Frequency of actionable secondary findings in 7472 Korean genomes derived from the National Project of Bio Big Data pilot study.

Exome and genome sequencing (ES/GS) in genetic medicine and research leads to discovering genomic secondary findings (SFs) unrelated to the purpose of the primary test. There is a lack of agreement to return the SF results for individuals undergoing the test. The aim of this study is to investigate the frequency of actionable secondary findings using GS data obtained from the rare disease study and the Korean Genome and Epidemiology Study (KoGES) in the National Project of Bio Big Data pilot study. Pathogenic (P) or likely pathogenic (LP) variants of 78 SF genes recommended by the American College of Medical Genetics and Genomics (ACMG) were screened in the rare disease study and KoGES. The pathogenicity of SF gene variants was determined according to the ACMG interpretation. The overall SF rate was 3.75% for 280 individuals with 298 P/LP variants of 41 ACMG SF genes which were identified among 7472 study participants. The frequencies of genes associated with cardiovascular, cancer, and miscellaneous phenotypes were 2.17%, 1.22%, and 0.58%, respectively. The most frequent SF gene was TTN followed by BRCA2. The frequency of actionable SFs among participants with rare disease and general population participants in the Korean population presented here will assist in reporting results of medically actionable SFs in genomic medicine.

Optimal allocation and operation of sewer monitoring sites for wastewater-based disease surveillance: A methodological proposal.

Wastewater-based epidemiology (WBE) is drawing increasing attention as a promising tool for an early warning of emerging infectious diseases such as COVID-19. This study demonstrated the utility of a spatial bisection method (SBM) and a global optimization algorithm (i.e., genetic algorithm, GA), to support better designing and operating a WBE program for disease surveillance and source identification. The performances of SBM and GA were compared in determining the optimal locations of sewer monitoring manholes to minimize the difference among the effective spatial monitoring scales of the selected manholes. While GA was more flexible in determining the spatial resolution of the monitoring areas, SBM allows stepwise selection of optimal sampling manholes with equiareal subcatchments and lowers computational cost. Upon detecting disease outbreaks at a regular sewer monitoring site, additional manholes within the catchment can be selected and monitored to identify source areas with a required spatial resolution. SBM offered an efficient method for rapidly searching for the optimal locations of additional sampling manholes to identify the source areas. This study provides strategic and technical elements of WBE including sampling site selection with required spatial resolution and a source identification method.

Simple differentiation method using FBS identifies DUSP6 as a marker for fine-tuning of FGF-ERK signaling activity in human pluripotent stem cells.

Assessment of differentiation potential is a basic requirement to obtain qualified human pluripotent stem cells (hPSCs). Here, we report a simple differentiation method using fetal bovine serum (FBS) to estimate differentiation potential and propensity of hPSCs. PluriTest using RNA-sequencing showed that cells differentiated after treatment with 5% FBS. Expression patterns of three germ layer markers revealed that cells cultured in Knockout Serum Replacement-containing medium (KSR) with mouse feeder cells had higher differentiation potential than cells cultured in a chemically defined medium (E8) with recombinant matrix proteins, especially into the mesoderm and endoderm lineages. Analysis of differentially expressed genes between KSR and E8 identified DUSP6 as a marker for where cells had been cultured. Expression of DUSP6 correlated with FGF-ERK signaling activity. Fine-tuning of FGF-ERK signaling activity to a range that can shut down DUSP6 transcription but sustain NANOG transcription partially increased the differentiation potential. Our data suggest that differentiation with 5% FBS is good to estimate differentiation potential and propensity at the early stage, and that DUSP6 is an excellent marker to monitor ERK signaling activity.

Socio-economic factors of high trash generation in the city of Los Angeles.

Trash is one of major pollutants in urban runoff. Some studies have been conducted to verify the different impacts of land use on trash generation in a qualitative way and focused on the performance of trash control measures. Few studies have explored the human impacts on trash generation or developed a quantitative model to describe the phenomenon. This paper examined the impact of human activity on trash generation. Spatial regimes on high trash generation areas were identified using the selected variables from best subset model regression and validated with Moran's I scatter plot and spatial analysis of variance. Bidirectional spatial lag regression with regimes was performed to develop the final model to explain the spatial distribution of trash generation and identify its major causes. The result showed that economic status and occupation of the population were correlated with trash accumulation and the dominant land use type, and the distance to rivers most affected trash generation. The effects of these indicators were different within and outside the high trash generation areas.

Genetic analysis of parathyroid and pancreatic tumors in a patient with multiple endocrine neoplasia type 1 using whole-exome sequencing.

BACKGROUND: Multiple endocrine neoplasia type 1 (MEN1) syndrome is an autosomal dominant hereditary disorder characterized by the presence of endocrine tumors affecting the parathyroid, pancreas, and pituitary. A heterozygous germline inactivating mutation in the MEN1 gene (first hit) may be followed by somatic loss of the remaining normal copy or somatic mutations in the MEN1 gene (second hit). Whole-exome sequencing has been successfully used to elucidate the mutations associated with the different types of tumors. CASE PRESENTATION: We performed whole-exome sequencing (WES) on three parathyroid tumors, one pancreatic insulinoma, and a blood sample taken from the same patient with MEN1 to study tumor heterogeneity in MEN1 originating from different tumors. We identified a novel frame-shift deletion (c.1382_1383delAG, p.E461GfsX69) in the MEN1 gene using WES, which was confirmed by Sanger sequencing. WES and the SNP array revealed somatic LOH on chromosome 11 in parathyroid tumors (left upper, left lower, and right upper parathyroid). However, we did not detect a somatic MEN1 gene mutation or LOH in the pancreatic insulinoma. WES revealed two somatic functional variants outside the MEN1 gene in the pancreatic insulinoma. CONCLUSIONS: This study revealed heterogeneity among tumors in the same patient with MEN1, suggesting that different tumor-specific tumorigenic mechanisms may contribute to the pathogenesis of MEN1 tumors. The present study supports the clinical applicability of the WES strategy to research on multiple tumor samples and blood.

Proactive modeling of water quality impacts of extreme precipitation events in a drinking water reservoir.

Extreme precipitation events are of concern to managers of drinking water sources because these occurrences can affect both water supply quantity and quality. However, little is known about how these low probability events impact organic matter and nutrient loads to surface water sources and how these loads may impact raw water quality. This study describes a method for evaluating the sensitivity of a water body of interest from watershed input simulations under extreme precipitation events. An example application of the method is illustrated using the Wachusett Reservoir, an oligo-mesotrophic surface water reservoir in central Massachusetts and a major drinking water supply to metropolitan Boston. Extreme precipitation event simulations during the spring and summer resulted in total organic carbon, UV-254 (a surrogate measurement for reactive organic matter), and total algae concentrations at the drinking water intake that exceeded recorded maximums. Nutrient concentrations after storm events were less likely to exceed recorded historical maximums. For this particular reservoir, increasing inter-reservoir transfers of water with lower organic matter content after a large precipitation event has been shown in practice and in model simulations to decrease organic matter levels at the drinking water intake, therefore decreasing treatment associated oxidant demand, energy for UV disinfection, and the potential for formation of disinfection byproducts.

Recessive C10orf2 mutations in a family with infantile-onset spinocerebellar ataxia, sensorimotor polyneuropathy, and myopathy.

Recessive mutations in chromosome 10 open reading frame 2 (C10orf2) are relevant in infantile-onset spinocerebellar ataxia (IOSCA). In this study, we investigated the causative mutation in a Korean family with combined phenotypes of IOSCA, sensorimotor polyneuropathy, and myopathy. We investigated recessive mutations in a Korean family with two individuals affected by IOSCA. Causative mutations were investigated using whole exome sequencing. Electrophysiological analyses and muscle and nerve biopsies were performed, along with magnetic resonance imaging (MRI) of the brain and lower extremities. Compound heterozygous mutations c.1460C>T and c.1485-1G>A in C10orf2 were identified as causative of IOSCA. Skeletal muscle showed mitochondrial DNA (mtDNA) deletions. Both patients showed a period of normal development until 12-15 months, followed by ataxia, athetosis, hearing loss, and intellectual disability. Electrophysiological findings indicated motor and sensory polyneuropathies. Muscle biopsy revealed variations in the size and shape of myofibers with scattered, small, and angulated degenerating myofibers containing abnormal mitochondria; these observations are consistent with myopathy and may be the result of mtDNA deletions. Sural nerve biopsy revealed an axonal neuropathy. High-signal-intensity lesions in the middle cerebellar peduncles were correlated with clinical severity, and MRI of the lower legs was compatible with the hypothesis of length-dependent axonal degeneration. We identified novel compound heterozygous mutations of the C10orf2 gene as the cause of IOSCA with sensorimotor polyneuropathy and myopathy. Signs of motor neuropathy and myopathy were discovered for the first time in IOSCA patients with C10orf2 mutations. These results suggest that the clinical spectrum of IOSCA caused by C10orf2 mutations may be more variable than previously reported.

Identification of CDH23 mutations in Korean families with hearing loss by whole-exome sequencing.

BACKGROUND: Patient genetic heterogeneity renders it difficult to discover disease-cause genes. Whole-exome sequencing is a powerful new strategy that can be used to this end. The purpose of the present study was to identify a hitherto unknown mutation causing autosomal recessive nonsyndromic hearing loss (ARNSHL) in Korean families. METHODS: We performed whole-exome sequencing in 16 individuals from 13 unrelated small families with ARNSHL. After filtering out population-specific polymorphisms, we focused on known deafness genes. Pathogenic effects of the detected mutations on protein structure or function were predicted via in silico analysis. RESULTS: We identified compound heterozygous CDH23 mutations in hearing-loss genes of two families. These include two previously reported pathological mutations, p.Pro240Leu and p.Glu1595Lys, as well as one novel mutation, p.Asn342Ser. The p.Pro240Leu mutation was found in both families. We also identified 26 non-synonymous variants in CDH23 coding exons from 16 hearing-loss patients and 30 Korean exomes. CONCLUSION: The present study is the first to show that CDH23 mutations cause hearing loss in Koreans. Although the precise contribution made by such mutations needs to be determined using a larger patient cohort, our data indicate that mutations in the CDH23 gene are one of the most important causes of non-syndromic hearing loss in East Asians. Further exome sequencing will identify common mutations or polymorphisms and contribute to the molecular diagnosis of, and development of new therapies for, hereditary hearing loss.

Multispectral remote sensing of harmful algal blooms in Lake Champlain, USA.

ABSTRACT: This study developed satellite remote sensing models to detect cyanobacterial blooms via chlorophyll a in Lake Champlain. Landsat Enhanced Thematic Mapper Plus data was used to retrieve chlorophyll a concentrations, phytoplankton, and cyanobacteria biovolume by calibrating and validating with coincident observation data. Correlation analysis results showed that band 2 (green band) and the band ratio of 2/1 (green/blue) were most highly correlated to chlorophyll a concentration (r = 0.76 and 0.82, respectively). Multiple regression results identified band 2 and 3 (red), and band ratio of 2/1 and 3/1 (red/blue) as critical information to estimate chlorophyll a concentrations. The regression models accounted for 72 to 83% of the variability in chlorophyll a observations, allowing for estimates of phytoplankton and cyanobacteria levels in the lake. Satellite image processing results successfully showed the temporal and spatial distribution of chlorophyll a, phytoplankton, and cyanobacteria in the lake. This information can be used to evaluate the effect of pollution sources and weather conditions, and assist decision making for water management.

Multivariate analyses for monitoring EDCs and PPCPs in a lake water.

The analysis of endocrine disrupting compounds (EDCs) and pharmaceutical and personal care products (PPCP), present at trace level in surface waters, is often expensive, time-consuming, and complex. Implementing effective monitoring strategies for these compounds is essential to determine the types of analytes, sampling locations, and sampling frequencies. Multivariate analyses were used to investigate the patterns of EDCs and PPCPs in Lake Mead, Nevada, for these purposes. The results of cluster analysis and principal component analysis to identify the patterns among compounds demonstrated that selected pharmaceuticals tended to be present together with each other, whereas hormones did not show patterns with other compounds. The results of cluster analysis and discriminant analysis to investigate the spatial variation of EDCs and PPCPs eliminated redundant sampling locations, verifying the current selection of sampling locations in Lake Mead. The results of autocorrelation provided optimal sampling frequencies for EDCs and PPCPs, suggesting either monthly or quarterly monitoring of these compounds in Lake Mead. The patterns of the compounds could be site specific; depending on weather and hydrological conditions of the water systems, but this study's approaches will facilitate effective assessment and monitoring of EDCs and PPCPs in surface water.

Assessment of nutrient distributions in Lake Champlain using satellite remote sensing.

The introduction of nutrients to lakes causing eutrophic conditions is a major problem around the world. Proper monitoring and modeling are important to effectively manage eutrophication in lake waters. The goal is to develop remote sensing models for nutrients, total phosphorus and total nitrogen, in Lake Champlain. The remote sensing models were created using multivariate linear regression with the unique band combinations of Landsat Enhanced Thematic Mapper Plus (ETM+) imagery based on the empirical relationship with the field observations. The resulting models successfully showed nutrient distributions in the most eutrophic part of Lake Champlain, Missisquoi Bay, with reasonable adjusted coefficient of determination values (R(2)=0.81 and 0.75 for total phosphorus and total nitrogen, respectively). The results show the feasibility and the utility of satellite imagery to detect spatial distributions of lake water quality constituents, which can be used to better understand nutrient distributions in Lake Champlain. This approach can be applicable to other lakes experiencing eutrophication assisting decision making when implementing Best Management Practices and other mitigation techniques to lakes.

Optimizing coagulant dosage using deep learning models with large-scale data.

Water treatment plants are facing challenges that necessitate transition to automated processes using advanced technologies. This study introduces a novel approach to optimize coagulant dosage in water treatment processes by employing a deep learning model. The study utilized minute-by-minute data monitored in real time over a span of five years, marking the first attempt in drinking water process modeling to leverage such a comprehensive dataset. The deep learning model integrates a one-dimensional convolutional neural network (Conv1D) and gated recurrent unit (GRU) to effectively extract features and model complex time-series data. Initially, the model predicted coagulant dosage and sedimentation basin turbidity, validated against a physicochemical model. Subsequently, the model optimized coagulant dosage in two ways: 1) maintaining sedimentation basin turbidity below the 1.0 NTU guideline, and 2) analyzing changes in sedimentation basin turbidity resulting from reduced coagulant dosage (5-20%). The findings of the study highlight the effectiveness of the deep learning model in optimizing coagulant dosage with substantial reductions in coagulant dosage (approximately 22% reduction and 21 million KRW/year). The results demonstrate the potential of deep learning models in enhancing the efficiency and cost-effectiveness of water treatment processes, ultimately facilitating process automation.

Whole-exome sequencing identifies MYO15A mutations as a cause of autosomal recessive nonsyndromic hearing loss in Korean families.

BACKGROUND: The genetic heterogeneity of hearing loss makes genetic diagnosis expensive and time consuming using available methods. Whole-exome sequencing has recently been introduced as an alternative approach to identifying causative mutations in Mendelian disorders. METHODS: To identify the hidden mutations that cause autosomal recessive nonsyndromic hearing loss (ARNSHL), we performed whole-exome sequencing of 13 unrelated Korean small families with ARNSHL who were negative for GJB2 or SLC26A4 mutations. RESULTS: We found two novel compound heterozygous mutations, IVS11 + 1 and p.R2146Q, of MYO15A in one (SR903 family) of the 13 families with ARNSHL. In addition to these causative mutations, 13 nonsynonymous variants, including variants with uncertain pathogenicity (SR285 family), were identified in the coding exons of MYO15A from Korean exomes. CONCLUSION: This is the first report of MYO15A mutations in an East Asian population. We suggest that close attention should be paid to this gene when performing genetic testing of patients with hearing loss in East Asia. The present results also indicate that whole-exome sequencing is a valuable method for comprehensive medical diagnosis of a genetically heterogeneous recessive disease, especially in small-sized families.

Genetic compatibility between Anopheles lesteri from Korea and Anopheles paraliae from Thailand.

To assess differentiation and relationships between Anopheles lesteri and Anopheles paraliae we established three and five iso-female lines of An. lesteri from Korea and An. paraliae from Thailand, respectively. These isolines were used to investigate the genetic relationships between the two taxa by crossing experiments and by comparing DNA sequences of ribosomal DNA second internal transcribed spacer (ITS2) and mitochondrial DNA cytochrome c oxidase subunit I (COI) and subunit II (COII). Results of reciprocal and F1-hybrid crosses between An. lesteri and An. paraliae indicated that they were compatible genetically producing viable progenies and complete synaptic salivary gland polytene chromosomes without inversion loops in all chromosome arms. The pairwise genetic distances of ITS2, COI and COII between these morphological species were 0.040, 0.007-0.017 and 0.008-0.011, respectively. The specific species status of An. paraliae in Thailand and/or other parts of the continent are discussed.

Prioritizing subwatersheds for stormwater pollution to Wachusett Reservoir.

The Wachusett Reservoir is a primary drinking water resource for the greater Boston, Massachusetts, area. With a drainage area of 280 km2, the watershed has been gradually urbanized with increased residential, commercial, industrial, and transportation land uses. Increased impervious surface area as a result of urbanization results in increased runoff volume and pollutant loads to the reservoir. This study estimated annual stormwater pollutant mass loads in the watershed to prioritize sub-basins and to identify areas susceptible to stormwater pollution. Catchment Prioritization Index (CPI) was calculated using annual stormwater pollutant mass loads, which were further used to identify clustered hotspots through application of the Getis-Ord Gi* statistic. Validation with observed data showed higher levels of fecal coliform bacteria loading from identified hotspots. This approach will be useful to prioritize sub-basins for future (1) development of stormwater monitoring strategies and (2) best management practices (BMPs) in the watershed.

Coagulant dosage determination using deep learning-based graph attention multivariate time series forecasting model.

Determination of coagulant dosage in water treatment is a time-consuming process involving nonlinear data relationships and numerous factors. This study provides a deep learning approach to determine coagulant dosage and/or the settled water turbidity using long-term data between 2011 and 2021 to include the effect of various weather conditions. A graph attention multivariate time series forecasting (GAMTF) model was developed to determine coagulant dosage and was compared with conventional machine learning and deep learning models. The GAMTF model (R2 = 0.94, RMSE = 3.55) outperformed the other models (R2 = 0.63 - 0.89, RMSE = 4.80 - 38.98), and successfully predicted both coagulant dosage and settled water turbidity simultaneously. The GAMTF model improved the prediction accuracy by considering the hidden interrelationships between features and the past states of features. The results demonstrate the first successful application of multivariate time series deep learning model, especially, a state-of-the-art graph attention-based model, using long-term data for decision-support systems in water treatment processes.

KMD: Korean Mutation Database for genes related to diseases.

The number of known disease-causing mutations has increased dramatically. However, there have been few organized mutation databases developed that are available to the public or not-for-profit entities. Thus, clinicians and diagnostic laboratories had to spend time searching many publications and databases to determine whether a mutation has been previously reported. To assist in genetic diagnoses, the systematic collection and curation of mutations are necessary. The Korean Mutation Database (KMD; http://kmd.cdc.go.kr) is a country-specific database of human gene mutations that was established in September 2009. The KMD is a database consolidating mutations of genes related to diseases in Korea; it now contains more than 1,600 mutations from 245 genes. We collected mutation data from diagnostic laboratories and published journals over recent decades in Korea. KMD has been open to the public for searches and registration of mutation data without charge. Our aim is to provide organized information for clinicians and researchers who are interested in genetic diseases. It will be useful not only for researchers in Korea but also for researchers in countries with similar ethnic backgrounds. Ultimately, KMD will be an essential base to improve researches in genetic diseases, developments of diagnostics, and therapeutic optimization.

Exome sequencing is an efficient tool for genetic screening of Charcot-Marie-Tooth disease.

Charcot-Marie-Tooth disease (CMT) is one of the most common inherited neuropathies and is a genetically and clinically heterogeneous disorder with variable inheritance modes. As several molecules have been reported to have therapeutic effects on CMT, depending on the underlying genetic causes, exact genetic diagnostics have become very important for executing personalized therapy. Whole-exome sequencing has recently been introduced as an available method to identify rare or novel genetic defects from genetic disorders. Particularly, CMT is a model disease to apply exome sequencing because more than 50 genes (loci) are involved in its development with weak genotype-phenotype correlation. This study performed the exome sequencing in 25 unrelated CMT patients who revealed neither 17p12 duplication/deletion nor several major CMT genes. This study identified eight causative heterozygous mutations (32%). This detection rate seems rather high because each sample was tested before the study for major genetic causes. Therefore, this study suggests that the exome sequencing can be a highly exact, rapid, and economical molecular diagnostic tool for CMT patients who are tested for major genetic causes.

Genetic loci associated with lipid concentrations and cardiovascular risk factors in the Korean population.

BACKGROUND: Dyslipidaemia, a key risk factor for cardiovascular disease (CVD), is strongly influenced by genetic factors. OBJECTIVE: To identify genetic factors affecting blood lipid concentrations and CVD risk factors in the Korean population by a candidate gene association analysis. METHODS: 21 single nucleotide polymorphisms (SNPs) that have been reported as associated with lipid concentrations in people of European ancestry were selected and their associations with CVD risk factors in Korean populations assessed. Genotype data from 7616 subjects without diabetes or lipid-lowering drugs were obtained from the Korean Association Resource (KARE) project. RESULTS: After adjustment for age and gender, five SNPs were identified that were associated with high-density lipoprotein-cholesterol (HDL-C; rs4420638: p=2.09×10⁻7), 11 SNPs with low-density lipoprotein-cholesterol (LDL-C; rs12654264: p=1.29×10⁻8) and eight SNPs with triglycerides (TG; rs4420638: p=1.80×10⁻6). Through analysis of multiple associations with lipid traits, after adjustment for age, gender, body mass index, smoking, alcohol consumption and hypertension, five SNPs (rs693, rs17321515, rs174547, rs688, rs4420638) were identified that were strongly associated with at least two of the following: HDL-C, LDL-C and TG. Of these, rs693, which lies in the APOB gene, was also significantly associated with the homoeostasis model assessment for insulin resistance (p=6.68×10⁻6) and γ-glutamyl transpeptidase (p=2.34×10⁻6), and rs174547, which lies in the FADS1 gene and was significantly associated with fasting plasma glucose (p=1.48×10⁻6). CONCLUSION: Several SNPs associated with lipid traits and CVD risk factors were identified. These findings may form the basis for further investigations to identify the causative polymorphisms in dyslipidaemia and CVD.

Functional expression and characterization of an iron-containing superoxide dismutase of Acanthamoeba castellanii.

Acanthamoeba spp. are free-living amoebae, but opportunistic infections of some strains of the organisms cause severe diseases such as acanthamoebic keratitis, pneumonitis, and granulomatous amoebic encephalitis in human. In this study, we identified a gene encoding iron superoxide dismutase of Acanthamoeba castellanii (AcFe-SOD) and characterized biochemical and functional properties of the recombinant enzyme. Multiple sequence alignment of the deduced amino acid sequence of AcFe-SOD with those of previously reported iron-containing SODs (Fe-SODs) from other protozoan parasites showed that AcFe-SOD shared common metal-binding residues and motifs that are conserved in Fe-SODs. The genomic length of the AcFe-SOD gene was 926 bp consisting of five exons interrupted by four introns. The recombinant AcFe-SOD showed similar biochemical characteristics with its native enzyme and shared typical biochemical properties with other characterized Fe-SODs, including molecular structure, broad pH optimum, and sensitivity to hydrogen peroxide. Immunolocalization analysis revealed that the enzyme localized in the cytosol of the trophozoites. Activity and expression level of the enzyme were significantly increased under oxidative stressed conditions. These results collectively suggest that AcFe-SOD may play essential roles in the survival of the parasite not only by protecting itself from endogenous oxidative stress but also by detoxifying oxidative killing of the parasite by host immune effector cells.