Investigation of groundwater quality in the Southern Coast of the Black Sea: application of computational health risk assessment in Giresun, Türkiye.

Potentially toxic elements (PTEs), especially arsenic in drinking water, pose significant global health risks, including cancer. This study evaluates the groundwater quality in Giresun province on the Black Sea coast of Türkiye by analyzing twelve groundwater resources. The mean concentrations of macronutrients (mg/L) were: Ca (10.53 ± 6.63), Na (6.81 ± 3.47), Mg (3.39 ± 2.27), and K (2.05 ± 1.10). The mean levels of PTEs (µg/L) were: Al (40.02 ± 15.45), Fe (17.65 ± 14.35), Zn (5.63 ± 2.59), V (4.74 ± 5.85), Cu (1.57 ± 0.81), Mn (1.02 ± 0.76), As (0.93 ± 0.73), Cr (0.75 ± 0.57), Ni (0.41 ± 0.18), Pb (0.36 ± 0.23), and Cd (0.10 ± 0.05). All PTE levels complied with WHO drinking water safety guidelines, and overall water quality was excellent. The heavy metal evaluation index (HEI < 10) and heavy metal pollution index (HPI < 45) indicate low pollution levels across all stations. Irrigation water quality was largely adequate, as shown by the magnesium hazard (MH), sodium adsorption ratio (SAR), Na%, and Kelly's ratio (KR). The total hazard index (THI) values consistently remained below 1, indicating no non-carcinogenic health risks. However, at station 10 (city center), the cancer risk (CR) for adults due to arsenic was slightly above the threshold (1.44E-04). Using principal component analysis (PCA), positive matrix factorization (PMF), and geographic information system (GIS) mapping, the study determined that most PTEs originated from natural geological formations or a combination of natural and human sources, with minimal impact from human activities. These findings highlight the safety and reliability of the groundwater sources studied, emphasizing their potential as a long-term, safe water supply for nearby populations.

Rapid genome sequencing for critically ill infants: an inaugural pilot study from Turkey.

Introduction: Rare and ultra-rare genetic conditions significantly contribute to infant morbidity and mortality, often presenting with atypical features and genetic heterogeneity that complicate management. Rapid genome sequencing (RGS) offers a timely and cost-effective approach to diagnosis, aiding in early clinical management and reducing unnecessary interventions. This pilot study represents the inaugural use of next-generation sequencing (NGS) as a diagnostic instrument for critically ill neonatal and pediatric ICU patients in a Turkish hospital setting. Methods: Ten infants were enrolled based on predefined inclusion criteria, and trio RGS was performed. The mean age of the participants was 124 days, with congenital abnormalities being the most common indication for testing. Three patients had consanguineous parents. The mean turnaround time from enrollment to delivery of results was 169 h, with a diagnostic yield of 50%. Results: Three patients received a definitive molecular diagnosis, impacting their clinical management. Two patients benefited from the exclusion of Mendelian conditions, leading to alternative diagnoses. Discussion: This study demonstrates the feasibility and results of RGS in Turkish hospital settings, emphasizing the importance of timely genetic diagnosis in reducing the diagnostic odyssey for families and improving patient care. Further research is needed to evaluate the cost-effectiveness and applicability of RGS in the Turkish healthcare system for children with diseases of uncertain etiology.

Toxicological risk assessment using spring water quality indices in plateaus of Giresun Province/Türkiye: a holistic hydrogeochemical data analysis.

Water scarcity is a growing concern due to rapid urbanization and population growth. This study assesses spring water quality at 20 stations in Giresun province, Türkiye, focusing on potentially toxic elements and physicochemical parameters. The Water Quality Index rated most samples as "excellent" during the rainy season and "good" during the dry season, except at stations 4 (40° 35' 12″ North/38° 26' 34″ East) and 19 (40° 44' 28″ North/38° 06' 53″ West), indicating "poor" quality. Mean macro-element concentrations (mg/L) were: Ca (34.27), Na (10.36), Mg (8.26), and K (1.48). Mean trace element values (µg/L) were: Al (1093), Zn (110.54), Fe (67.45), Mn (23.03), Cu (9.79), As (3.75), Ni (3.00), Cr (2.84), Pb (2.70), Co (1.93), and Cd (0.76). Health risk assessments showed minimal non-carcinogenic risks, while carcinogenic risk from arsenic slightly exceeded safe limits (CR = 1.75E-04). Higher arsenic concentrations during the rainy season were due to increased recharge, arsenic-laden surface runoff, and human activities. Statistical analyses (PCA, PCC, HCA) suggested that metals and physico-chemical parameters originated from lithogenic, anthropogenic, or mixed sources. Regular monitoring of spring water is recommended to mitigate potential public health risks from waterborne contaminants.

Appraisal of metallic accumulation in the surface sediment of a fish breeding dam in Türkiye: A stochastical approach to ecotoxicological risk assessment.

This study examines the levels and patterns of potentially toxic elements (PTEs) in surface sediment of Almus Dam Lake (ADL), a key fish breeding site in Türkiye. PTE concentrations in sediment were ranked: Hg (0.05 ± 0.01) < Cd (0.16 ± 0.01) < Pb (9.34 ± 1.42) < As (18.75 ± 15.65) < Cu (63.30 ± 15.17) < Ni (72.64 ± 20.54) < Zn (86.66 ± 11.95) < Cr (108.35 ± 36.40) < Mn (1008 ± 151) < Fe (53,998 ± 6468), with no significant seasonal or spatial differences. Ecological risk indices (mHQ, EF, Igeo, CF, PLI, Eri, mCd, NPI, PERI, MPI, and TRI) showed low contamination levels. Health risk assessments, including LCR, HQ, and THI, indicated minimal risks to humans from sediment PTEs. Statistical analyses (PCA, HCA, SCC) identified natural, transportation, and anthropogenic PTE sources, with slight impacts from agriculture and fish farming. This research underlines contamination status of ADL and emphasizes the need for targeted management strategies, offering critical insights for environmental safeguarding.

Metal pollution assessment in the surface sediments of a river system in Türkiye: Integrating toxicological risk assessment and source identification.

This study investigates potentially toxic elements (PTEs) in the surface sediments of the Abdal River system, a critical water source for Samsun province, Türkiye, due to the presence of the Çakmak Dam. PTE concentrations, measured in mg/kg, show significant variability: Hg (0.03) < Cd (0.26) < As (10.98) < Pb (13.88) < Cu (48.61) < Ni (62.45) < Zn (70.97) < Cr (96.28) < Mn (1015) < Fe (38357). Seasonal variations were observed, in particular increased concentrations of As, Cd and Pb in summer (p < 0.05). Contamination and ecological risk indices (mHQ, EF, Igeo, CF, PLI, Eri, mCd, NPI, PERI, MPI, and TRI) indicate moderate to low levels of contamination, suggesting potential ecological effects. Health risk assessments suggest minimal risks to human health from sediment PTEs. Statistical analyses (PCC, PCA and HCA) improve the understanding of the sediment environment and contamination sources, while the coefficient of variation assists in source identification.

LC-MS/MS Investigation of nitrosamine impurities in certain Sartan group medicinal products available in Istanbul, Türkiye.

Nitrosamines (NAs) are molecules that include the nitroso functional group. In 2018, the US Food and Drug Administration (FDA) received its first report of NAs in pharmaceuticals. The fact that NA impurities are likely human carcinogens is relevant to these compounds. Furthermore, prolonged exposure to NA contaminants above safe limits may raise the risk of cancer. The goal of this article was to assess the amounts of six different NAs in Sartan group medicines purchased from formal pharmacies in Istanbul, Türkiye, using a validated LC-MS/MS assay. An LC-MS/MS-based analytical assay was undertaken. The separation was performed with a HR ODS 150mm×3.0mm and 5-analytical columns, providing effective separation of major peaks from NA impurities. In mobile phase A, formic acid was 0.10% in water, while in mobile phase B, formic acid was 0.10% in methanol. The flow rate was 0.4mL/minute, and the total runtime was 18minutes with the gradient elution mode. The validation was conducted in line with ISO/IEC 17025 requirements. Up to 100µg/L, linearity was determined using correlation coefficients (r2>0.995) for all NAs. The limit of quantification values for all NAs analyses were below 1.0µg/L. The mean recovery value obtained during the spike experiment was 95.18%, demonstrating the accuracy of the procedure. In addition, the accuracy was shown by a certified reference analysis, which yielded relative standard deviation and relative error values of 1.82% and 3.34%, respectively. During the intermediate precision testing, bias and relative standard deviation were 0.96 and 2.87%, respectively. Of the 75 study samples involving Sartan group medical products, no nitrosamine impurities were detected, demonstrating that pharmaceutical companies have adequate medication safety precautions in place in accordance with FDA and European Medicines Agency (EMA) regulations published to prevent NA contaminants in human medicinal products.

Potentially hazardous elements in sediments and Ceratophyllum demersum: an ecotoxicological risk assessment in Miliç Wetland, Samsun, Türkiye.

Potentially hazardous elements (PHEs) are non-biodegradable and accumulate in places like water, soil, and plants where they endanger environmental health. There are a considerable number of wetlands having both national and worldwide importance in Türkiye. Regarding PHE accumulation, sediments and Ceratophyllum demersum were examined in the Miliç Wetland (MW), situated in a basin with intense hazelnut and rice farming, which is next to the international highway on the Central Black Sea Coast of Türkiye. The quantification of PHEs in the study subjects was undertaken using a validated inductively coupled plasma-mass spectrometry (ICP-MS) method, and mean concentrations (mg/kg) of PHEs in the sediments were in the order of Al (13,133) > Fe (10,790) > Mn (205.84) > Cu (17.95) > Cr (16.40) > Zn (15.55) > Ni (11.74) > Pb (9.17) > Co (6.30) > As (2.07) > Cd (0.19). The ecotoxicological risk was assessed using sediment quality guidelines (SQGs) and certain geological indices, indicating mostly low ecological risk, low pollution, and no hazardous risk. Based on the modified hazard quotient (mHQ) classification of values, Ni showed low contamination, while Cd, Pb, As, and Cu displayed very low contamination, and Zn presented minor contamination. The findings of total lifetime cancer risk (LCR), hazard quotient (HQ), and hazard index (HI) identified that exposure of adults or children to sediments containing PHEs would not represent a major health risk. As a recommendation, it is necessary to avoid the direct entrance of agricultural pesticides and fertilizers to enhance the sediment quality of the MW. Since the highway was constructed close to MW, this is considered a significant source of human-caused pollution. Consequently, all PHEs analyzed, except for Cd, displayed a bioconcentration factor (BCF) value of more than 1000, indicating that Ceratophyllum demersum is a promising plant for phytoremediation in PHE-polluted ecological systems involving wetlands, and it can efficiently be employed as an indicator species in biological screening investigations.

Ecotoxicological risk assessment for sediments of Çavuslu stream in Giresun, Turkey: association between garbage disposal facility and metallic accumulation.

The objective of this paper was to stress the possible potential toxic element (PTE) accumulation in the surface sediments of the Çavuslu Stream (ÇS), as well as examining the source identification of whether or not any association between garbage disposal facility (GDF) and ecotoxicity or human health risk in Giresun, Turkey. The sediment specimens were analyzed by inductively coupled plasma mass spectroscopy (ICP-MS) followed by microwave digestion. The descending order of metals (mg/kg) in sediments were as follows: Fe (38,791 ± 3269) > Al (27,753 ± 4051) > Mn (730.90 ± 114.60) > Cr (233.39 ± 53.32) > V (176.40 ± 19.66) > Cu (85.22 ± 6.06) > Ni (72.87 ± 11.50) > Zn (46.45 ± 3.68) > Co (21.96 ± 3.33) > Pb (12.17 ± 1.97) > As (3.12 ± 1.45) > Sb (0.22 ± 0.06) > Cd (0.17 ± 0.02) > Hg (0.04 ± 0.01). Among these elements, certain metals (V, Cr, Cu, and Ni) in the sediments were above the average shale. Cr and Ni levels were above their corresponding threshold effect level (TEL) and probable effect level (PEL) values while Cu concentration exceeding its TEL, indicating that benthic organisms in the sediment of ÇS have likely toxic responses. Based on the results from contamination factor (CF), enrichment factor (EF), and geo-accumulation factor (Igeo) values of PTEs, the sediment was frequently classified into moderate contamination, moderate enrichment, and unpolluted to moderately polluted group. Pollution load index (PLI), integrated pollution index (IPI), and ecological risk index (Eri) indicated low pollution or low potential ecological risk. Toxicity risk index (TRI) and toxic unit analysis (TUs) suggested moderate toxicity. The outcomes of hazard quotient (HQ), total hazard index (THI), and lifetime cancer risk (LCR) stressed out that PTEs would not pose a significant health risk when adults are exposed to sediments in ÇS. However, a non-cancerogenic health risk for children was considered as the collective effect of 14 PTE (THI = 1.47 > 1). Multivariate statistical analysis (principal component analysis (PCA), Pearson's correlation coefficient (PCC), and hierarchical cluster analysis (HCA)) outlined that the metallic accumulation in the sediments of ÇS was related to lithological, geological, and anthropogenic impacts. Therefore, the GDF is likely a major reason in terms of anthropogenic pollution in the sediments of the ÇS.

Assessing reference levels of nickel and chromium in cord blood, maternal blood and placenta specimens from Ankara, Turkey

Objective: Placenta is a temporary organ that connects the developing fetus and the mother. However, it cannot protect the embryo against chromium (Cr) and nickel (Ni) exposure. Quantification of Cr and Ni in biological and ecological subjects is challenging. Thus, the first goal of this study was to provide a validated Graphite Furnace Atomic Absorption Spectrometry (GFAAS) method to determine Cr and Ni in mother-newborn specimens. The second goal was to assess the reference Ni and Cr contents in cord blood, maternal blood, and placenta samples in a population from Ankara. Material and Methods: Biological samples were collected from 100 healthy mother-newborn pairs. Metal levels were quantified by GFAAS. Method validation of this toxicological analysis was performed by the use of certified reference materials, and assessed through accuracy, precision, specificity, range, quantitation, and detection limits. Results: Mean Cr levels of maternal blood, placentas, and cord blood were 0.337±0.222 µg/L, 0.221±0.160 µg/kg, 0.121±0.096 µg/L, respectively while mean Ni concentrations were 0.128±0.093 µg/L, 0.124±0.067 µg/kg, 0.099±0.067 µg/L, respectively. The method showed linearity with excellent correlation coefficients (r2) for Cr (0.9994) and Ni (0.9999). Satisfactory recovery and coefficient of variation for Cr and Ni were 102.85% and 102.35%; 1.75% and 2.91%, respectively. Relative error did not exceed 3%, demonstrating the accuracy of the method. Control charts were drawn to assess inter-day stability. The predicted reference ranges for Cr and Ni concentrations in maternal blood, placenta and cord blood were: Cr 0.033-0.75 µg/L; 0.032-0.526 µg/kg; 0.031-0.309 µg/L and for Ni were 0.011-0.308 µg/L; 0.024-0.251 µg/kg; 0.066-0.209 µg/L, respectively. Conclusion: The reported reference values of biological specimens in this paper will provide complementary aid to health professionals in terms of assessment of environmental and occupational exposure.

Characterization of differentially expressed genes to Cu stress in Brassica nigra by Arabidopsis genome arrays.

Phytoremediation is an efficient and promising cleanup technology to extract or inactivate heavy metals and several organic and inorganic pollutants from soil and water. In this study, different Brassica nigra L. ecotypes, including Diyarbakir, collected from mining areas were exposed to different concentrations of copper and harvested after 72 h of Cu stress for the assessment of phytoremediation capacity. The Diyarbakir ecotype was called as "metallophyte" because of surviving at 500 µM Cu. To better understand Cu stress mechanism, ArabidopsisATH1 genome array was used to compare the gene expression in root and shoot tissues of B. nigra under 25 µM Cu. The response to Cu was much stronger in roots (88 genes showing increased or decreased mRNA levels) than in leaf tissues (24 responding genes). These genes were classified into the metal transport and accumulation-related genes, signal transduction and metabolism-related genes, and transport facilitation genes. Glutathione pathway-related genes (γ-ECS, PC, etc.) mRNAs were identified as differentially expressed in root and shoot tissues. QRT-PCR validation experiments showed that γ-ECS and PC expression was upregulated in the shoot and leaf tissues of the 100 µM Cu-subjected B. nigra-tolerant ecotype. This is the first study showing global expression profiles in response to Cu stress in B. nigra by Arabidopsis genome array. This work presented herein provides a well-illustrated insight into the global gene expression to Cu stress response in plants, and identified genes from microarray data will serve as molecular tools for the phytoremediation applications in the future.

GPR56 homozygous nonsense mutation p.R271* associated with phenotypic variability in bilateral frontoparietal polymicrogyria.

Öncü-Öner T, Ünalp A, Porsuk-Doru I, Agilkaya S, Güleryüz H, Saraç A, Ergüner B, Yüksel B, Hiz-Kurul S, Cingöz S. GPR56 homozygous nonsense mutation p.R271* associated with phenotypic variability in bilateral frontoparietal polymicrogyria. Turk J Pediatr 2018; 60: 229-237. Polymicrogyria is a disorder of neuronal migration characterized by excessive cortical folding and partially fused gyri separated by shallow sulci. Homozygous mutations in the GPR56 gene, which regulates migration of neural precursor cells, are associated with bilateral frontoparietal polymicrogyria (BFPP) syndrome including white matter changes, brainstem and cerebellar involvement. Herein, we describe three siblings of consanguineous parents with a homozygous germline mutation (p.R271*) located in the seventh exon of the GPR56 gene that was previously detected in only one Portuguese patient. Phenotypic/genotypic relationships were analysed according to the clinical characteristics in only index patient. While earlier reported patient was exhibiting seizures provoked by hot water, macrocephaly, cerebellar/brainstem hypoplasia and corpus callosum abnormalities, the index patient showed only hypoplasia of brainstem, focal onset bilateral tonic clonic seizure. Despite the phenotypic similarities in two patients, the potential causes of the variation in the expression of the p.R271* variant between the two affected families might be genetic or epigenetic factors beyond the GPR56 gene. Consequently, the present findings show that the same mutation in GPR56 gene can have different phenotypic effects. Therefore, additional functional studies are needed to detect the phenotypic spectrum of the p.R271* mutation in GPR56, and provide insight into the mechanism of normal cortical development and regional patterning of the cerebral cortex.

Comparative transcriptome analysis of Zea mays in response to petroleum hydrocarbon stress.

The use of plants for the improvement of soils contaminated with hydrocarbons has been a primary research focus in phytoremediation studies. Obtaining insights regarding genes that are differentially induced by petroleum hydrocarbon stress and understanding plant response mechanisms against petroleum hydrocarbons at molecular level is essential for developing better phytoremediation strategies to remove these hazardous contaminants. The purpose of this study was to analyze the transcriptomal profile changes under hydrocarbon stress in maize plants and identify the genes associated with the phytoremediative capacity. Zea mays GeneChips were used to analyze the global transcriptome profiles of maize treated with different concentrations of petroleum hydrocarbons. In total, 883, 1281, and 2162 genes were differentially induced or suppressed in the comparisons of 0 (control) vs. 1% crude petroleum, 1 vs. 5% crude petroleum, and 0 vs. 5% crude petroleum, respectively. The differentially expressed genes were functionally associated with the osmotic stress response mechanism, likely preventing the uptake of water from the roots, and the phytoremediative capacity of plants, e.g., secretory pathway genes. The results presented here show the regulatory mechanisms in the response to petroleum hydrocarbon pollution in soil. Our study provides global gene expression data of Z. mays in response to petroleum hydrocarbon stress that could be useful for further studies investigating the biodegradation mechanism in maize and other plants.

A probable new syndrome with the storage disease phenotype caused by the VPS33A gene mutation.

We present a novel multisystem disease in two siblings with clinical features resembling a lysosomal storage disease. These included coarse face, dysostosis multiplex, respiratory difficulty, proteinuria with glomerular foamy cells, neurological involvement with developmental delays, pyramidal signs, and severe chronic anemia. Detailed enzymatic analysis for lysosomal diseases and whole-exome sequencing studies excluded known lysosomal storage diseases in the proband. Subsequently, genome-wide genotyping and exome sequencing analysis of the family indicated two large homozygous regions on chromosomes 5 and 12, and strongly suggested that a homozygous p. R498W missense mutation in the VPS33A gene might be responsible for this novel disease. Segregation analysis in family members and mutation prediction tools' results also supported the damaging effect of the missense mutation on the function of the Vps33a protein, which plays a role in the vesicular transport system. Electron microscopic studies of the cornea of the proband showed findings supportive of dysfunction in vesicular transport. The clinical phenotype and genetic studies support the suggestion that the siblings most probably have a novel disease very likely caused by a VPS33A gene defect.

Loss-of-Function Mutations in ELMO2 Cause Intraosseous Vascular Malformation by Impeding RAC1 Signaling.

Vascular malformations are non-neoplastic expansions of blood vessels that arise due to errors during angiogenesis. They are a heterogeneous group of sporadic or inherited vascular disorders characterized by localized lesions of arteriovenous, capillary, or lymphatic origin. Vascular malformations that occur inside bone tissue are rare. Herein, we report loss-of-function mutations in ELMO2 (which translates extracellular signals into cellular movements) that are causative for autosomal-recessive intraosseous vascular malformation (VMOS) in five different families. Individuals with VMOS suffer from life-threatening progressive expansion of the jaw, craniofacial, and other intramembranous bones caused by malformed blood vessels that lack a mature vascular smooth muscle layer. Analysis of primary fibroblasts from an affected individual showed that absence of ELMO2 correlated with a significant downregulation of binding partner DOCK1, resulting in deficient RAC1-dependent cell migration. Unexpectedly, elmo2-knockout zebrafish appeared phenotypically normal, suggesting that there might be human-specific ELMO2 requirements in bone vasculature homeostasis or genetic compensation by related genes. Comparative phylogenetic analysis indicated that elmo2 originated upon the appearance of intramembranous bones and the jaw in ancestral vertebrates, implying that elmo2 might have been involved in the evolution of these novel traits. The present findings highlight the necessity of ELMO2 for maintaining vascular integrity, specifically in intramembranous bones.

Draft Genome Sequences of Two Heat-Resistant Mutant Strains (A52 and B41) of the Photosynthetic Hydrogen-Producing Bacterium Rhodobacter capsulatus.

The draft genome sequences of two heat-resistant mutant strains, A52 and B41, derived from Rhodobacter capsulatus DSM 1710, and with different hydrogen production levels, are reported here. These sequences may help understand the molecular basis of heat resistance and hydrogen production in R. capsulatus.

Phytoremediation of petroleum hydrocarbons by using a freshwater fern species Azolla filiculoides Lam.

In this study, the phytoremediation capacity of Azolla filiculoides Lam. for the water resources contaminated with petroleum hydrocarbons was investigated. The plants were grown in nitrogen-free Hoagland nutrient solution containing 0.005%, 0.01%, 0.05%, 0.1%, 0.2%, 0.3%, 0.4%, and 0.5% crude oil under greenhouse conditions for 15 days. Although the growth rate of the plants were not negatively influenced by the presence of crude oil in the media for the concentration of 0.005% and 0.01% v/v, a gradual impeding effect of crude oil in the growth media has been observed at concentrations 0.05-0.1%. More than 0.1% crude oil in the growth medium ostensibly retarded the growth. For example, 0.2% oil in the media reduced growth approximately 50% relative to the control, and the presence of crude oil at concentrations 0.3% or more were lethal. The data about the percentage of plant growth, fresh weight increase and root growth clearly indicated that the tolerance level of A. filiculoides plants to crude oil ranges between 0.1% and 0.2%. In comparison to control samples, the biodegradation rate of total aliphatic and aromatic (phenathrene) hydrocarbons at 0.05-0.2% oil concentrations, was 94-73% and 81-77%, respectively. On the other hand, in case of further increases in oil concentration in media, i.e.; 0.3-0.5%, the biodegradation rate was still higher in the experimental samples, respectively 71-63% and 75-71%. The high biodegradation rates of petroleum hydrocarbons in the experimental samples suggested that A. filiculoides plants could be a promising candidate to be used for the phytoremediation of low crude oil contaminated precious freshwater resources.

Robustness of Massively Parallel Sequencing Platforms.

The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications.

Novel POC1A mutation in primordial dwarfism reveals new insights for centriole biogenesis.

POC1A encodes a WD repeat protein localizing to centrioles and spindle poles and is associated with short stature, onychodysplasia, facial dysmorphism and hypotrichosis (SOFT) syndrome. These main features are related to the defect in cell proliferation of chondrocytes in growth plate. In the current study, we aimed at identifying the molecular basis of two patients with primordial dwarfism (PD) in a single family through utilization of whole-exome sequencing. A novel homozygous p.T120A missense mutation was detected in POC1A in both patients, a known causative gene of SOFT syndrome, and confirmed using Sanger sequencing. To test the pathogenicity of the detected mutation, primary fibroblast cultures obtained from the patients and a control individual were used. For evaluating the global gene expression profile of cells carrying p.T120A mutation in POC1A, we performed the gene expression array and compared their expression profiles to those of control fibroblast cells. The gene expression array analysis showed that 4800 transcript probes were significantly deregulated in cells with p.T120A mutation in comparison to the control. GO term association results showed that deregulated genes are mostly involved in the extracellular matrix and cytoskeleton. Furthermore, the p.T120A missense mutation in POC1A caused the formation of abnormal mitotic spindle structure, including supernumerary centrosomes, and changes in POC1A were accompanied by alterations in another centrosome-associated WD repeat protein p80-katanin. As a result, we identified a novel mutation in POC1A of patients with PD and showed that this mutation causes the formation of multiple numbers of centrioles and multipolar spindles with abnormal chromosome arrangement.

A clinical variant in SCN1A inherited from a mosaic father cosegregates with a novel variant to cause Dravet syndrome in a consanguineous family.

A consanguineous family from Turkey having two children with intellectual disability exhibiting myoclonic, febrile and other generalized seizures was recruited to identify the genetic origin of these phenotypes. A combined approach of SNP genotyping and exome sequencing was employed both to screen genes associated with Dravet syndrome and to detect homozygous variants. Analysis of exome data was extended further to identify compound heterozygosity. Herein, we report identification of two paternally inherited genetic variants in SCN1A (rs121917918; p.R101Q and p.I1576T), one of which was previously implicated in Dravet syndrome. Interestingly, the previously reported clinical variant (rs121917918; p.R101Q) displayed mosaicism in the blood and saliva of the father. The study supported the genetic diagnosis of affected children as Dravet syndrome possibly due to the combined effect of one clinically associated (rs121917918; p.R101Q) and one novel (p.I1576T) variants in SCN1A gene. This finding is important given that heterozygous variants may be overlooked in standard exome scans of consanguineous families. Thus, we are presenting an interesting example, where the inheritance of the condition may be misinterpreted as recessive and identical by descent due to consanguinity and mosaicism in one of the parents.

Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica.

BACKGROUND: Fasciola hepatica causes chronic liver disease, fasciolosis, leading to significant losses in the livestock economy and concerns for human health in many countries. The identification of F. hepatica genes involved in the parasite's virulence through modulation of host immune system is utmost important to comprehend evasion mechanisms of the parasite and develop more effective strategies against fasciolosis. In this study, to identify the parasite's putative virulence genes which are associated with host immunomodulation, we explored whole transcriptome of an adult F. hepatica using current transcriptome profiling approaches integrated with detailed in silico analyses. In brief, the comparison of the parasite transcripts with the specialised public databases containing sequence data of non-parasitic organisms (Dugesiidae species and Caenorhabditis elegans) or of numerous pathogens and investigation of the sequences in terms of nucleotide evolution (directional selection) and cytokine signaling relation were conducted. RESULTS: NGS of the whole transcriptome resulted in 19,534,766 sequence reads, yielding a total of 40,260 transcripts (N50 = 522 bp). A number of the parasite transcripts (n = 1,671) were predicted to be virulence-related on the basis of the exclusive homology with the pathogen-associated data, positive selection or relationship with cytokine signaling. Of these, a group of the virulence-related genes (n = 62), not previously described, were found likely to be associated with immunomodulation based on in silico functional categorisation, showing significant sequence similarities with various immune receptors (i.e. MHC I class, TGF-ß receptor, toll/interleukin-1 receptor, T-cell receptor, TNF receptor, and IL-18 receptor accessory protein), cytokines (i.e. TGF-ß, interleukin-4/interleukin-13 and TNF-α), cluster of differentiations (e.g. CD48 and CD147) or molecules associated with other immunomodulatory mechanisms (such as regulation of macrophage activation). Some of the genes (n = 5) appeared to be under positive selection (Ka/Ks > 1), imitating proteins associated with cytokine signaling (through sequence homologies with thrombospondin type 1, toll/interleukin-1 receptor, TGF-ß receptor and CD147). CONCLUSIONS: With a comparative transcriptome profiling approach, we have identified a number of potential immunomodulator genes of F. hepatica (n = 62), which are firstly described here, could be employed for the development of better strategies (including RNAi) in the battle against both zoonotically and economically important disease, fasciolosis.