Non-Small Cell Lung Cancer: Targetable Variants in Concurrent Tissue and Liquid Biopsy Testing in a North Indian Cohort.

OBJECTIVES: Testing for EGFR, ALK, ROS1 and MET alterations in paired tissue and plasma samples of treatment-naïve patients of NSCLC and correlating their status with overall survival. MATERIALS AND METHODS: One hundred treatment-naïve patients were recruited after obtaining informed consent. Ten ml of blood was collected within a period of two weeks from histological diagnosis, prior to the start of any treatment. DNA & RNA extraction was done from formalin-fixed paraffin embedded (FFPE) tissue and total cell-free nucleic acid extraction was done from plasma samples. EGFR mutation, ALK, ROS1 and MET rearrangements were tested by ARMS (Amplification Refractory Mutation System) PCR. All statistical analyses were conducted in R version 4.1.1. RESULTS: A total of 61 cases showed molecular alterations in tissue samples which included EGFR mutations (47), ALK rearrangements (12), ROS1 fusion (2). MET alteration was not detected. Forty-three cases showed EGFR mutations in plasma, 26 of which were concurrently positive in tissue. Concordance observed was 62%. ALK-EML4 rearrangement, ROS1 fusion and MET were not detected in plasma samples. Sensitivity and specificity for detection of EGFR mutation in plasma were 55.3% and 67.9% respectively. Univariate Cox regression analysis showed a positive association between EGFR mutation in tissue and overall survival (HR = 0.4; 95% CI: 0.2-0.7; p = 0.003) and improved overall survival in those who received targeted therapy (HR = 0.29; 95% CI: 0.1-0.8; p = 0.02). CONCLUSION: Concurrent testing in tissue and liquid biopsy in NSCLC increased the detection of EGFR mutations (47% to 64%). This has substantial implications in deciding treatment and administration targeted therapy and the consequent overall survival.

A Rapid Method for Determination of Serum Methotrexate Using Ultra-High-Performance Liquid Chromatography-Tandem Mass Spectrometry and Its Application in Therapeutic Drug Monitoring.

Objectives Methotrexate (MTX) has anticancer therapeutic potential with multiple doses-related adverse effects and toxicities. Immunoassays for therapeutic monitoring of serum MTX have their own limitations. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is considered as the reference method; however, commercially availability of them is limited. We aimed to adapt/develop an in-house LC-MS/MS method for therapeutic monitoring of serum MTX. Materials and Methods Serum protein precipitation was performed using acetonitrile-water containing 250 µM solution of aminoacetophenone as internal standard (IS). Chromatographic separation was achieved on a C18 column with mobile phase of 0.1% solution of formic acid (solvent A) and acetonitrile (solvent B) at a flow rate of 0.4 mL/min. MS was performed under positive ion mode with mass transition for MTX and IS as m/z 455.1→308.1 and 136.2→94.1, respectively. The method was validated by following Bioanalytical Method Validation Guidance for Industry, 2018 and applied on leukemia patients' samples on MTX therapy. Results The correlation coefficient of eight serially diluted calibration standards of 0.09 to 12.5 µM was >0.99 and had linearity with > 95% precision and accuracy at analytical quality control levels. The lower limit of MTX quantification achieved was 0.09 µM with good intensity and sharp peak as compared with blank sample. The total run time of the assay was 5 minutes. The serum MTX levels obtained by this method in leukemia patients exhibited clinical correlation and an excellent agreement with commercial immunoassay used in parallel. Conclusion We were able to develop a rapid, sensitive, and cost-effective LC-MS/MS method suitable for therapeutic drug monitoring of MTX in routine clinical diagnostic laboratories.

Sensitivity and specificity of phrenic nerve electrophysiology to predict mechanical ventilation in the Guillain-Barré syndrome.

INTRODUCTION/AIMS: In Guillain-Barré syndrome (GBS), the sensitivity and specificity of phrenic compound muscle action potential (CMAP) measurements to predict endotracheal mechanical ventilation are unknown. Hence, we sought to estimate sensitivity and specificity. METHODS: We performed a 10-year retrospective analysis of adult GBS patients from our single-center laboratory database (2009 to 2019). The phrenic nerve amplitudes and latencies before ventilation were recorded along with other clinical and demographic features. Receiver operating curve (ROC) analysis with area under the curve (AUC) was used to determine the sensitivity and specificity with 95% confidence interval (CI) for phrenic amplitudes and latencies in predicting the need for mechanical ventilation. RESULTS: Two hundred five phrenic nerves were analyzed in 105 patients. The mean age was 46.1 ± 16.2 years, with 60% of them being male. Fourteen patients (13.3%) required mechanical ventilation. The average phrenic amplitudes were lower in the ventilated group (P = .003), but average latencies did not differ (P = .133). ROC analysis confirmed that phrenic amplitudes could predict respiratory failure (AUC = 0.76; 95% CI, 0.61 to 0.91; P < .002), but phrenic latencies could not (AUC = 0.60; 95% CI, 0.46 to 0.73; P = .256). The best threshold for amplitude was ≥0.6 mV, with sensitivity, specificity, and positive and negative predictive values of 85.7%, 58.2%, 24.0%, and 96.4%, respectively. DISCUSSION: Our study suggests that phrenic CMAP amplitudes can predict the need for mechanical ventilation in GBS. In contrast, phrenic CMAP latencies are not reliable. The high negative predictive value of phrenic CMAP amplitudes ≥0.6 mV can preclude mechanical ventilation, making these a useful adjunct to clinical decision-making.

Mineral-Bound Trace Metals as Cofactors for Anaerobic Biological Nitrogen Fixation.

Nitrogenase is the only known biological enzyme capable of reducing N2 to bioavailable NH3. Most nitrogenases use Mo as a metallocofactor, while alternative cofactors V and Fe are also viable. Both geological and bioinformatic evidence suggest an ancient origin of Mo-based nitrogenase in the Archean, despite the low concentration of dissolved Mo in the Archean oceans. This apparent paradox would be resolvable if mineral-bound Mo were bioavailable for nitrogen fixation by ancient diazotrophs. In this study, the bioavailability of mineral-bound Mo, V, and Fe was determined by incubating an obligately anaerobic diazotroph Clostridium kluyveri with Mo-, V-, and Fe-bearing minerals (molybdenite, cavansite, and ferrihydrite, respectively) and basalt under diazotrophic conditions. The results showed that C. kluyveri utilized mineral-associated metals to express nitrogenase genes and fix nitrogen, as measured by the reverse transcription quantitative polymerase chain reaction and acetylene reduction assay, respectively. C. kluyveri secreted chelating molecules to extract metals from the minerals. As a result of microbial weathering, mineral surface chemistry significantly changed, likely due to surface coating by microbial exudates for metal extraction. These results provide important support for the ancient origin of Mo-based nitrogenase, with profound implications for coevolution of the biosphere and geosphere.

Outcome Measures and Inclusion/Exclusion Criteria in Benign Prostatic Hyperplasia Trials on ClinicalTrials.gov.

INTRODUCTION: For benign prostatic hyperplasia, clinical trials help assess new medical and surgical treatment options. The U.S. National Library of Medicine maintains ClinicalTrials.gov to provide access to prospective trials on diseases. This study investigates registered benign prostatic hyperplasia trials to determine if there are widespread differences in outcome measures and study criteria. METHODS: Interventional research with known study status on ClinicalTrials.gov identified by the keywords "benign prostatic hyperplasia" was examined. Inclusion/exclusion criteria, primary outcomes, secondary outcomes, study status, study enrollment, country of origin, and intervention category were studied. RESULTS: Of the 411 studies identified, International Prostate Symptom Score was the most common study outcome and was the primary or secondary study outcome in 65% of trials. Maximum urinary flow was the second most common study outcome (40.1% of studies). No other outcomes were measured as the primary or secondary outcome for more than 30% of studies. The most common inclusion criteria were a minimum International Prostate Symptom Score (48.9%), maximum urinary flow (34.8%), and minimum prostate volume (25.8%). Among studies using a minimum International Prostate Symptom Score, 13 was the most common minimum (35.3%) and a range of 7-21 was noted. The most common maximum urinary flow for inclusion was 15 mL/s (78 trials). CONCLUSIONS: Among clinicals trials on benign prostatic hyperplasia registered on ClinicalTrials.gov, a majority of studies utilized International Prostate Symptom Score as a primary or secondary outcome. Unfortunately, there were major differences in the inclusion criteria; these dissimilarities between trials may limit comparability of results across trials.

Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes.

Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (31 commercially important, 7 vulnerable and 13 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.

Bioavailability of mineral-associated trace metals as cofactors for nitrogen fixation by Azotobacter vinelandii.

Life on Earth depends on N2 -fixing microbes to make ammonia from atmospheric N2 gas by the nitrogenase enzyme. Most nitrogenases use Mo as a cofactor; however, V and Fe are also possible. N2 fixation was once believed to have evolved during the Archean-Proterozoic times using Fe as a cofactor. However, δ15 N values of paleo-ocean sediments suggest Mo and V cofactors despite their low concentrations in the paleo-oceans. This apparent paradox is based on an untested assumption that only soluble metals are bioavailable. In this study, laboratory experiments were performed to test the bioavailability of mineral-associated trace metals to a model N2 -fixing bacterium Azotobacter vinelandii. N2 fixation was observed when Mo in molybdenite, V in cavansite, and Fe in ferrihydrite were used as the sole sources of cofactors, but the rate of N2 fixation was greatly reduced. A physical separation between minerals and cells further reduced the rate of N2 fixation. Biochemical assays detected five siderophores, including aminochelin, azotochelin, azotobactin, protochelin, and vibrioferrin, as possible chelators to extract metals from minerals. The results of this study demonstrate that mineral-associated trace metals are bioavailable as cofactors of nitrogenases to support N2 fixation in those environments that lack soluble trace metals and may offer a partial answer to the paradox.

Disparity in hospital admissions and length of stay based on income status for emergency department hypertensive crisis visits.

OBJECTIVE: Racial, gender, and socioeconomic status have been shown to impact the delivery of care. How this impacts the management of hypertensive crisis remains unclear. We aim to identify disparities on admission frequency and length of stay (LOS) among those presenting with hypertensive crisis, as a function of household income. METHODS: This is a cross-sectional analysis of 2016 emergency department visits and supplemental inpatient data from the Nationwide Emergency Department Sample. Median household income quartiles were established. A multivariable logistic regression model was used to estimate odds of admission in each income quartile. A multivariable linear regression model was used to predict LOS. RESULTS: After applying sample weighting, the total number of emergency department visits was 33 727 with 6906, 25 443, and 1378 visits for hypertensive emergency, hypertensive urgency, and unspecified crisis, respectively. There were 13 191, 8889, 6400, 5247 visits in the (first) lowest, second, third , and fourth (highest) income quartiles, respectively. The median age for the study population was 60. The most common comorbidity was chronic kidney disease. Individuals with the highest income, had a lower likelihood of admission, compared with the lowest quartile (adjusted odds ratio: 0.41, 95% CI 0.22-0.74). There was a significant association between income quartile and LOS among hypertensive emergency patients (beta coefficient: 0.407, P value = 0.019). CONCLUSION: In this study, patients with lower income were more likely to be admitted, whereas those with higher income exhibited a longer LOS. Clinicians must be made aware these disparities to ensure equitable delivery of care.

Incomplete denitrification phenotypes in diverse Thermus species from diverse geothermal spring sediments and adjacent soils in southwest China.

A few members of the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite (NO2-) or nitrous oxide (N2O). However, the denitrification abilities of the genus as a whole remain poorly characterized. Here, we describe diverse denitrification phenotypes and genotypes of a collection of 24 strains representing ten species, all isolated from a variety of geothermal systems in China. Confirmed terminal products of nitrate reduction were nitrite or N2O, while nitric oxide (NO) was inferred as the terminal product in some strains. Most strains produced N2O; complete denitrification was not observed. Denitrification phenotypes were largely consistent with the presence of denitrification genes, and strains of the same species often had the same denitrification phenotypes and largely syntenous denitrification gene clusters. Genes for nirS and nirK coexisted in three Thermus brockianus and three Thermus oshimai genomes, which is a unique hallmark of some denitrifying Thermus strains and may be ecologically important. These results show that incomplete denitrification phenotypes are prominent, but variable, within and between Thermus species. The incomplete denitrification phenotypes described here suggest Thermus species may play important roles in consortial denitrification in high-temperature terrestrial biotopes where sufficient supply of oxidized inorganic nitrogen exists.

The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes.

The walking catfish Clarias magur (Hamilton, 1822) (magur) is an important catfish species inhabiting the Indian subcontinent. It is considered as a highly nutritious food fish and has the capability to walk to some distance, and survive a considerable period without water. Assembly, scaffolding and several rounds of iterations resulted in 3,484 scaffolds covering ∼94% of estimated genome with 9.88 Mb largest scaffold, and N50 1.31 Mb. The genome possessed 23,748 predicted protein encoding genes with annotation of 19,279 orthologous genes. A total of 166 orthologous groups represented by 222 genes were found to be unique for this species. The Computational Analysis of gene Family Evolution (CAFE) analysis revealed expansion of 207 gene families and 100 gene families have rapidly evolved. Genes specific to important environmental and terrestrial adaptation, viz. urea cycle, vision, locomotion, olfactory and vomeronasal receptors, immune system, anti-microbial properties, mucus, thermoregulation, osmoregulation, air-breathing, detoxification, etc. were identified and critically analysed. The analysis clearly indicated that C. magur genome possessed several unique and duplicate genes similar to that of terrestrial or amphibians' counterparts in comparison to other teleostean species. The genome information will be useful in conservation genetics, not only for this species but will also be very helpful in such studies in other catfishes.

The Effect of Spring Water Geochemistry on Copper Proteins in Tengchong Hot Springs, China.

Copper (Cu) is an essential trace metal cofactor for a variety of proteins; however, excess Cu is toxic to most organisms. Cu homeostasis is maintained by a complex machinery of Cu binding proteins that control the uptake, transport, sequestration, and efflux of Cu ions. Despite the importance of Cu binding proteins in electron transfer, substrate oxidation, superoxide dismutation, and denitrification, little information exists about microbial Cu utilization in extreme environments, where the geochemical conditions may affect Cu bioavailability. Using metagenomic data from 9 hot springs in Tengchong, China, which range in temperature from 42°C to 96°C and in pH from 2.3 to 9, the effects of pH, temperature, and spring geochemistry on the distribution of Cu binding domains of proteins and oxidoreductases were studied. Dissolved Cu and Cu binding domains were detected across all temperature and pH gradients. Cu binding domains of cytochrome c oxidase subunits, heavy-metal-associated domains, and nitrous oxide reductase were detected at all sites. DoxB, a quinol oxidase, and other quinol oxidase subunits were the dominant Cu binding oxidoreductase subunits present at low-pH and high-temperature sites, whereas cbb3-type cytochrome c oxidase subunits were dominant at high-pH and high-temperature sites. Additionally, aa3-type cytochrome c oxidase was more prominent than cbb3-type cytochrome c oxidase under circumneutral-pH conditions. This suggests that the type of cytochrome c oxidase pathway and the Cu proteins employed by microbes to carry out important functions such as energy acquisition and efflux of excess Cu are affected by the physicochemical conditions of the springs.IMPORTANCE Copper is present in a variety of proteins and is required to carry out essential functions by all organisms. However, in hot spring environments, copper availability may be limited due to the high temperatures and the wide range in pH. The significance of our research is in relating the physicochemical environment to the distribution of copper proteins across hot spring environments, which provides increased understanding of primary functions and adaptions in these environments.

Electrostatic Surface Potential of Macrophages Correlates with Their Functional Phenotype.

Macrophages exist in various functional phenotypes, which could be identified by specific surface molecules. Previous studies have shown that modulation of surface charges could alter the phagocytic function of macrophages. In this study, we show that activation of both human peripheral blood monocyte and THP-1-derived macrophages with lipopolysaccharide (LPS) or IL-1ß resulted in a significant decrease in the zeta potential compared to freshly isolated monocytes and unstimulated macrophages. Interestingly, interaction with bacteria significantly increased the zeta potential of such cells irrespective of activation conditions. Similarly, IFNγ-treated pro-inflammatory macrophages showed lesser negative zeta potential compared to untreated control. A moderate reduction was also seen in IL-4-treated anti-inflammatory subtype. Additionally, in an LPS-induced systemic inflammation model, bone marrow cells isolated after 2 h of LPS injection showed significant reduction in zeta potential compared to naïve cells. Furthermore, electrostatic potential measurement of surface proteins associated with pro-inflammatory and anti-inflammatory macrophages, using in silico modeling under physiological and protonation conditions, showed that the average electrostatic potential of pro-inflammatory type surface proteins was less negative than anti-inflammatory subtype. These data suggest that the expression of different protein molecules on macrophages under different environments may contribute to the zeta potential and that this quick and low-cost technique could be used in monitoring macrophage functional phenotypes.

Clinical evaluation of 4D MRI in the delineation of gross and internal tumor volumes in comparison with 4DCT.

PURPOSE: To evaluate clinical utility of respiratory-correlated (RC) four-dimensional magnetic resonance imaging (4DMRI) for lung tumor delineation and motion assessment, in comparison with the current clinical standard of 4D computed tomography (4DCT). METHODS AND MATERIALS: A prospective T2-weighted (T2w) RC-4DMRI technique was applied to acquire coronal 4DMRI images for 14 lung cancer patients (16 lesions) during free breathing (FB) under an IRB-approved protocol, together with a breath-hold (BH) T1w 3DMRI and axial 4DMRI. Clinical simulation CT and 4DCT were acquired within 2 h. An internal navigator was applied to trigger amplitude-binned 4DMRI acquisition whereas a bellows or real-time position management (RPM) was used in the 4DCT reconstruction. Six radiation oncologists manually delineated the gross and internal tumor volumes (GTV and ITV) in 399 3D images using programmed clinical workflows under a tumor delineation guideline. The ITV was the union of GTVs within the breathing cycle without margin. Average GTV and motion range were assessed and ITV variation between 4DMRI and 4DCT was evaluated using the Dice similarity index, mean distance agreement (MDA), and volume difference. RESULTS: The mean tumor volume is similar between 4DCT (GTV4DCT  = 1.0, as the reference) and T2w-4DMRI (GTVT2wMR  = 0.97), but smaller in T1w MRI (GTVT1wMR  = 0.76), suggesting possible peripheral edema around the tumor. Average GTV variation within the breathing cycle (22%) in 4DMRI is slightly greater than 4DCT (17%). GTV motion variation (-4 to 12 mm) and ITV variation (∆VITV =-25 to 95%) between 4DCT and 4DMRI are large, confirmed by relatively low ITV similarity (Dice = 0.72 ± 0.11) and large MDA = 2.9 ± 1.5 mm. CONCLUSION: Average GTVs are similar between T2w-4DMRI and 4DCT, but smaller by 25% in T1w BH MRI. Physician training and breathing coaching may be necessary to reduce ITV variability between 4DMRI and 4DCT. Four-dimensional magnetic resonance imaging is a promising and viable technique for clinical lung tumor delineation and motion assessment.

Retention failures in cement- and screw-retained fixed restorations on dental implants in partially edentulous arches: A systematic review with meta-analysis.

PURPOSE: This systematic review aimed to evaluate retention failures in cement- and screw-retained fixed restorations on dental implants in partially edentulous arches. METHODS: The relevant articles were retrieved from MEDLINE (PubMed), Cochrane Library, and EBSCO electronic databases for articles published from January 1995 to January 2016 and were restricted to randomized controlled trials and retrospective and prospective studies on human subjects that were reported in English. A further hand search was conducted on individual journals and reference list of the articles found. Reviewed studies which reported retention failures in fixed implant-supported prostheses using screw and cement retention mechanism. Information on the type and nature of restoration, as well as different luting cement, were also collected. RESULTS: Thirty-three articles were finalized, 20 short-term clinical studies (up to 5 years) and 13 long-term studies (≥5 years). Out of 33 studies, 16 studies were included in meta-analysis, 8 in short-term and 8 in long-term studies. The results of the meta-analysis for short-term studies showed statistically significant difference between cement-retained and screw-retained prosthesis, with the forest plot favoring cement-retained prostheses (risk ratio [RR]: 0.26; confidence interval [CI]: 0.09-0.74; P < 0.0001; I2 = 79%). In long-term studies, the forest plot revealed statistically significant difference between both retention systems favoring cement-retained prostheses (RR: 0.31; CI: 0.13-0.76; P = 0.03; I2 = 56%). CONCLUSION: Analysis of the short- and long-term studies shows lesser retention failures with cement-retained prostheses when compared to screw-retained prostheses. Further, multicentric, high-quality randomized controlled studies with long-term observations and modified cementation protocols can yield higher grades of recommendation to avoid retention failures.

Abundance and taxonomic affiliation of molybdenum transport and utilization genes in Tengchong hot springs, China.

The nitrogen, sulfur and carbon cycles all rely on critical microbial transformations that are carried out by enzymes that require molybdenum (Mo) as a cofactor. Despite Mo importance in these biogeochemical cycles, little information exists about microbial Mo utilization in extreme environments where, due to geochemical conditions, bioavailable Mo may be limited. Using metagenomic data from nine hot springs in Tengchong, Yunnan Province, China, which range in temperature from 42°C to 96°C and pH from 2.3 to 9, the effects of pH, temperature and spring geochemistry on the abundance and taxonomic affiliation of genes related to Mo were studied. Dissolved Mo was only detected at sites with circumneutral pH. However, processes and organisms that require Mo were detected at all sites across all temperature and pH gradients. All sites contained xanthine dehydrogenase, formate dehydrogenase, carbon-monoxide dehydrogenase, nitrate reductase, sulfite oxidase and methionine-sulfoxide reductase despite different community compositions. This suggests that different microbial communities, resulting from different physicochemical conditions, may be performing similar metabolic functions. Furthermore, the abundance and taxonomic diversity of Mo-related annotations increased with higher concentrations of Mo. This study shows that despite geochemical conditions that can limit Mo bioavailability, microbes require Mo for a variety of processes.

WGSSAT: A High-Throughput Computational Pipeline for Mining and Annotation of SSR Markers From Whole Genomes.

Mining and characterization of Simple Sequence Repeat (SSR) markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. Whole genome sequencing (WGS)-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, noncoding RNA (ncRNA), core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic, and core gene region) along with primer identification and mining of cross-species markers. The program also generates a detailed statistical report along with visualization of mapped SSRs, genes, core genes, and RNAs. The features of WGSSAT were demonstrated using Takifugu rubripes data. This yielded a total of 139 057 SSR, out of which 113 703 SSR primer pairs were uniquely amplified in silico onto a T. rubripes (fugu) genome. Out of 113 703 mined SSRs, 81 463 were from coding region (including 4286 exonic and 77 177 intronic), 7 from RNA, 267 from core genes of fugu, whereas 105 641 SSR and 601 SSR primer pairs were uniquely mapped onto the medaka genome. WGSSAT is tested under Ubuntu Linux. The source code, documentation, user manual, example dataset and scripts are available online at https://sourceforge.net/projects/wgssat-nbfgr.