Identification of Sequence Variants in Genetic Disease-Causing Genes Using Targeted Next-Generation Sequencing

Identification of gene variants plays an important role in research on and diagnosis of genetic diseases. A combination of enrichment of targeted genes and next-generation sequencing (targeted DNA-HiSeq) results in both high efficiency and low cost for targeted sequencing of genes of interest.To identify mutations associated with genetic diseases, we designed an array-based gene chip to capture all of the exons of 193 genes involved in 103 genetic diseases. To evaluate this technology, we selected 7 samples from seven patients with six different genetic diseases resulting from six disease-causing genes and 100 samples from normal human adults as controls. The data obtained showed that on average, 99.14% of 3,382 exons with more than 30-fold coverage were successfully detected using Targeted DNA-HiSeq technology, and we found six known variants in four disease-causing genes and two novel mutations in two other disease-causing genes (the STS gene for XLI and the FBN1 gene for MFS) as well as one exon deletion mutation in the DMD gene. These results were confirmed in their entirety using either the Sanger sequencing method or real-time PCR.Targeted DNA-HiSeq combines next-generation sequencing with the capture of sequences from a relevant subset of high-interest genes. This method was tested by capturing sequences from a DNA library through hybridization to oligonucleotide probes specific for genetic disorder-related genes and was found to show high selectivity, improve the detection of mutations, enabling the discovery of novel variants, and provide additional indel data. Thus, targeted DNA-HiSeq can be used to analyze the gene variant profiles of monogenic diseases with high sensitivity, fidelity, throughput and speed

New insight into kinetics behavor of the structural formation process in Agar gelation

A time-resolved experimental study on the kinetics and relaxation of the structural formation process in gelling Agar-water solutions was carried out using our custom-built torsion resonator. The study was based on measurements of three naturally cooled solutions with agar concentrations of 0.75%, 1.0% and 2.0% w/w. It was found that the natural-cooling agar gelation process could be divided into three stages, sol stage (Stage I), gelation zone (Stage II) and gel stage (Stage III), based on the time/temperature evolutions of the structural development rate (SDR). An interesting fluctuant decaying behavior of SDR was observed in Stage II and III, indicative of a sum of multiple relaxation processes and well described by a multiple-order Gaussisn-like equation: . More interestingly, the temperature dependences of the fitted values of Wn in Stage II and Stage III were found to follow the different Arrhenius laws, with different activation energies of EaII= 39-74 KJ/mol and EaIII~7.0 KJ/mol. The two different Arrhenius-like behaviors respectively suggest that dispersions in Stage II be attributed to the relaxation of the self-assembly of agar molecules or the growth of junction zones en route to gelation, in which the formation or fission of hydrogen bonding interactions plays an important role; and that dispersions in Stage III be attributed to the relaxation dynamics of water released from various size domains close to the domain of the viscous flow of water during the syneresis process.Comment: 24 pages, 4 figures, 1 tabl

Prevalence and trend of hepatitis C virus infection among blood donors in Chinese mainland: a systematic review and meta-analysis

<p>Abstract</p> <p>Background</p> <p>Blood transfusion is one of the most common transmission pathways of hepatitis C virus (HCV). This paper aims to provide a comprehensive and reliable tabulation of available data on the epidemiological characteristics and risk factors for HCV infection among blood donors in Chinese mainland, so as to help make prevention strategies and guide further research.</p> <p>Methods</p> <p>A systematic review was constructed based on the computerized literature database. Infection rates and 95% confidence intervals (95% CI) were calculated using the approximate normal distribution model. Odds ratios and 95% CI were calculated by fixed or random effects models. Data manipulation and statistical analyses were performed using STATA 10.0 and ArcGIS 9.3 was used for map construction.</p> <p>Results</p> <p>Two hundred and sixty-five studies met our inclusion criteria. The pooled prevalence of HCV infection among blood donors in Chinese mainland was 8.68% (95% CI: 8.01%-9.39%), and the epidemic was severer in North and Central China, especially in Henan and Hebei. While a significant lower rate was found in Yunnan. Notably, before 1998 the pooled prevalence of HCV infection was 12.87% (95%CI: 11.25%-14.56%) among blood donors, but decreased to 1.71% (95%CI: 1.43%-1.99%) after 1998. No significant difference was found in HCV infection rates between male and female blood donors, or among different blood type donors. The prevalence of HCV infection was found to increase with age. During 1994-1995, the prevalence rate reached the highest with a percentage of 15.78% (95%CI: 12.21%-19.75%), and showed a decreasing trend in the following years. A significant difference was found among groups with different blood donation types, Plasma donors had a relatively higher prevalence than whole blood donors of HCV infection (33.95% <it>vs </it>7.9%).</p> <p>Conclusions</p> <p>The prevalence of HCV infection has rapidly decreased since 1998 and kept a low level in recent years, but some provinces showed relatively higher prevalence than the general population. It is urgent to make efficient measures to prevent HCV secondary transmission and control chronic progress, and the key to reduce the HCV incidence among blood donors is to encourage true voluntary blood donors, strictly implement blood donation law, and avoid cross-infection.</p

Fates and ecological effects of current-use pesticides (CUPs) in a typical river-estuarine system of Laizhou Bay, North China

Current-use pesticides (CUPS) are widely applied in agriculture; however, little is known about their environmental behaviors, especially in the freshwater-seawater transitional zone. Water and sediment samples were collected in an intensively human impacted river (Xiaoqing River) from the headwaters to Laizhou Bay to investigate the distributions and environmental fates of four CUPs: trifluralin, chlorothalonil, chlorpyrifos, and dicofol. These CUPS were frequently detected in water and sediment samples. Sigma CUPs in water and sediment samples ranged from 1.20 to 100.2 ng L-1 and 6.6-2972.5 ng g(-1) dry weight (dw), respectively. Chlorpyrifos and chlorothalonil were the most abundant CUPs in water and sediment samples, respectively. Spatial distribution of CUPs in the Xiaoqing River aquatic ecosystem was mainly influenced by point sources, agricultural activities, the dilution effect by seawater, and environmental parameters. Field-based sediment water partitioning coefficients, normalized by organic carbon (log Koc), were calculated. Interestingly, temperature and salinity exhibited significant impacts on the distribution of log Koc of the four CUPs. The effect of temperature on the distribution of log Koc of the four CUPs varied between the CUPs. In most water samples, the levels of chlorpyrifos exceed the freshwater screening benchmarks. Hence, urgent control measures need to be devised and implemented. (C) 2019 Elsevier Ltd. All rights reserved

Halogenated flame retardants in the sediments of the Chinese Yellow Sea and East China Sea

With the phasing out of traditional polybrominated diphenyl ethers (PBDE5), significant volumes of alternative brominated flame retardants (aBFRs) are being used and released into the environment compartment, especially in coastal regions. The levels and distribution of PBDE5, aBFRs, and dechlorane plus (DPs) were investigated in the surface sediments of the Yellow Sea (YS) and East China Sea (ECS) to examine the distribution and sources of these hydrophobic contaminants. The level and distribution of pollutants in the sediments of YS and ECS show obvious regional differences. As a major replacement for decabromodiphenyl ether (BDE 209), decabromodiphenyl ethane (DBDPE) was the dominant compound observed in the surface sediments, with a concentration one order of magnitude higher than that of BDE 209. High concentrations were found in the depositional zones of the YS, indicating that these contaminants may originate from land-based pollution sources (likely from the Laizhou Bay manufacturing base) near the Bohai Sea. The pollutants can be carried by the coastal current together with the sediment from the Yellow River, transported through the Bohai Strait and deposited in the mud zone of Northern and Southern YS. Low levels of halogenated flame retardants (HFRs) were found in the estuary of the Yangtze River and ECS, indicating that Yangtze River contributes less HFRs to the region. Riverine discharge, atmospheric deposition, surface runoff, ocean current system, and mud area deposition effects may be significant factors influencing the distributions of HFRs. (C) 2019 Elsevier Ltd. All rights reserved