilarity indices and Metastats analyses of the first (A–C) and second (D–F) subsampling datasets (A and D) without, and with Metastats analyses for representative (B and E) GLOTUs and (C and F) clinical features (skin, diet and lifestyle). The vector length indicates the strength of th...