Small Panel Research Articles

Development of a dual antigen lateral flow immunoassay for detecting Yersinia pestis.

Yersinia pestis is the causative agent of plague, a zoonosis associated with small mammals. Plague is a severe disease, especially in the pneumonic and septicemic forms, where fatality rates approach 100% if left untreated. The bacterium is primarily transmitted via flea bite or through direct contact with an infected host. The 2017 plague outbreak in Madagascar resulted in more than 2,400 cases and was highlighted by an increased number of pneumonic infections. Standard diagnostics for plague include laboratory-based assays such as bacterial culture and serology, which are inadequate for administering immediate patient care for pneumonic and septicemic plague. The goal of this study was to develop a sensitive rapid plague prototype that can detect all virulent strains of Y. pestis. Monoclonal antibodies (mAbs) were produced against two Y. pestis antigens, low-calcium response V (LcrV) and capsular fraction-1 (F1), and prototype lateral flow immunoassays (LFI) and enzyme-linked immunosorbent assays (ELISA) were constructed. The LFIs developed for the detection of LcrV and F1 had limits of detection (LOD) of roughly 1-2 ng/mL in surrogate clinical samples (antigens spiked into normal human sera). The optimized antigen-capture ELISAs produced LODs of 74 pg/mL for LcrV and 61 pg/mL for F1 when these antigens were spiked into buffer. A dual antigen LFI prototype comprised of two test lines was evaluated for the detection of both antigens in Y. pestis lysates. The dual format was also evaluated for specificity using a small panel of clinical near-neighbors and other Tier 1 bacterial Select Agents. LcrV is expressed by all virulent Y. pestis strains, but homologs produced by other Yersinia species can confound assay specificity. F1 is specific to Y. pestis but is not expressed by all virulent strains. Utilizing highly reactive mAbs, a dual-antigen detection (multiplexed) LFI was developed to capitalize on the diagnostic strengths of each target.

Neuraminidase inhibitor treatment is associated with decreased mortality in COVID-19 patients: a retrospective analysis.

AimsThe aim of this study was to investigate the effects of Neuraminidase inhibitors (NI) on COVID-19 in a retrospective study.Methods and resultsThe study included an overall COVID-19 patients (n = 3267) and a 1:1 propensity score-matched patients (n = 972). The levels of plasma N-acetylneuraminic acid and neuraminidase expression were further evaluated in a panel of hospitalized and 1-month post-infection recovered COVID-19 subjects. The mortality rate in the overall patients was 9.6% (313/3267) and 9.2% (89/972) in the propensity-score matched patients. The NI treatment lowered the mortality rate (5.7% vs. 10.3%) and the critically ill conversion rate (14.1% vs. 19.7%) compare to those in the non-NI group in the overall patients and evaluated in the propensity score-matched patients when applying the multivariate Cox model for adjusting imbalanced confounding factors. Furthermore, NI treatment was associated with attenuated cytokine storm levels and acute heart injury but not liver or kidney injuries. Further analysis in a small panel of patients found the levels of N-acetylneuraminic acid and neuraminidase (dominantly the NEU3 isoform) were elevated in the hospitalized COVID-19 subjects and recovered at the 1-month post-infection stage, suggesting increasing desialylation in COVID-19 patients.ConclusionThese results suggest that NI treatment is associated with decreased mortality in COVID-19 subjects, especially for those subjects with acute heart injury.

Small Molecule Signatures of Mice Lacking T-cell p38 Alternate Activation, a Model for Immunosuppression Conditions, after Total-Body Irradiation.

Several diagnostic biodosimetry tools have been in development that may aid in radiological/nuclear emergency responses. Of these, correlating changes in non-invasive biofluid small-molecule signatures to tissue damage from ionizing radiation exposure show promise for inclusion in predictive biodosimetry models. Integral to dose reconstruction has been determining how genotypic variation in the general population will affect model performance. Here, we used a mouse model that lacks the T-cell receptor specific alternative p38 pathway [p38αβY323F, double knock-in (DKI) mice] to determine how attenuated autoimmune and inflammatory responses may affect dose reconstruction. We exposed adult male DKI mice (8-10 weeks old) to 2 and 7 Gy in parallel with wild-type mice and assessed perturbations in urine (days 1, 3, 7) and serum (day 1) using a global metabolomics approach. A multidimensional scaling plot showed excellent separation of radiation-exposed groups in wild-type mice with slightly dampened responses in DKI mice. Validated metabolite panels were developed for urine [N6,N6,N6-trimethyllysine (TML), N1-acetylspermidine, spermidine, carnitine, acylcarnitine C21H35NO5, aminohippuric acid] and serum [phenylalanine, glutamine, propionylcarnitine, lysophosphatidylcholine (LysoPC 14:0), LysoPC (22:5)] to determine the area under the receiver operating characteristic curve (AUROC). For both urine and serum, excellent sensitivity and specificity (AUROC > 0.90) was observed for 0 Gy vs. 7 Gy groups irrespective of genotype using identical metabolite panels. Similarly, excellent to fair classification (AUROC > 0.75) was observed for ≤2 Gy vs. 7 Gy mice for both genotypes, however, model performance declined (AUROC < 0.75) between genotypes after irradiation. Overall, these results suggest immunosuppression should not compromise small molecule multiplex panels used in dose reconstruction for biodosimetry.

Numerical Study on the Effect of Different Steel Reinforcement Arrangement in Reinforced Concrete Wall Subjected to Blast Load

Reinforced concrete (RC) is the most preferred construction material for the civilian structural construction such as building and bridge because it is economical to build and possesses high strength. There have been several verified numerical studies on RC, but most have all been limited to the scope of a small rectangular or small square RC panel clamped at the edges. As a result, there is still a need for a complete RC structure for example RC wall with its foundation to represent as a single stand structure. With available validated complete RC structure experimentally and numerical data on blast pressure profile, detail numerical study is possible to investigate in depth. In AUTODYN commercial software, arbitrary Lagrange Euler (ALE) solvers are used to analyse the interaction between air and RC wall structure. The RC walls were built with the same moment resistance but a different hooked direction on vertical flexural steel reinforcement into the foundation. The numerical result indicated that in the hooked-in direction, the average strain at the back side of the wall peaked at 1.0625×10-3 at first 5 msec after impact, which is half of what it was in the hooked- out direction. Furthermore, the numerical simulation coincided with the experimental findings, where the proper steel arrangement for the RC wall subjected to blast was hooked-in.

NetAUC: A network-based multi-biomarker identification method by AUC optimization.

Complex diseases are caused by a variety of factors, and their diagnosis, treatment and prognosis are usually difficult. Proteins play an indispensable role in living organisms and perform specific biological functions by interacting with other proteins or biomolecules, their dysfunction may lead to diseases, it is a natural way to mine disease-related biomarkers from protein-protein interaction network. AUC, the area under the receiver operating characteristics (ROC) curve, is regarded as a gold standard to evaluate the effectiveness of a binary classifier, which measures the classification ability of an algorithm under arbitrary distribution or any misclassification cost. In this study, we have proposed a network-based multi-biomarker identification method by AUC optimization (NetAUC), which integrates gene expression and the network information to identify biomarkers for the complex disease analysis. The main purpose is to optimize two objectives simultaneously: maximizing AUC and minimizing the number of selected features. We have applied NetAUC to two types of disease analysis: 1) prognosis of breast cancer, 2) classification of similar diseases. The results show that NetAUC can identify a small panel of disease-related biomarkers which have the powerful classification ability and the functional interpretability.

A Comparative Analysis between Battery- and Solar-Powered Wireless Sensors for Soil Water Monitoring

Wireless sensor networks (WSN) have found wide applications in many fields (such as agriculture) over last few years, and research interest is constantly increasing. However, power supply to the sensor nodes remains an issue to be resolved. Batteries are usually used to power the sensor nodes, but they have a limited lifetime, so solar energy harvesters are a good alternative solution. This study provides a comparative analysis between battery and solar energy harvesters for sensor nodes used for soil water monitoring. Experimental results show that small-sized solar panels with low-power energy harvester circuits and rechargeable batteries distinctly outperform secondary batteries in outdoor and continuous-operation applications. The power level of the energy storage device of sensor node 1, which was powered by a small PV panel, remained constantly close to 90% for all days. The power of the other three nodes, which were powered by a rechargeable battery, was initially at 100% of the charge and gradually started to reduce. Sensor node 1 performed a total of 1288 activations during the experimental period, while sensor nodes 2 and 4 behaved satisfactorily and performed a total of 781 and 803 activations, respectively. In contrast, sensor node 3 did not exhibit the same behavior throughout the experiments.

Identification of the most specific markers to differentiate primary pulmonary carcinoma from metastatic gastrointestinal carcinoma to the lung

BackgroundA number of biomarkers have the potential of differentiating between primary lung tumours and secondary lung tumours from the gastrointestinal tract, however, a standardised panel for that purpose does not exist yet. We aimed to identify the smallest panel that is most sensitive and specific at differentiating between primary lung tumours and secondary lung tumours from the gastrointestinal tract.MethodsA total of 170 samples were collected, including 140 primary and 30 non-primary lung tumours and staining for CK7, Napsin-A, TTF1, CK20, CDX2, and SATB2 was performed via tissue microarray. The data was then analysed using univariate regression models and a combination of multivariate regression models and Receiver Operating Characteristic (ROC) curves.ResultsUnivariate regression models confirmed the 6 biomarkers’ ability to independently predict the primary outcome (p < 0.001). Multivariate models of 2-biomarker combinations identified 11 combinations with statistically significant odds ratios (ORs) (p < 0.05), of which TTF1/CDX2 had the highest area under the curve (AUC) (0.983, 0.960–1.000 95% CI). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 75.7, 100, 100, and 37.5% respectively. Multivariate models of 3-biomarker combinations identified 4 combinations with statistically significant ORs (p < 0.05), of which CK7/CK20/SATB2 had the highest AUC (0.965, 0.930–1.000 95% CI). The sensitivity, specificity, PPV, and NPV were 85.1, 100, 100, and 41.7% respectively. Multivariate models of 4-biomarker combinations did not identify any combinations with statistically significant ORs (p < 0.05).ConclusionsThe analysis identified the combination of CK7/CK20/SATB2 to be the smallest panel with the highest sensitivity (85.1%) and specificity (100%) for predicting tumour origin with an ROC AUC of 0.965 (p < 0.001; SE: 0.018, 0.930–1.000 95% CI).

Reforming the workers’ compensation process for occupational lung disease among miners in South Africa: an efficiency study of claims assessment

The large burden of silicosis and tuberculosis (TB) in the South African mining industry, coupled with an under-resourcing of the compensation agencies responsible for certifying occupational lung disease, have resulted in serious backlogs. This work aimed to measure the efficiency gains from triaging occupational lung disease claims using claim type, years of mining exposure and computer aided detection (CAD) to save on scarce medical adjudicators. During 2020, the compensation authority started to triage claims for TB and those of miners with < 10years of service to two-person panels instead of the four-person panel plus radiologist used previously. Efficiency gain was calculated in medical person-units saved and reduction in delays. Different service thresholds predictive of silicosis were simulated, as well as the impact of pre-classification of chest X-rays with CAD using different combinations of sensitivity and specificity. The new triage system saved 20.3% in person-time units and reduced delays by 10-20days. Without CAD the greatest efficiency gain (28%) was projected from dispensing with a mining service threshold and routing all non-TB claims to the small panels at the outset. Simulation of four different CAD sensitivity/specificity combinations yielded efficiency gains of 18.2-36.1%, with 31.1% judged the most realistic. Use of sensitivity of close to 100% would not be feasible because of the very low resulting specificity. Pre-adjudication triage of claims at the compensation agency is capable of saving a substantial proportion of adjudicator time and reducing certification delays. Additional efficiency gains are achievable by referring all claims to small panels to begin with and improvement of CAD performance for this ex-miner population.

Étude de deux petits panneaux de l’entourage de Goya : mise en lumière de pratiques d’atelier

L’étude technique de deux petits panneaux de l’entourage de Goya, le Christ au mont des Oliviers (Paris, musée du Louvre) et la Dernière communion de san José de Calasanz (Bayonne, musée Bonnat-Helleu) a permis de mettre en évidence des pratiques communes d’atelier portant tant sur le support et la préparation que sur le mode de cadrage. Elles éclairent la pratique de l’atelier de Goya vers 1819.

EFFECTIVENESS OF PREDICTING THE PRODUCTIVE QUALITIES OF BEEF CATTLE BY QTL ASSOCIATED SNP

The article presents the results of assessing the possibilities of predicting the meat productivity of Kazakh white-headed and Auliekol cattle by increasing alleles of QTL associated SNP. 4 polymorphic sites were selected for each of the breeds. Priority in the selection of targets were given to those with a higher frequency of occurrence of an alternative allele (at least 15%), location in different functional regions of the genome and genes, and distribution by chromosomes, as well as belonging to known QTL. Analysis of the genotypes of the sample showed that homozygosity for all 4 minor alleles (increasing) were not detected simultaneously in any animal in the sample. It was also not possible to identify animals carrying 7 alleles at the same time. The presence of 3 or more "increasing" alleles in animals of the Kazakh white-headed breed, regardless of the specific polymorphic variant, indicated that its live weight index in 12 months would exceed the average for the sample by 10 kg, and in comparison, with animals that do not carry any such allele – by 15 kg. The identification of 5 or more increasing alleles may probably indicate an even more significant increase in the live weight of the animal at 12 months (20 kg). The Auliekol breed, as in the case of the Kazakh white-headed breed, approximates the trait value to the upper limit of the trait norm as the number of increasing alleles increase. In this case, it can be stated that for the development and application of small diagnostic panels to predict increased productivity of animals, it is enough to detect from 3 to 6 increasing alleles. However, due to the insufficient amount of data, it is worth treating this data with caution at this stage of work. Increasing the sample will allow more specific data to be obtained in the future.

The use of a photovoltaic system in a single family house in Poland – case study

Renewable energy is becoming widely used all over the world nowadays. More single-family houses use such sources to generate heat and electricity. The article presents a case study of a house located in central Poland, in which a photovoltaic system was used, additionally with other renewable sources, such as a small wind turbine, biomass boiler and solar panels. The article describes the advantages of using renewable energy sources in the building sector considered and presents the results of experimental studies of electricity generation in a given period of time with their analysis. It turned out that the production of electricity using photovoltaic panels in autumn can support high electricity demand at this time.

‘Where are the dead flies!’: perceptions of local communities towards the deployment of Tiny Targets to control tsetse in the Democratic Republic of the Congo

The National Programme for the control of human African trypanosomiasis in Democratic Republic of Congo includes a large-scale vector control operation using Tiny Targets. These are small panels of insecticide-impregnated...

Development of Epigenetic Clocks for Key Ruminant Species.

Robust biomarkers of chronological age have been developed in humans and model mammalian species such as rats and mice using DNA methylation data. The concept of these so-called “epigenetic clocks” has emerged from a large body of literature describing the relationship between genome-wide methylation levels and age. Epigenetic clocks exploit this phenomenon and use small panels of differentially methylated cytosine (CpG) sites to make robust predictions of chronological age, independent of tissue type. Here, we present highly accurate livestock epigenetic clocks for which we have used the custom mammalian methylation array “HorvathMammalMethyl40” to construct the first epigenetic clock for domesticated goat (Capra hircus), cattle (Bos taurus), Red (Cervus elaphus) and Wapiti deer (Cervus canadensis) and composite-breed sheep (Ovis aries). Additionally, we have constructed a ‘farm animal clock’ for all species included in the study, which will allow for robust predictions to be extended to various breeds/strains. The farm animal clock shows similarly high accuracy to the individual species’ clocks (r > 0.97), utilizing only 217 CpG sites to estimate age (relative to the maximum lifespan of the species) with a single mathematical model. We hypothesise that the applications of this livestock clock could extend well beyond the scope of chronological age estimates. Many independent studies have demonstrated that a deviation between true age and clock derived molecular age is indicative of past and/or present health (including stress) status. There is, therefore, untapped potential to utilize livestock clocks in breeding programs as a predictor for age-related production traits.

Molecular Evaluation of Endometrial Dedifferentiated Carcinoma, Endometrioid Carcinoma, Carcinosarcoma, and Serous Carcinoma Using a Custom-Made Small Cancer Panel.

It is often difficult to histologically differentiate among endometrial dedifferentiated carcinoma (DC), endometrioid carcinoma (EC), serous carcinoma (SC), and carcinosarcoma (CS) due to the presence of solid components. In this study, we aimed to categorize these carcinomas according to The Cancer Genome Atlas (TCGA) classification using a small custom-made cancer genome panel (56 genes and 17 microsatellite regions) for integrated molecular diagnosis. A total of 36 endometrial cancer cases with solid components were assessed using IHC, next-generation sequencing (NGS), and the custom-made panel. Among 19 EC cases, six were categorized as MMR-deficient (MMR-d) and eight were classified as having a nonspecific molecular profile. Three EC cases were classified as POLE mutation (POLEmut)-type, which had a very high tumor mutation burden (TMB) and low microsatellite instability (MSI). Increased TMB and MSI were observed in all three DC cases, classified as MMR-d with mutations in MLH1 and POLD1. Except for one case classified as MMR-d, all SC cases exhibited TP53 mutations and were classified as p53 mutation-type. SC cases also exhibited amplification of CCND1, CCNE1, and MYC. CS cases were classified as three TCGA types other than the POLEmut-type. The IHC results for p53 and ARID1A were almost consistent with their mutation status. NGS analysis using a small panel enables categorization of endometrial cancers with solid proliferation according to TCGA classification. As TCGA molecular classification does not consider histological findings, an integrated analytical procedure including IHC and NGS may be a practical diagnostic tool for endometrial cancers.

Development and Validation of a Targeted 'Liquid' NGS Panel for Treatment Customization in Patients with Metastatic Colorectal Cancer.

The detection of actionable mutations in tumor tissue is a prerequisite for treatment customization in patients with metastatic colorectal cancer (mCRC). Analysis of circulating tumor DNA (ctDNA) for the identification of such mutations in patients’ plasma is an attractive alternative to invasive tissue biopsies. Despite having the high analytical sensitivity required for ctDNA analysis, digital polymerase chain reaction (dPCR) technologies can only detect a very limited number of hotspot mutations, whilst a broader mutation panel is currently needed for clinical decision making. Recent advances in next-generation sequencing (NGS) have led to high-sensitivity platforms that allow screening of multiple genes at a single assay. Our goal was to develop a small, cost- and time-effective NGS gene panel that could be easily integrated in the day-to-day clinical routine in the management of patients with mCRC. We designed a targeted panel comprising hotspots in six clinically relevant genes (KRAS, NRAS, MET, BRAF, ERBB2 and EGFR) and validated it in a total of 68 samples from 30 patients at diagnosis, first and second disease progression. Results from our NGS panel were compared against plasma testing with BEAMing dPCR regarding the RAS gene status. The overall percent of agreement was 83.6%, with a positive and negative percent agreement of 74.3% and 96.2%, respectively. Further comparison of plasma NGS with standard tissue testing used in the clinic showed an overall percent agreement of 86.7% for RAS status, with a positive and negative percent agreement of 81.2% and 92.8%, respectively. Thus, our study strongly supports the validity and efficiency of an affordable targeted NGS panel for the detection of clinically relevant mutations in patients with mCRC.

In Vitro Anti-SARS-CoV-2 Activity of Selected Metal Compounds and Potential Molecular Basis for Their Actions Based on Computational Study.

Metal-based drugs represent a rich source of chemical substances of potential interest for the treatment of COVID-19. To this end, we have developed a small but representative panel of nine metal compounds, including both synthesized and commercially available complexes, suitable for medical application and tested them in vitro against the SARS-CoV-2 virus. The screening revealed that three compounds from the panel, i.e., the organogold(III) compound Aubipyc, the ruthenium(III) complex KP1019, and antimony trichloride (SbCl3), are endowed with notable antiviral properties and an acceptable cytotoxicity profile. These initial findings prompted us to perform a computational study to unveil the likely molecular basis of their antiviral actions. Calculations evidenced that the metalation of nucleophile sites in SARS-CoV-2 proteins or nucleobase strands, induced by Aubipyc, SbCl3, and KP1019, is likely to occur. Remarkably, we found that only the deprotonated forms of Cys and Sec residues can react favorably with these metallodrugs. The mechanistic implications of these findings are discussed.

Simulation of Self-Consumption in Small Photovoltaic Panel Energy Application: A Case Study in Estonia

Simulation of Self-Consumption in Small Photovoltaic Panel Energy Application: A Case Study in Estonia

Targeting peripheral immune organs with self-assembling prodrug nanoparticles ameliorates allogeneic heart transplant rejection

Organ transplantation has become a mainstay of therapy for patients with end-stage organ diseases. However, long-term administration of immunosuppressive agents, a scheme for improving the survival of transplant recipients, has been compromised by severe side effects and posttransplant complications. Therapeutic delivery targeting immune organs has the potential to address these unmet medical issues. Here, through screening of a small panel of mammalian target of rapamycin complex kinase inhibitor (TORKinib) compounds, a TORKinib PP242 is identified to be able to inhibit T cell function. Further chemical derivatization of PP242 using polyunsaturated fatty acids (i.e., docosahexaenoic acid) transforms this water-insoluble hydrophobic agent into a self-assembling nanoparticle (DHA-PP242 nanoparticle [DPNP]). Surface PEGylation of DPNP with amphiphilic copolymers renders the nanoparticles aqueously soluble for preclinical studies. Systemically administered DPNP shows tropism for macrophages within peripheral immune organs. Furthermore, DPNP regulates differentiation of adoptively transferred T cells in a macrophage-dependent manner in Rag1-/- mouse model. In an experimental model of heart transplantation, DPNP significantly extends the survival of grafts through inducing immune suppression, thus reducing the inflammatory response of the recipients. These findings suggest that targeted delivery of TORKinibs exploiting prodrug-assembled nanoparticle scaffolds may provide a therapeutic option against organ rejection.

Safety Levels and Occupant Injury Risk for Light Commercial Vehicles in the ASEAN Region: Results of Crashworthiness Data

The logistics industry in Malaysia has greatly evolved in recent years. With regard to the freight industry, business operations depend on transportation service using commercial vehicles to deliver products in a timely manner. Technically categorised as N1 vehicle, the Light Commercial Vehicle (LCV) or light duty truck is designed to carry goods with maximum load not exceeding 3.5 tons. To maximize cargo size, the occupant cabin space has been pushed forward, hence, becoming a ‘flat head type’ vehicle. Nevertheless, the flat head vehicle fared poorly in terms of its crashworthiness performance during a frontal collision. In the ASEAN region, the automotive market for LCVs or the ‘People Mover’ trails behind passenger cars (M1 category) from the safety aspect where most small lorries or panel vans are sold with the lowest safety standards due to undemanding requirements and regulations imposed on this vehicle category. To examine the current issue surrounding this vehicles category in ASEAN, this paper shall discuss 1) the results of crashworthiness data for LCVs based on the assessment conducted by ASEAN NCAP and Japan NCAP and 2) review the leg injury analysis involving five LCVs tested by ASEAN NCAP. The vehicles with the worst performance for both NCAPs were compared, namely the TATA Super Ace (ASEAN NCAP) which came with no safety features, and the Daihatsu Hijet Cargo DX (Japan NCAP) which was equipped with ABS, airbag for both driver and front passenger, seatbelt pretensioner for driver and front passenger, as well as seatbelt load limiter for the driver and front passenger. The results showed that the driver and front passenger of the TATA Super Ace sustained very serious lower extremity, chest, and head injuries compared to Japan NCAP’s low performing LCV. In addition, five LCV models (TATA Super Ace, Chana Era Star II, DFSK V25L, Suzuki Carry, and Cherry Transcab) were tested by ASEAN NCAP without the fitment of any protection to the driver and front passenger during frontal crashes. As a result, the occupants, especially the driver, faced a very high risk of sustaining serious lower extremity, chest, and head injuries. The crash test results led to all five LCV models tested being awarded zero-star safety rating. The injury analysis also proved that the driver fatality was greatly affected by severe injuries, or AIS 3+ in the head, lower extremity and chest. It can be concluded that the safety of LCVs in ASEAN is a cause for serious concern where improvements are urgently needed to ensure that this vehicle category is equipped with sufficient safety features.

Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers.

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.