High Amplification Rates Research Articles

The Epidemiology of Biliary Tract Cancer and Associated Prevalence of MDM2 Amplification: A Targeted Literature Review.

Biliary tract cancer (BTC) is a rare and aggressive malignancy that is anatomically classified as gallbladder cancer (GBC), extra- and intra-hepatic cholangiocarcinoma (eCCA and iCCA) and ampullary cancer (AC). BTC is often diagnosed at an advanced stage when treatment options are limited and patients have a poor prognosis, so the identification of new drug targets is of critical importance. BTC is molecularly diverse and harbours different therapeutically actionable biomarkers, including mouse double minute 2 homolog (MDM2), which is currently being investigated as a drug target. The aim of this targeted review was to evaluate and synthesise evidence on the epidemiology of BTC and its subtypes in different geographic regions and on the frequency of MDM2 amplifications in BTC tumours. Epidemiological studies (N=33) consistently demonstrated high incidence rates in South and Central Asia for BTC overall (up to 9.00/100,000) and for all subtypes, with much lower rates in Europe and the US. Among the different types of BTC, the highest global incidence was observed for CCA, mainly driven by iCCA (1.4/100,000), followed by GBC (1.2/100,000) and AC (0.18-0.93 per 100,000). Studies of MDM2 in BTC (N=19) demonstrated variable frequency of MDM2 amplification according to subtype, with consistently high MDM2 amplification rates in GBC (up to 17.5%), and lower rates in CCA (up to 4.4%). The results from this literature review highlight the geographic heterogeneity of BTC and the need for standardised clinicopathologic assessment and reporting to allow cross-study comparisons.

Robotic Manipulation of Cumulus–Oocyte Complexes for Cumulus Cell Removal

The removal of cumulus cells from cumulus–oocyte complexes is a critical step in clinical in vitro fertilization. Since the oocyte is partially occluded by the surrounding cumulus cells and individual cumulus cells are small in size, it is difficult for embryologists to assess the oocyte's maturity before cumulus cell removal and to completely remove all the cumulus cells manually . Furthermore, it is easy for the oocyte to become lost inside the micropipette during aspiration due to the inaccuracy of manual control. To deal with these difficulties, a robotic system was developed to completely remove cumulus cells from mature oocytes. In this study, an EPSANet50 network was developed to accurately assess the maturity of oocytes, avoiding the removal of cumulus cells around the immature oocyte. An adaptive controller was designed to accurately position oocytes at the target position, reducing the loss of oocytes inside the micropipette. An improved Yolov5s network was proposed to quantify the number and size of cumulus cells and assess the completeness of cumulus cell removal. The experimental results on mouse cumulus–oocyte complexes showed that the robotic system had a higher success rate (98.0 ± 1.8% vs. 85.3 ± 2.4%) and lower discard rate (4.1 ± 2.7% vs. 19.6 ± 3.5%) than the manual operation. Moreover, a higher amplification rate and lower non-specific rate were also achieved by the robotic system in the subsequent genetic testing procedure, indicating reduced genetic contamination from the cumulus cells.

Evaluation of ITS1 rDNA primers for the detection and identification of African trypanosomes in mammalian hosts and tsetse flies.

Although several primers targeted to the internal transcribed-spacer 1 (ITS1) of the ribosomal DNA (rDNA) have been designed to improve the detection of African trypanosomes, no study tried to compare their agreement level and ability to amplify different trypanosome species in tsetse flies and mammals in various epidemiological settings. This study was designed to fill this gap, by targeting tsetse-infested areas of Cameroon. For this, archived DNA samples reporting at-least one trypanosome species with species-specific PCR primers were reviewed. Ten sets of primers targeting different ITS1 rDNA sequences of trypanosomes were selected for assessment using single-round and nested-PCR method. Amplification rates (sensitivity) and agreement level of different ITS1 assays were compared using Cohen's-Kappa and McNemar's x2 statistic. Little agreement level (k = 0.05–0.52) were observed between different ITS1-primers PCRs detection of African trypanosome species despite significant (X2=54.3, p = 0.0001) high amplification rate 91.6 % (339/370). This sensitivity varied from quite low for T. simiae (11.9 %) and T. vivax (27.3 %) to fairly good for T. congolence (51.9 %), Trypanozoon (32.4 %) and T. theileri (40.3 %). Primers set targeting ITS1-A sequence of trypanosome species recorded the highest sensitivity (50.5 %) with fairly good agreement compared to 39.2 % for ITS1-C (k = 0.52), 32.4 % for ITS1-R (k = 0.47), 29.7 % for ITS1-N (k = 0.48) and 23.0 % for ITS1-KIN (k = 0.43) respectively. This study revealed a diversity in the sensitivity of different trypanosome species with different sets of ITS-primers enhancing the need to use the same sets of primers in different bio-ecological settings. The use of nested-PCR instead of single-round PCR enabled improvement of trypanosome infections detection in both tsetse and mammals. Among the sets of ITS1-primers tested, those designed by to amplify ITS1-A can be considered as the most appropriate for the detection of trypanosome infections in mammals and tsetse flies.

Development and Characterization of 12 Microsatellite Markers for an Economically Important Fish, Caranx ignobilis, in the Philippines

The giant trevally (Caranx ignobilis) is an important food fish that faces increasing demand due to human population growth, necessitating genetic monitoring. This study intends to spearhead the development of microsatellite markers to assess the genetic variation of C. ignobilis populations. A total of 150 C. ignobilis specimens from six localities in the Philippines were analyzed. Based on next-generation sequencing data, 12 primer pairs were developed with high amplification rates and polymorphism across different loci. This study introduces the first microsatellite markers exclusively for C. ignobilis, which can be used for monitoring and management purposes.

Boron nitride nanoplate-based improvement of the specificity and sensitivity in loop-mediated isothermal amplification for Vibrio parahaemolyticus detection

BackgroundNucleic acid testing based on DNA amplification is gradually entering people's modern life for clinical diagnosis, food safety monitoring and infectious disease prevention. Polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) are the most powerful techniques that have been the gold standard for quantitative nucleic acid analysis. However, the high nonspecific amplification rate caused by the formation of primer dimers, hairpin structures and mismatched hybridization severely restricts their real-world applications. It is highly desirable to explore a way for improving the specificity and sensitivity of PCR and LAMP assays. ResultsIn this work, we demonstrated that a nanomaterial boron nitride nanoplate (BNNP), due to its unique surface properties, can interact with the main components of the amplification reaction, such as single stranded primers and Bst DNA polymerase, and increase the thermal conductivity of the solution. As a result, the presence of BNNPs dramatically improved the specificity of PCR and LAMP. And BNNPs maintained the specificity even after five rounds of PCR. Moreover, the sensitivity of LAMP was also enhanced by BNNPs, and the detection limit of BNNP-based LAMP was two orders of magnitude lower than that of classical LAMP. Then the BNNP-based LAMP was applied to detect Vibrio parahaemolyticus in contaminated seafood samples with high specificity and a 10-fold increase in sensitivity. SignificanceThis is the first systematic demonstration of BNNPs as a promising additive to enhance the efficiency and fidelity of PCR and LAMP amplification reactions, thereby greatly expanding the application of nucleic acid detection in a wide range of laboratory and clinical settings.

De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum.

Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.

Characterization, validation, and cross-species transferability of EST-SSR markers developed from Lycoris aurea and their application in genetic evaluation of Lycoris species

BackgroundThe Lycoris genus includes many ornamentally and medicinally important species. Polyploidization and hybridization are considered modes of speciation in this genus, implying great genetic diversity. However, the lack of effective molecular markers has limited the genetic analysis of this genus.ResultsIn this study, mining of EST-SSR markers was performed using transcriptome sequences of L. aurea, and 839 primer pairs for non-redundant EST-SSRs were successfully designed. A subset of 60 pairs was randomly selected for validation, of which 44 pairs could amplify products of the expected size. Cross-species transferability of the 60 primer pairs among Lycoris species were assessed in L. radiata Hreb, L. sprengeri Comes ex Baker, L. chinensis Traub and L. anhuiensis, of which between 38 to 77% of the primers were able to amplify products in these Lycoris species. Furthermore, 20 and 10 amplification products were selected for sequencing verification in L. aurea and L. radiata respectively. All products were validated as expected SSRs. In addition, 15 SSRs, including 10 sequence-verified and 5 unverified SSRs were selected and used to evaluate the genetic diversity of seven L. radiata lines. Among these, there were three sterile lines, three fertile lines and one line represented by the offspring of one fertile line. Unweighted pair group method with arithmetic mean analysis (UPGMA) demonstrated that the outgroup, L. aurea was separated from L. radiata lines and that the seven L. radiata lines were clustered into two groups, consistent with their fertility. Interestingly, even a dendrogram with 34 individuals representing the seven L. radiata lines was almost consistent with fertility.ConclusionsThis study supplies a pool of potential 839 non-redundant SSR markers for genetic analysis of Lycoris genus, that present high amplification rate, transferability and efficiency, which will facilitate genetic analysis and breeding program in Lycoris.

Observing production and growth of Tollmien–Schlichting waves in subsonic flat plate boundary layer via exciters-free high fidelity numerical simulation

A numerical solution of the Navier–Stokes equations describing the instability of a two-dimensional subsonic flow about a flat plate is presented. It is obtained with the 16th-order multioperators-based scheme without introducing artificial exciters. It shows how small numerical disturbances produced by the scheme generate downstream from the leading edge a succession of wave packets formed by the Tollmien–Schlichting waves. When travelling downstream, the packets demonstrate high amplification rates and the occurrence of separation bubbles. The details of their coming into being, the spatial–temporal progress and the spectra are described.

Genome-wide developed microsatellites reveal a weak population differentiation in the hoverfly Eupeodes corollae (Diptera: Syrphidae) across China.

The hoverfly, Eupeodes corollae, is a worldwide natural enemy of aphids and a plant pollinator. To provide insights into the biology of this species, we examined its population genetic structure by obtaining 1.15-GB random genomic sequences using next-generation sequencing and developing genome-wide microsatellite markers. A total of 79,138 microsatellite loci were initially isolated from the genomic sequences; after strict selection and further testing of 40 primer pairs in eight individuals, 24 polymorphic microsatellites with high amplification rates were developed. These microsatellites were used to examine the population genetic structure of 96 individuals from four field populations collected across southern to northern China. The number of alleles per locus ranged from 5 to 13 with an average of 8.75; the observed and expected heterozygosity varied from 0.235 to 0.768 and from 0.333 to 0.785, respectively. Population genetic structure analysis showed weak genetic differentiation among the four geographical populations of E. corollae, suggesting a high rate of gene flow reflecting likely widespread migration of E. corollae in China.

Development of a DNA mini-barcoding protocol targeting COI for the identification of elasmobranch species in shark cartilage pills

Many elasmobranch (shark and ray) species are considered threatened and their identification in processed products is important for conservation and authentication purposes. However, identification of elasmobranch species in shark cartilage pills has proven difficult using existing methodologies. The objective of this study was to develop a DNA mini-barcoding protocol using a ~130 bp region of the cytochrome c oxidase subunit I (COI) gene for species identification in shark cartilage pills. A total of 22 shark cartilage products underwent DNA extraction in duplicate using the DNeasy Blood and Tissue Kit (Qiagen). The effectiveness of a clean-up step following DNA extraction was analyzed by comparing DNA purity values and polymerase chain reaction (PCR) amplification rates. Next, five different mini-barcode primer sets were compared based on amplification rates, and the three top-performing primer sets were used in DNA sequencing. The incorporation of a clean-up step following DNA extraction showed a slight advantage over DNA extraction alone, with a higher amplification rate (52.3% vs. 47.8%) and A260/A230 value (3.3 vs. 0.6). The three primer sets selected for DNA mini-barcoding showed DNA sequencing rates of 54.5–65.9% among the 44 duplicate samples. When the results for all three primer sets were combined, 18 of the 22 shark cartilage products were identified to the species or genus level. On an individual basis, the best-performing primer set identified 16 of the 22 products to the species or genus level. Overall, the protocol developed in this study increased the identification rate for elasmobranches in cartilage products by more than 2-fold as compared to previous research.

Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients

BackgroundCurrent HCV treatments are genotype specific although potential pan-genotype treatments have recently been described. Therefore, genotyping is an essential tool for the therapeutic management of HCV infection and a variety of technologies have been developed for HCV genotypes determination. Sequences analysis of HCV sub-genomic regions is considered as gold standard and is widely used for HCV genotyping. Here, we compared HCV genotyping using core and NS5B regions in routine practice in HCV-positive Cameroonian patients.MethodsAll plasma samples received at Centre Pasteur of Cameroon (CPC) in 2016 for HCV genotyping were included. Viral loads were determined using the Abbott Real Time assay. Further, genotyping was based on the amplification and sequencing of core and NS5B regions following by phylogenetic analysis of corresponding sequences.ResultsA total of 369 samples were received during the study period with high viral load values (median: 930,952 IU/ml; IQR: 281,833-2,861,179). Positive amplification was obtained in at least one genomic region (core or NS5B) for all the samples with similar amplification rate in the two genomic regions (p = 0.34). Phylogenetic analysis showed that among the 369 samples, 146 (39.6%) were classified as genotype 4, 132 (35.8%) as genotype 1, 89 (24.1%) as genotype 2, in both core and NS5B regions. Interestingly, for two samples (0.54%) discordant genotypes were obtained in both regions with the core region classified as genotype 4 while the NS5B was identified as genotype 1 indicating the presence of putative HCV recombinant virus or multiple infections in these samples. Discrimination of HCV subtypes was most likely possible with NS5B compared to core region.ConclusionsWe found high amplification rates of HCV in both core and NS5B regions, and a good concordance was obtained at genotype level using both regions except for two samples where putative 1–4 recombinants/multiple infections were detected. Therefore, HCV genotyping based on at least two genomic regions could help to identify putative recombinants and improve therapeutic management of HCV infection.

Nuclear and plastidial SNP and INDEL markers for genetic tracking studies of Jacaranda copaia

Nuclear and plastidial single nucleotide polymorphism (SNP) and INDEL markers were developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing for population genetics and timber tracking purposes in the Neotropical timber species Jacaranda copaia. We used 407 nuclear SNPs, 29 chloroplast, and 31 mitochondrial loci to genotype 92 individuals from Brazil, Bolivia, French Guiana, and Peru. Based on high amplification rates and genetic differentiation among populations, 113 nuclear SNPs, 11 chloroplast, and 4 mitochondrial loci were selected, and their use validated for genetic tracking of timber origin.

Screening of polymorphic microsatellites and their application for Saccharina angustata and Saccharina longissima population genetic analysis

Saccharina angustata and S. longissima are ecologically and economically important seaweeds. So far, no microsatellite marker was available to S. angustata and S. longissima due to a lack of genomic data. Here, we developed polymorphic simple sequence repeats (SSRs) in S. longissima and S. angustata and applied these markers for further population genetic analysis. Cross-amplification tests showed that 11 SSR loci exhibited high amplification rate in S. angustata and S. longissima. Polymorphic information content values (PIC) of 11 loci showed 10 loci (PIC = 0.552–0.908), except for SJ31 (PIC = 0.482), have high polymorphism (PIC > 0.5). Polymorphism tests indicated that 10 loci have high polymorphism in three varieties of S. japonica and two related species. Genetic diversity analysis confirmed the validation of these markers in accessing the genetic diversity level of these kelps. STRUCTURE and NJ tree results indicated these 10 microsatellites are effective in evaluating the genetic relationship among different kelp populations. As results, these 10 polymorphic microsatellite markers are valid to Saccharina genetic analysis.

InDel markers: An extended marker resource for molecular breeding in chickpea.

Chickpea is one of the most important food legumes that holds the key to meet rising global food and nutritional demand. In order to deploy molecular breeding approaches in crop improvement programs, user friendly and cost effective marker resources remain prerequisite. The advent of next generation sequencing (NGS) technology has resulted in the generation of several thousands of markers as part of several large scale genome sequencing and re-sequencing initiatives. Very recently, PCR based Insertion-deletions (InDels) are becoming a popular gel based genotyping solution because of their co-dominant, inexpensive, and highly polymorphic nature. With an objective to expand marker resources for genomics assisted breeding (GAB) in chickpea, whole genome re-sequencing data generated on five parental lines of one interspecific (ICC 4958 × PI 489777) and two intra-specific (ICC 283 × ICC 8261 and ICC 4958 × ICC 1882) mapping populations, were used for identification of InDels. A total of 231,658 InDels were identified using Dindel software with default parameters. Further, a total of 8,307 InDels with ≥20 bp size were selected for development of gel based markers, of which primers could be designed for 7,523 (90.56%) markers. On average, markers appeared at a frequency of 1,038 InDels/LG with a maximum number of markers on CaLG04 (1,952 InDels) and minimum on CaLG08 (360 InDels). In order to validate these InDels, a total of 423 primer pairs were randomly selected and tested on the selected parental lines. A high amplification rate of 80% was observed ranging from 46.06 to 58.01% polymorphism rate across parents on 3% agarose gel. This study clearly reflects the usefulness of available sequence data for the development of genome-wide InDels in chickpea that can further contribute and accelerate a wide range of genetic and molecular breeding activities in chickpea.

A high-gain and high-fidelity coherent state comparison amplifier

Optical signals are subject to a distance-dependent loss as they propagate through transmission media. High-intensity, classical, optical signals can routinely be amplified to overcome the degradation caused by this loss. However, quantum optical states cannot be deterministically amplified and any attempt to do so will introduce intrinsic noise that spoils the desired quantum properties. Non-deterministic optical amplification, based on post-selection of the output depending on certain conditioning detection outcomes, is an emerging enabling technology in quantum measurement and quantum communications. Here we present an investigation into the properties of a simple, modular optical state comparison amplifier operating on weak coherent states. This amplifier requires no complex quantum resources and is based on linear optical components allowing for a high amplification rate at high gain and fidelity. We examine the amplifier’s performance in different configurations and develop an accurate analytical model that accounts for typical experimental scenarios.

Microsatellite Marker for Cross-Species Amplification: Study Case for Indonesian Sundaland Python (Serpentes: Pythonidae)

The python of Indonesian Sundaland has been traded for its distinct skin colour and patterns. The need for rapid method in cross-species amplification for Indonesian Sundaland python is useful to contribute in management of sustainability harvesting system. In this research, we screened 10 microsatellite primers which are previously used for Australian, New Guinean, Chinese and Burmese pythons and 7 potentially amplifiable primers for African and Asian reptiles. Python breitensteini showed a greater number of alleles (2-8 alleles) than Python bivittatus (1-3 alleles) and Python brongersmai (1-2 alleles). The observed and expected heterozygosity for all species were ranged from 0 to 1.00 and 0 to 0.79, respectively. According to the high cross-species amplification rates, 15 out of 17 primers were useful in assessing the genetic diversity and conservation genetic of Indonesian Sundaland python. Among the 15 primers, MS3 generated the highest number of allele for P. breitensteini (8 alleles), P. bivittatus (3 alleles), and P. brongersmai (2 alleles). We proposed MS3 locus as a suitable marker for Indonesian Sundaland python. Keywords: microsatellite, Python, Sundaland.

Forensic genetic analysis of bone remain samples

DNA typing from degraded human remains is still challenging forensic DNA scientists not only in the prospective of DNA purification but also in the interpretation of established DNA profiles and data manipulation, especially in mass fatalities. In this report, we presented DNA typing protocol to investigate many skeletal remains in different degrees of decomposing. In addition, we established the grading system aiming for prior determination of the association between levels of decomposing and overall STR amplification efficacy. A total of 80 bone samples were subjected to DNA isolation using the modified DNA IQ™ System (Promega, USA) for bone extraction following with STR analysis using the AmpFLSTR Identifiler® (Thermo Fisher Scientific, USA). In low destruction group, complete STR profiles were observed as 84.4% whereas partial profiles and non-amplified were found as 9.4% and 6.2%, respectively. Moreover, in medium destruction group, both complete and partial STR profiles were observed as 31.2% while 37.5% of this group was unable to amplify. Nevertheless, we could not purify DNA and were unable to generate STR profile in any sample from the high destroyed bone samples. Compact bones such as femur and humerus have high successful amplification rate superior than loose/spongy bones. Furthermore, costal cartilage could be a designate specimen for DNA isolation in a case of the body that was discovered approximately to 3 days after death which enabled to isolate high quality and quantity of DNA, reduce time and cost, and do not require special tools such as freezer mill.

The status of Her2 amplification and Kras mutations in mucinous ovarian carcinoma

Jayson GC et al. remarked in Lancet that nearly 100% of mucinous ovarian cancer cases have Kras mutation as well as a high frequency of Her2 amplification. Using the Abbott PathVysion Her2 DNA Probe Kit and Kras mutant-enriched PCR Kits (FemtoPath®), 21 samples of primary ovarian mucinous cystadenocarcinomas from Taiwanese patients were examined to determine the status of Her2 amplification and Kras mutations. Our results showed the Her2 amplification rates were 33.33%, while the Kras mutation rates were 61.90%. We present here our results in order to enlighten the readership that the ~100% Kras mutant frequency and the high Her2 amplification rate reported by Jayson et al. may be too exaggerated to be applicable into all populations. Additionally, we report another 2 novel Kras mutations (A11V, V14I).

Multilocus genotyping of Giardia duodenalis (Lambl, 1859) from symptomatic human infections in Slovenia.

Giardiasis is a common gastrointestinal infection of humans and animals with a worldwide distribution. Eight genetic groups (known as assemblages A to H) are currently recognised within the species complex of Giardia duodenalis (Lambl, 1859), of which assemblages A and B are responsible for infection of humans and other mammalian hosts. Genotyping data on giardiasis are not available from Slovenia. In this work, we have characterised isolates of G. duodenalis from 85 human symptomatic cases collected during 2002-2013. Genomic DNAs were first tested by a real-time (rt) PCR assay and then by conventional PCR at three loci (beta-giardin, bg; triose phosphate isomerase, tpi; and glutamate dehydrogenase, gdh). We found that the threshold cycle (Ct) values in rt-PCR testing were higher for samples collected during 2002-2005 and that this was paralleled by a low amplification rate in conventional PCR (6 of 32, i.e. 19%). In contrast, lower Ct values and higher amplification rate (45 of 53; 85%) were observed for samples collected during 2006-2013, suggesting an adverse effect of prolonged freezing of stools. Assemblages A and B were found with an almost identical frequency in the 51 genotyped samples. In agreement with previous studies, sequences from assemblage B isolates were characterised by larger genetic variability and by the presence of heterogeneous positions, which made assignment to specific genotypes difficult. Less variability was observed in sequences from assemblage A isolates, which belonged to the human-specific subassemblage AII. These data showed that the genotypes of G. duodenalis that circulate in humans in Slovenia are similar to those previously identified in Europe.

Shear wave velocity mapping of Hat Yai district, southern Thailand: implication for seismic site classification

Soil characteristics play an important role in the degree of ground shaking due to local site amplification during an earthquake. The objectives of this work are to study shear wave velocity (Vs) distribution in the near surface, and to develop a seismic site classification map for soil effect characterization and seismic hazard assessment in Hat Yai district, southern Thailand. The Vs determination based on the multichannel analysis of surface waves technique, has been carried out and analyzed at 70 measuring sites throughout the district. On the basis of the weighted-average Vs in the upper 30 m depth (Vs30), a seismic site classification map, based on the National Earthquake Hazards Reduction Program (NEHRP) standard has been developed. It is found that the NEHRP site class in Hat Yai can be classified into four groups in accordance with the value of Vs30 within the range of about 150 to 1160 m s−1. Most parts of the study area are typically classified as site class C and D. Site class C is mostly found within the colluvial and terrace deposits in the western and eastern part of the area, whereas site class D is concentrated in the alluvial sediment of the middle and northern flood plain areas. A small portion of site class B is observed in the western mountain ranges, where there is a thin overburden on the firm rock. There is a remarkably low Vs30 value at only one site, located near the main stream in the northern part of the study area. The results imply that the soil characteristics in the central and northern Hat Yai district pose a medium to high amplification rate with respect to the other regions. Although Vs data alone are insufficient to verify the potential of the amplification of ground shaking, this study provides an initial attempt to understand seismic hazards in the study area.