The primary problem during the evolvement of next-generation Internet is the contradiction between growing requirements for Internet and the insufficient development of network theory and technology. As the fundamenta...The primary problem during the evolvement of next-generation Internet is the contradiction between growing requirements for Internet and the insufficient development of network theory and technology. As the fundamental principles to guide the developing direction of Internet, the study of Internet architecture is always a focus in the research community. To address the core issue of network scalability, we propose multi-dimension scalable architecture of next-generation Internet, the main idea of which is to extend the single-dimension scalability of traditional Internet on interconnection to multi-dimension scalability of next-generation Internet. The multi-dimension scalability is composed of scale-scalability, performance-scalability, security-scalability, function-scalability, and service-scalability. We suggest five elements, namely, IPv6, authentic IPv6 addressing, scalable processing capacity of routers, end-to-end connectionless Quality-of-Service control, and 4over6 mechanism to realize the multi-dimension scalability. The current research results show that the multi-dimension scalable architecture composed of these five elements will bring great influence on next-generation Internet.展开更多
The security of the seed industry is crucial for ensuring national food security.Currently,developed countries in Europe and America,along with international seed industry giants,have entered the Breeding 4.0 era.This...The security of the seed industry is crucial for ensuring national food security.Currently,developed countries in Europe and America,along with international seed industry giants,have entered the Breeding 4.0 era.This era integrates biotechnology,artificial intelligence(AI),and big data information technology.In contrast,China is still in a transition period between stages 2.0 and 3.0,which primarily relies on conventional selection and molecular breeding.In the context of increasingly complex international situations,accurately identifying core issues in China's seed industry innovation and seizing the frontier of international seed technology are strategically important.These efforts are essential for ensuring food security and revitalizing the seed industry.This paper systematically analyzes the characteristics of crop breeding data from artificial selection to intelligent design breeding.It explores the applications and development trends of AI and big data in modern crop breeding from several key perspectives.These include highthroughput phenotype acquisition and analysis,multiomics big data database and management system construction,AI-based multiomics integrated analysis,and the development of intelligent breeding software tools based on biological big data and AI technology.Based on an in-depth analysis of the current status and challenges of China's seed industry technology development,we propose strategic goals and key tasks for China's new generation of AI and big data-driven intelligent design breeding.These suggestions aim to accelerate the development of an intelligent-driven crop breeding engineering system that features large-scale gene mining,efficient gene manipulation,engineered variety design,and systematized biobreeding.This study provides a theoretical basis and practical guidance for the development of China's seed industry technology.展开更多
The scope of the Internet of Things(IoT)applications varies from strategic applications,such as smart grids,smart transportation,smart security,and smart healthcare,to industrial applications such as smart manufacturi...The scope of the Internet of Things(IoT)applications varies from strategic applications,such as smart grids,smart transportation,smart security,and smart healthcare,to industrial applications such as smart manufacturing,smart logistics,smart banking,and smart insurance.In the advancement of the IoT,connected devices become smart and intelligent with the help of sensors and actuators.However,issues and challenges need to be addressed regarding the data reliability and protection for signicant nextgeneration IoT applications like smart healthcare.For these next-generation applications,there is a requirement for far-reaching privacy and security in the IoT.Recently,blockchain systems have emerged as a key technology that changes the way we exchange data.This emerging technology has revealed encouraging implementation scenarios,such as secured digital currencies.As a technical advancement,the blockchain network has the high possibility of transforming various industries,and the next-generation healthcare IoT(HIoT)can be one of those applications.There have been several studies on the integration of blockchain networks and IoT.However,blockchain-as-autility(BaaU)for privacy and security in HIoT systems requires a systematic framework.This paper reviews blockchain networks and proposes BaaU as one of the enablers.The proposed BaaU-based framework for trustworthiness in the next-generation HIoT systems is divided into two scenarios.The rst scenario suggests that a healthcare service provider integrates IoT sensors such as body sensors to receive and transmit information to a blockchain network on the IoT devices.The second proposed scenario recommends implementing smart contracts,such as Ethereum,to automate and control the trusted devices’subscription in the HIoT services.展开更多
The Internet of things has particularly novel implications in the area of public health. This is due to (1) The rapid and widespread adoption of powerful contemporary Smartphone’s;(2) The increasing availability and ...The Internet of things has particularly novel implications in the area of public health. This is due to (1) The rapid and widespread adoption of powerful contemporary Smartphone’s;(2) The increasing availability and use of health and fitness sensors, wearable sensor patches, smart watches, wireless-enabled digital tattoos and ambient sensors;and (3) The nature of public health to implicitly involve connectivity with and the acquisition of data in relation to large numbers of individuals up to population scale. Of particular relevance in relation to the Internet of Things (IoT) and public health is the need for privacy and anonymity of users. It should be noted that IoT capabilities are not inconsistent with maintaining privacy, due to the focus of public health on aggregate data not individual data and broad public health interventions. In addition, public health information systems utilizing IoT capabilities can be constructed to specifically ensure privacy, security and anonymity, as has been developed and evaluated in this work. In this paper we describe the particular characteristics of the IoT that can play a role in enabling emerging public health capabilities;we describe a privacy-preserving IoT-based public health information system architecture;and provide a privacy evaluation.展开更多
BACKGROUND Pepsinogen(PG)and the PG I/II ratio(PGR)are critical indicators for diagnosing Helicobacter pylori infection and chronic atrophic gastritis,and assessing gastric cancer risk.Existing reference intervals(RIs...BACKGROUND Pepsinogen(PG)and the PG I/II ratio(PGR)are critical indicators for diagnosing Helicobacter pylori infection and chronic atrophic gastritis,and assessing gastric cancer risk.Existing reference intervals(RIs)often overlook age,sex,and demographic variations.Partitioned RIs,while considering these factors,fail to capture the gradual age-related physiological changes.Next-generation RIs offer a solution to this limitation.AIM To investigate age-and sex-specific dynamics of PG and establish next-generation RIs for adults and the elderly in northern China.METHODS After screening,708 healthy individuals were included in this observational study.Serum PG was measured using chemiluminescence immunoassay.Age-and sex-related effects on PG were analyzed with a two-way analysis of variance.RI partitioning was determined by the standard deviation ratio(SDR).Traditional RIs were established using a non-parametric approach.Generalized Additive Models for Location,Scale,and Shape(GAMLSS)modeled age-related trends and continuous reference percentiles for PG I and PG II.Reference limit flagging rates for both RI types were compared.RESULTS PG I and PG II levels were influenced by age(P<0.001)and sex(P<0.001),while PGR remained stable.Age-specific RIs were required for PG I(SDR=0.366)and PG II(SDR=0.424).Partitioned RIs were established for PG I and PG II,with a single RI for PGR.GAMLSS modeling revealed distinct age-dependent trajectories:PG I increased from a median of 39.75μg/L at age 20 years to 49.75μg/L at age 60 years,a 25.16%increase,after which it plateaued through age 80 years.In contrast,PG II showed a continuous rise throughout the age range,with the median value increasing from 5.07μg/L at age 20 years to 8.36μg/L at age 80 years,corresponding to a 64.89%increase.Continuous reference percentiles intuitively reflected these trends and were detailed in this study.Next-generation RIs demonstrated superior accuracy compared to partitioned RIs when applied to specific age subgroups.CONCLUSION This study elucidates the age-and sex-specific dynamics of PG and,to our knowledge,is the first to establish next-generation RIs for PG,supporting more individualized interpretation in laboratory medicine.展开更多
BACKGROUND Leuconostoc garlicum is commonly found in fermented foods and very few infected patients have been reported,who typically present symptoms such as fever and fatigue.Conventional clinical examinations often ...BACKGROUND Leuconostoc garlicum is commonly found in fermented foods and very few infected patients have been reported,who typically present symptoms such as fever and fatigue.Conventional clinical examinations often struggle to identify this bacterium,and routine anti-infective treatments are generally ineffective.Both diagnostic challenges and therapeutic limitations pose significant difficulties for clinicians.CASE SUMMARY We report a patient ultimately diagnosed with Leuconostoc garlicum infection.The primary manifestations included persistent fever,cough and fatigue.These symptoms lasted for 2 months.He received anti-infective treatment at a community hospital,but this was ineffective.After inquiring about the patient's medical history and conducting a physical examination,the patient underwent laboratory tests.Complete blood count tests revealed that the patient had a high proportion of neutrophils,C-reactive protein level was 235.9 mg/L,erythrocyte sedimentation rate was 67 mm/h,respiratory pathogen testing was negative,and he was then thought to have an infectious disease.However,conventional anti-infective treatments were ineffective.After excluding infectious neurological diseases,urologic diseases and digestive problems,we ultimately focused our attention on the lungs.A lung computed tomography scan indicated pulmonary inflammation.Bronchoalveolar lavage fluid for next-generation sequencing suggested lung infection with Leuconostoc garlicum.The patient's symptoms gradually improved following treatment with piperacillin tazobactam and linezolid.During the follow-up period,the patient's temperature remained normal.CONCLUSION For patients with suspected bacterial infection and experiencing fever,conventional anti-infective treatment can be ineffective in controlling their symptoms,and an infection due to rare bacteria or drug-resistant bacteria should be considered.Next-generation sequencing enables rapid and precise identification of infection-related pathogens in febrile patients.展开更多
In rice fields,rice plants usually grow alongside wild weeds and are attacked by various invertebrate species.Viruses are abundant in plants and invertebrates,playing crucial ecological roles in controlling microbial ...In rice fields,rice plants usually grow alongside wild weeds and are attacked by various invertebrate species.Viruses are abundant in plants and invertebrates,playing crucial ecological roles in controlling microbial abundance and maintaining community structures.To date,only 16 rice viruses have been documented in rice-growing regions.These viruses pose serious threats to rice production and have traditionally been identified only from rice plants and insect vectors by isolation techniques.Advances in next-generation sequencing(NGS)have made it feasible to discover viruses on a global scale.Recently,numerous viruses have been identified in plants and invertebrates using NGS technologies.In this review,we discuss viral studies in rice plants,invertebrate species,and weeds in rice fields.Many novel viruses have been discovered in rice ecosystems through NGS technologies,with some also detected using metatranscriptomic and small RNA sequencing.These analyses greatly expand our understanding of viruses in rice fields and provide valuable insights for developing efficient strategies to manage insect pests and virus-mediated rice diseases.展开更多
Objective and Background Early and accurate diagnosis of spinal infections,including spinal tuberculosis,is pivotal for effective treatment but remains challenging.This study aims to assess the diagnostic yield of met...Objective and Background Early and accurate diagnosis of spinal infections,including spinal tuberculosis,is pivotal for effective treatment but remains challenging.This study aims to assess the diagnostic yield of metagenomic next-generation sequencing(mNGS)compared with that of conventional microbiological tests(CMTs)in identifying pathogens associated with spinal pathologies,with a special focus on infections leading to surgical interventions.Methods We enrolled 85 patients who underwent spinal surgery,comprising 63 patients with clinically diagnosed spinal infections,including patients with spinal tuberculosis,and 22 patients with noninfectious spinal conditions.The procedures involved irrigation and debridement for persistent wound drainage,with subsequent DNA extraction from plasma and joint fluid for mNGS and CMT analysis.Results Significantly increased C-reactive protein(CRP)levels were observed in patients with infections.The mNGS approach showed greater diagnostic sensitivity(92.06%)for detecting pathogens,including Mycobacterium tuberculosis,than did CMTs(36.51%).Despite its low specificity,mNGS had considerable negative predictive value(70.59%),underscoring its utility in ruling out infections.Conclusions The mNGS offers superior sensitivity over CMTs in the diagnosis of a variety of spinal infections,notably spinal tuberculosis.This study highlights the potential of mNGS in enhancing the diagnosis of complex spinal infections,thereby informing targeted treatment strategies.展开更多
In this study,an amine-reactive poly(pentafluorophenyl acrylate)(PPFPA)platform was developed for advanced surface engineering of next-generation sequencing(NGS)chips.Through post-polymerization modification,PPFPA was...In this study,an amine-reactive poly(pentafluorophenyl acrylate)(PPFPA)platform was developed for advanced surface engineering of next-generation sequencing(NGS)chips.Through post-polymerization modification,PPFPA was functionalized with dual moieties:azide groups for covalent immobilization of DBCO-modified DNA primers via click chemistry and tunable hydrophilic side chains to optimize biocompatibility and surface properties.Systematic screening revealed that hydrophobic azide carriers combined with neutral hydroxyl groups maximized the DNA immobilization efficacy,approaching the performance of commercial polyacrylamide-based polymers.The negatively charged carboxyl groups severely impede DNA primer attachment.Higher molecular weight derivatives further enhance the efficacy of DNA immobilization.In NGS validation,optimized surface modification polymers achieved robust surface density of clustered DNA and high sequencing accuracy,surpassing quality benchmarks and comparable to those of conventional analogs.This platform demonstrates significant potential for tailoring high-sensitivity surfaces for genomic applications,advancing clinical diagnostics,and personalized medicine.展开更多
This study investigates the diversity of gut microbiota in Metaphire peguana,an earthworm species commonly found in agricultural areas of Thailand.Earthworms play a critical role in soil ecosystems by supporting nutri...This study investigates the diversity of gut microbiota in Metaphire peguana,an earthworm species commonly found in agricultural areas of Thailand.Earthworms play a critical role in soil ecosystems by supporting nutrient cycling and breaking down organic matter.Understanding the microbial diversity in their gut is essential for exploring their ecological contributions.Using Next Generation Sequencing(NGS),we analyzed the mycobiome in the gut of M.peguana.Our findings revealed a high diversity of fungal species,primarily belonging to two major phyla:Ascomycota and Basidiomycota.Ascomycota was the most abundant phylum,comprising 40.1% of the total fungal species identified.A total of 33 distinct fungal species were identified,which underscores the richness of microbial life within the earthworm gut.This study successfully created the first genetic database of the microbial community in M.peguana,providing a foundation for future research in agricultural applications.The microbial species identified,particularly siderophoreproducing fungi,could have significant implications for improving soil fertility and promoting sustainable agricultural practices.The use of NGS technology has enabled comprehensive profiling of microbial communities,allowing for precise identification of fungi that may play essential roles in soil health.Furthermore,the study paves the way for future studies on the potential applications of earthworm gut microbiomes in biotechnology,especially in enhancing soil nutrient availability and plant growth.The findings of this research contribute to the broader understanding of the ecological roles of earthworms and their microbiomes in soil ecosystems.展开更多
Cystic echinococcosis (CE) is a prevalent zoonotic disease caused by Echinococcus granulosus, with a cosmopolitan distribution. The parasite is transmitted cyclically between canines and numerous intermediate herbivor...Cystic echinococcosis (CE) is a prevalent zoonotic disease caused by Echinococcus granulosus, with a cosmopolitan distribution. The parasite is transmitted cyclically between canines and numerous intermediate herbivorous livestock animals. Also, other Taeniid tapeworms could infect domestic dogs and they pose significant veterinary and public health concerns worldwide. This study aimed to develop a sensitive molecular method for detecting Echinococcus spp. DNA in dog fecal samples using next-generation sequencing (NGS). A set of PCR primers targeting conserved regions of Taeniid tapeworms’ 18s rRNA genes was designed and tested for amplifying genomic DNA from various tapeworm species. The PCR system demonstrated high sensitivity, amplifying DNA from all tested tapeworm species, with differences observed in amplified band sizes. The primers were adapted for NGS analysis by adding forward and reverse adapters, enabling the sequencing of amplified DNA fragments. Application of the developed PCR system to dog fecal samples collected from Yatta town, Palestine, revealed the presence of E. granulosus DNA in five out of 50 samples. NGS analysis confirmed the specificity of the amplified DNA fragments, showing 98% - 99% similarity with the 18s rDNA gene of E. granulosus. This study demonstrates the utility of NGS-based molecular methods for accurate and sensitive detection of Echinococcus spp. in dog fecal samples, providing valuable insights for epidemiological surveillance and control programs of echinococcosis in endemic regions.展开更多
The improvement of soybean seed carotenoid contents is very important due to the beneficial role of carotenoids in human health and nutrition. However, the genetic architecture underlying soybean carotenoid biosynthes...The improvement of soybean seed carotenoid contents is very important due to the beneficial role of carotenoids in human health and nutrition. However, the genetic architecture underlying soybean carotenoid biosynthesis remains largely unknown. In the present study, we employed next generation sequencing-based bulked-segregant analysis to identify new genomic regions governing seed carotenoids in 1,551 natural soybean accessions. The genomic DNA samples of individual plants with extreme phenotypes were pooled to form two bulks with high(50 accessions) and low(50 accessions) carotenoid contents for Illumina sequencing. A total of 125.09 Gb of clean bases and 89.82% of Q30 were obtained, and the average alignment efficiency was 99.45% with an average coverage depth of 62.20× and 99.75% genome coverage. Based on the G prime statistic algorithm(G') method analysis, 16 candidate genomic loci with a total length 20.41 Mb were found to be related to the trait. Of these loci, the most significant regions displaying the highest elevated G' values were found in chromosome 06 at a position of 18.53–22.67 Mb, and chromosome 19 at genomic region intervals of 8.36–10.94, 12.06–13.79 and 18.45–20.26 Mb. These regions were then used to identify the key candidate genes. In these regions, 250 predicted genes were found and analyzed to obtain 90 significantly enriched(P<0.05) Gene Ontology(GO) terms. Based on ANNOVAR analysis, 50 genes with non-synonymous and stopgained mutations were preferentially selected as potential candidate genes. Of those 50 genes, following their gene annotation functions and high significant haplotype variations in various environments,five genes were identified as the most promising candidate genes regulating soybean seed carotenoid accumulation, and they should be investigated in further functional validation studies. Collectively, understanding the genetic basis of carotenoid pigments and identifying genes underpinning carotenoid accumulation via a bulked-segregant analysis-based sequencing(BSA-seq) approach provide new insights for exploring future molecular breeding efforts to produce soybean cultivars with high carotenoid content.展开更多
Next-generation sequencing(NGS) technology is capable of sequencing millions or billions of DNA molecules simultaneously.Therefore, it represents a promising tool for the analysis of molecular targets for the initial ...Next-generation sequencing(NGS) technology is capable of sequencing millions or billions of DNA molecules simultaneously.Therefore, it represents a promising tool for the analysis of molecular targets for the initial diagnosis of disease, monitoring of disease progression, and identifying the mechanism of drug resistance. On behalf of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology(CSCO) and the China Actionable Genome Consortium(CAGC), the present expert group hereby proposes advisory guidelines on clinical applications of NGS technology for the analysis of cancer driver genes for precision cancer therapy. This group comprises an assembly of laboratory cancer geneticists, clinical oncologists, bioinformaticians,pathologists, and other professionals. After multiple rounds of discussions and revisions, the expert group has reached a preliminary consensus on the need of NGS in clinical diagnosis, its regulation, and compliance standards in clinical sample collection. Moreover, it has prepared NGS criteria, the sequencing standard operation procedure(SOP), data analysis, report, and NGS platform certification and validation.展开更多
This article reviews basic concepts, general applications, and the potential impact of next-generation sequencing （NGS） technologies on genomics, with particular reference to currently available and possible future ...This article reviews basic concepts, general applications, and the potential impact of next-generation sequencing （NGS） technologies on genomics, with particular reference to currently available and possible future platforms and bioinformatics. NGS technologies have demon- strated the capacity to sequence DNA at unprecedented speed, thereby enabling previously unimaginable scientific achievements and novel biological applications. But, the massive data produced by NGS also presents a significant challenge for data storage, analyses, and management solutions. Advanced bioinformatic tools are essential for the successful application of NGS technology. As evidenced throughout this review, NGS technologies will have a striking impact on genomic research and the entire biological field. With its ability to tackle the unsolved challenges unconquered by previous genomic technologies, NGS is likely to unravel the complexity of the human genome in terms of genetic variations, some of which may be confined to susceptible loci for some common human conditions. The impact of NGS technologies on genomics will be far reaching and likely change the field for years to come.展开更多
BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of ...BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of concomitant viral infection on the survival rate of intensive care unit (ICU) sepsis patients.METHODS: A total of 74 ICU patients with sepsis who were admitted to our institution from February1, 2018 to June 30, 2019 were enrolled. Separate blood samples were collected from patients for bloodcultures and metagenomic NGS when the patients’ body temperature was higher than 38 °C. Patients’demographic data, including gender, age, ICU duration, ICU scores, and laboratory results, were recorded.The correlations between pathogen types and sepsis severity and survival rate were evaluated.RESULTS: NGS produced higher positive results (105 of 118;88.98%) than blood cultures(18 of 118;15.25%) over the whole study period. Concomitant viral infection correlated closelywith sepsis severity and had the negative effect on the survival of patients with sepsis. However,correlation analysis indicated that the bacterial variety did not correlate with the severity of sepsis.CONCLUSIONS: Concurrent viral load correlates closely with the severity of sepsis and thesurvival rate of the ICU sepsis patients. This suggests that prophylactic administration of antiviraldrugs combined with antibiotics may be benefi cial to ICU sepsis patients.展开更多
Two major types of cancer occur in the esophagus: squamous cell carcinoma, which is associated with chronic smoking and alcohol consumption, and adenocarcinoma, which typically arises in gastric reflux-associated Barr...Two major types of cancer occur in the esophagus: squamous cell carcinoma, which is associated with chronic smoking and alcohol consumption, and adenocarcinoma, which typically arises in gastric reflux-associated Barrett's esophagus. Although there is increasing incidence of esophageal adenocarcinoma in Western counties, esophageal squamous cell carcinoma(ESCC) accounts for most esophageal malignancies in East Asia, including China and Japan. Technological advances allowing for massively parallel, high-throughput next-generation sequencing(NGS) of DNA have enabled comprehensive characterization of somatic mutations in large numbers of tumor samples. Recently, several studies were published in which whole exome or whole genome sequencing was performed in ESCC tumors and compared with matched normal DNA. Mutations were validated in several genes, including in TP53, CDKN2 A, FAT1, NOTCH1, PIK3 CA, KMT2 D and NFE2L2, which had been previously implicated in ESCC. Several new recurrent alterations have also been identified in ESCC. Combining the clinicopathological characteristics of patients with information obtained from NGS studies may lead to the development of effective diagnostic and therapeutic approaches for ESCC. As this research becomes more prominent, it is important that gastroenterologist become familiar with the various NGS technologies and the results generated using these methods. In the present study, we describe recent research approaches using NGS in ESCC.展开更多
Reliable and accurate pre-implantation genetic diagnosis （PGD） of patient＇s embryos by next-generation sequencing （NGS） is dependent on efficient whole genome amplification （WGA） of a representative biopsy samp...Reliable and accurate pre-implantation genetic diagnosis （PGD） of patient＇s embryos by next-generation sequencing （NGS） is dependent on efficient whole genome amplification （WGA） of a representative biopsy sample. However, the performance of the current state of the art WGA methods has not been evaluated for sequencing. Using low template DNA （15 pg） and single cells, we showed that the two PCR-based WGA systems SurePlex and MALBAC are superior to the REPLI-g WGA multiple displacement amplification （MDA） system in terms of consistent and reproducible genome coverage and sequence bias across the 24 chromosomes, allowing better normalization of test to reference sequencing data. When copy number variation sequencing （CNV-Seq） was applied to single cell WGA products derived by either SurePlex or MALBAC amplification, we showed that known disease CNVs in the range of 3-15 Mb could be reliably and accurately detected at the correct genomic positions. These findings indicate that our CNV-Seq pipeline incorporating either SurePlex or MALBAC as the key initial WGA step is a powerful methodology for clinical PGD to identify euploid embryos in a patient＇s cohort for uterine transplantation,展开更多
Over the past decade, there has been a growing realization that studying the small RNA transcriptome is essential for understanding the complexity of transcriptional regulation. With an increased throughput and a redu...Over the past decade, there has been a growing realization that studying the small RNA transcriptome is essential for understanding the complexity of transcriptional regulation. With an increased throughput and a reduced cost, next-generation sequencing technology has provided an unprecedented opportunity to measure the extent and complexity of small RNA transcriptome. Meanwhile, the large amount of obtained data and varied technology platforms have also posed multiple challenges for effective data analysis and mining. To provide some insight into the small RNA transcriptome investigation, this review describes the major small RNA classes, experimental methods to identify small RNAs, and available bioinformatics tools and databases.展开更多
A large proportion of patients with idiopathic spermatogenic failure(SPGF;oligozoospermia or nonobstructive azoospermia[NOA])do not receive a diagnosis despite an extensive diagnostic workup.Recent evidence has shown ...A large proportion of patients with idiopathic spermatogenic failure(SPGF;oligozoospermia or nonobstructive azoospermia[NOA])do not receive a diagnosis despite an extensive diagnostic workup.Recent evidence has shown that the etiology remains undefined in up to 75%of these patients.A number of genes involved in germ-cell proliferation,spermatocyte meiotic divisions,and spermatid development have been called into play in the pathogenesis of idiopathic oligozoospermia or NOA.However,this evidence mainly comes from case reports.Therefore,this study was undertaken to identify the molecular causes of SPGF.To accomplish this,15 genes(USP9Y,NR5A1,KLHL10,ZMYND15,PLK4,TEX15,TEX11,MEIOB,SOHLH1,HSF2,SYCP3,TAF4B,NANOS1,SYCE1,and RHOXF2)involved in idiopathic SPGF were simultaneously analyzed in a cohort of 25 patients with idiopathic oligozoospermia or NOA,accurately selected after a thorough diagnostic workup.After next-generation sequencing(NGS)analysis,we identified the presence of rare variants in the NR5A1 and TEX11 genes with a pathogenic role in 3/25(12.0%)patients.Seventeen other different variants were identified,and among them,13 have never been reported before.Eleven out of 17 variants were likely pathogenic and deserve functional or segregation studies.The genes most frequently mutated were MEIOB,followed by USP9Y,KLHL10,NR5A1,and SOHLH1.No alterations were found in the SYCP3,TAF4B,NANOS1,SYCE1,or RH0XF2 genes.In conclusion,NGS technology,by screening a specific custom-made panel of genes,could help increase the diagnostic rate in patients with idiopathic oligozoospermia or NOA.展开更多
Gastric cancer(GC)is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide.There is an increasing understanding of the roles that genetic and epigenetic alterations...Gastric cancer(GC)is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide.There is an increasing understanding of the roles that genetic and epigenetic alterations play in GCs.Recent studies using nextgeneration sequencing(NGS)have revealed a number of potential cancer-driving genes in GC.Whole-exome sequencing of GC has identified recurrent somatic mutations in the chromatin remodeling gene ARID1A and alterations in the cell adhesion gene FAT4,a member of the cadherin gene family.Mutations in chromatin remodeling genes(ARID1A,MLL3 and MLL)have been found in 47%of GCs.Whole-genome sequencing and whole-transcriptome sequencing analyses have also discovered novel alterations in GC.Recent studies of cancer epigenetics have revealed widespread alterations in genes involved in the epigenetic machinery,such as DNA methylation,histone modifications,nucleosome positioning,noncoding RNAs and microRNAs.Recent advances in molecular research on GC have resulted in the introduction of new diagnostic and therapeutic strategies into clinical settings.The antihuman epidermal growth receptor 2(HER2)antibody trastuzumab has led to an era of personalized therapy in GC.In addition,ramucirumab,a monoclonal antibody targeting vascular endothelial growth factor receptor(VEGFR)-2,is the first biological treatment that showed survival benefits as a single-agent therapy in patients with advanced GC who progressed after firstline chemotherapy.Using NGS to systematically identify gene alterations in GC is a promising approach with remarkable potential for investigating the pathogenesis of GC and identifying novel therapeutic targets,as well as useful biomarkers.In this review,we will summarize the recent advances in the understanding of the molecular pathogenesis of GC,focusing on the potential use of these genetic and epigenetic alterations as diagnostic biomarkers and novel therapeutic targets.展开更多
基金This work is supported by the National Natural Science Foundation of China （Grant No. 90104002）, the National Grand Fundamental Research 973 Program of China （Grant No. 2003CB314801）.
文摘The primary problem during the evolvement of next-generation Internet is the contradiction between growing requirements for Internet and the insufficient development of network theory and technology. As the fundamental principles to guide the developing direction of Internet, the study of Internet architecture is always a focus in the research community. To address the core issue of network scalability, we propose multi-dimension scalable architecture of next-generation Internet, the main idea of which is to extend the single-dimension scalability of traditional Internet on interconnection to multi-dimension scalability of next-generation Internet. The multi-dimension scalability is composed of scale-scalability, performance-scalability, security-scalability, function-scalability, and service-scalability. We suggest five elements, namely, IPv6, authentic IPv6 addressing, scalable processing capacity of routers, end-to-end connectionless Quality-of-Service control, and 4over6 mechanism to realize the multi-dimension scalability. The current research results show that the multi-dimension scalable architecture composed of these five elements will bring great influence on next-generation Internet.
基金partially supported by the Construction of Collaborative Innovation Center of Beijing Academy of Agricultural and Forestry Sciences(KJCX20240406)the Beijing Natural Science Foundation(JQ24037)+1 种基金the National Natural Science Foundation of China(32330075)the Earmarked Fund for China Agriculture Research System(CARS-02 and CARS-54)。
文摘The security of the seed industry is crucial for ensuring national food security.Currently,developed countries in Europe and America,along with international seed industry giants,have entered the Breeding 4.0 era.This era integrates biotechnology,artificial intelligence(AI),and big data information technology.In contrast,China is still in a transition period between stages 2.0 and 3.0,which primarily relies on conventional selection and molecular breeding.In the context of increasingly complex international situations,accurately identifying core issues in China's seed industry innovation and seizing the frontier of international seed technology are strategically important.These efforts are essential for ensuring food security and revitalizing the seed industry.This paper systematically analyzes the characteristics of crop breeding data from artificial selection to intelligent design breeding.It explores the applications and development trends of AI and big data in modern crop breeding from several key perspectives.These include highthroughput phenotype acquisition and analysis,multiomics big data database and management system construction,AI-based multiomics integrated analysis,and the development of intelligent breeding software tools based on biological big data and AI technology.Based on an in-depth analysis of the current status and challenges of China's seed industry technology development,we propose strategic goals and key tasks for China's new generation of AI and big data-driven intelligent design breeding.These suggestions aim to accelerate the development of an intelligent-driven crop breeding engineering system that features large-scale gene mining,efficient gene manipulation,engineered variety design,and systematized biobreeding.This study provides a theoretical basis and practical guidance for the development of China's seed industry technology.
基金supported by the Deanship of Scientic Research(DSR),King Abdulaziz University,Jeddah,under Grant No.RG-2-611-41(A.OA.received the gran)。
文摘The scope of the Internet of Things(IoT)applications varies from strategic applications,such as smart grids,smart transportation,smart security,and smart healthcare,to industrial applications such as smart manufacturing,smart logistics,smart banking,and smart insurance.In the advancement of the IoT,connected devices become smart and intelligent with the help of sensors and actuators.However,issues and challenges need to be addressed regarding the data reliability and protection for signicant nextgeneration IoT applications like smart healthcare.For these next-generation applications,there is a requirement for far-reaching privacy and security in the IoT.Recently,blockchain systems have emerged as a key technology that changes the way we exchange data.This emerging technology has revealed encouraging implementation scenarios,such as secured digital currencies.As a technical advancement,the blockchain network has the high possibility of transforming various industries,and the next-generation healthcare IoT(HIoT)can be one of those applications.There have been several studies on the integration of blockchain networks and IoT.However,blockchain-as-autility(BaaU)for privacy and security in HIoT systems requires a systematic framework.This paper reviews blockchain networks and proposes BaaU as one of the enablers.The proposed BaaU-based framework for trustworthiness in the next-generation HIoT systems is divided into two scenarios.The rst scenario suggests that a healthcare service provider integrates IoT sensors such as body sensors to receive and transmit information to a blockchain network on the IoT devices.The second proposed scenario recommends implementing smart contracts,such as Ethereum,to automate and control the trusted devices’subscription in the HIoT services.
文摘The Internet of things has particularly novel implications in the area of public health. This is due to (1) The rapid and widespread adoption of powerful contemporary Smartphone’s;(2) The increasing availability and use of health and fitness sensors, wearable sensor patches, smart watches, wireless-enabled digital tattoos and ambient sensors;and (3) The nature of public health to implicitly involve connectivity with and the acquisition of data in relation to large numbers of individuals up to population scale. Of particular relevance in relation to the Internet of Things (IoT) and public health is the need for privacy and anonymity of users. It should be noted that IoT capabilities are not inconsistent with maintaining privacy, due to the focus of public health on aggregate data not individual data and broad public health interventions. In addition, public health information systems utilizing IoT capabilities can be constructed to specifically ensure privacy, security and anonymity, as has been developed and evaluated in this work. In this paper we describe the particular characteristics of the IoT that can play a role in enabling emerging public health capabilities;we describe a privacy-preserving IoT-based public health information system architecture;and provide a privacy evaluation.
文摘BACKGROUND Pepsinogen(PG)and the PG I/II ratio(PGR)are critical indicators for diagnosing Helicobacter pylori infection and chronic atrophic gastritis,and assessing gastric cancer risk.Existing reference intervals(RIs)often overlook age,sex,and demographic variations.Partitioned RIs,while considering these factors,fail to capture the gradual age-related physiological changes.Next-generation RIs offer a solution to this limitation.AIM To investigate age-and sex-specific dynamics of PG and establish next-generation RIs for adults and the elderly in northern China.METHODS After screening,708 healthy individuals were included in this observational study.Serum PG was measured using chemiluminescence immunoassay.Age-and sex-related effects on PG were analyzed with a two-way analysis of variance.RI partitioning was determined by the standard deviation ratio(SDR).Traditional RIs were established using a non-parametric approach.Generalized Additive Models for Location,Scale,and Shape(GAMLSS)modeled age-related trends and continuous reference percentiles for PG I and PG II.Reference limit flagging rates for both RI types were compared.RESULTS PG I and PG II levels were influenced by age(P<0.001)and sex(P<0.001),while PGR remained stable.Age-specific RIs were required for PG I(SDR=0.366)and PG II(SDR=0.424).Partitioned RIs were established for PG I and PG II,with a single RI for PGR.GAMLSS modeling revealed distinct age-dependent trajectories:PG I increased from a median of 39.75μg/L at age 20 years to 49.75μg/L at age 60 years,a 25.16%increase,after which it plateaued through age 80 years.In contrast,PG II showed a continuous rise throughout the age range,with the median value increasing from 5.07μg/L at age 20 years to 8.36μg/L at age 80 years,corresponding to a 64.89%increase.Continuous reference percentiles intuitively reflected these trends and were detailed in this study.Next-generation RIs demonstrated superior accuracy compared to partitioned RIs when applied to specific age subgroups.CONCLUSION This study elucidates the age-and sex-specific dynamics of PG and,to our knowledge,is the first to establish next-generation RIs for PG,supporting more individualized interpretation in laboratory medicine.
文摘BACKGROUND Leuconostoc garlicum is commonly found in fermented foods and very few infected patients have been reported,who typically present symptoms such as fever and fatigue.Conventional clinical examinations often struggle to identify this bacterium,and routine anti-infective treatments are generally ineffective.Both diagnostic challenges and therapeutic limitations pose significant difficulties for clinicians.CASE SUMMARY We report a patient ultimately diagnosed with Leuconostoc garlicum infection.The primary manifestations included persistent fever,cough and fatigue.These symptoms lasted for 2 months.He received anti-infective treatment at a community hospital,but this was ineffective.After inquiring about the patient's medical history and conducting a physical examination,the patient underwent laboratory tests.Complete blood count tests revealed that the patient had a high proportion of neutrophils,C-reactive protein level was 235.9 mg/L,erythrocyte sedimentation rate was 67 mm/h,respiratory pathogen testing was negative,and he was then thought to have an infectious disease.However,conventional anti-infective treatments were ineffective.After excluding infectious neurological diseases,urologic diseases and digestive problems,we ultimately focused our attention on the lungs.A lung computed tomography scan indicated pulmonary inflammation.Bronchoalveolar lavage fluid for next-generation sequencing suggested lung infection with Leuconostoc garlicum.The patient's symptoms gradually improved following treatment with piperacillin tazobactam and linezolid.During the follow-up period,the patient's temperature remained normal.CONCLUSION For patients with suspected bacterial infection and experiencing fever,conventional anti-infective treatment can be ineffective in controlling their symptoms,and an infection due to rare bacteria or drug-resistant bacteria should be considered.Next-generation sequencing enables rapid and precise identification of infection-related pathogens in febrile patients.
基金supported by the National Natural Science Foundation of China(Grant Nos.31972983 and 32072487)the Key Technology R&D Program of Zhejiang Province,China(Grant No.2021C02006)the Zhejiang Provincial Natural Science Foundation of China(Grant No.LY23C140001).
文摘In rice fields,rice plants usually grow alongside wild weeds and are attacked by various invertebrate species.Viruses are abundant in plants and invertebrates,playing crucial ecological roles in controlling microbial abundance and maintaining community structures.To date,only 16 rice viruses have been documented in rice-growing regions.These viruses pose serious threats to rice production and have traditionally been identified only from rice plants and insect vectors by isolation techniques.Advances in next-generation sequencing(NGS)have made it feasible to discover viruses on a global scale.Recently,numerous viruses have been identified in plants and invertebrates using NGS technologies.In this review,we discuss viral studies in rice plants,invertebrate species,and weeds in rice fields.Many novel viruses have been discovered in rice ecosystems through NGS technologies,with some also detected using metatranscriptomic and small RNA sequencing.These analyses greatly expand our understanding of viruses in rice fields and provide valuable insights for developing efficient strategies to manage insect pests and virus-mediated rice diseases.
基金supported by the Hubei Provincial Natural Science Foundation of China(No.2023AFB646)Knowledge Innovation Program of Wuhan(No.2023020201010155)Educational Research Program of Huazhong University of Science and Technology(No.2022135).
文摘Objective and Background Early and accurate diagnosis of spinal infections,including spinal tuberculosis,is pivotal for effective treatment but remains challenging.This study aims to assess the diagnostic yield of metagenomic next-generation sequencing(mNGS)compared with that of conventional microbiological tests(CMTs)in identifying pathogens associated with spinal pathologies,with a special focus on infections leading to surgical interventions.Methods We enrolled 85 patients who underwent spinal surgery,comprising 63 patients with clinically diagnosed spinal infections,including patients with spinal tuberculosis,and 22 patients with noninfectious spinal conditions.The procedures involved irrigation and debridement for persistent wound drainage,with subsequent DNA extraction from plasma and joint fluid for mNGS and CMT analysis.Results Significantly increased C-reactive protein(CRP)levels were observed in patients with infections.The mNGS approach showed greater diagnostic sensitivity(92.06%)for detecting pathogens,including Mycobacterium tuberculosis,than did CMTs(36.51%).Despite its low specificity,mNGS had considerable negative predictive value(70.59%),underscoring its utility in ruling out infections.Conclusions The mNGS offers superior sensitivity over CMTs in the diagnosis of a variety of spinal infections,notably spinal tuberculosis.This study highlights the potential of mNGS in enhancing the diagnosis of complex spinal infections,thereby informing targeted treatment strategies.
基金financially supported by the Science and Technology Commission of Shanghai Municipality(No.24ZR1401400)Shenzhen Salus Bio Med Company for their strong support in this study。
文摘In this study,an amine-reactive poly(pentafluorophenyl acrylate)(PPFPA)platform was developed for advanced surface engineering of next-generation sequencing(NGS)chips.Through post-polymerization modification,PPFPA was functionalized with dual moieties:azide groups for covalent immobilization of DBCO-modified DNA primers via click chemistry and tunable hydrophilic side chains to optimize biocompatibility and surface properties.Systematic screening revealed that hydrophobic azide carriers combined with neutral hydroxyl groups maximized the DNA immobilization efficacy,approaching the performance of commercial polyacrylamide-based polymers.The negatively charged carboxyl groups severely impede DNA primer attachment.Higher molecular weight derivatives further enhance the efficacy of DNA immobilization.In NGS validation,optimized surface modification polymers achieved robust surface density of clustered DNA and high sequencing accuracy,surpassing quality benchmarks and comparable to those of conventional analogs.This platform demonstrates significant potential for tailoring high-sensitivity surfaces for genomic applications,advancing clinical diagnostics,and personalized medicine.
文摘This study investigates the diversity of gut microbiota in Metaphire peguana,an earthworm species commonly found in agricultural areas of Thailand.Earthworms play a critical role in soil ecosystems by supporting nutrient cycling and breaking down organic matter.Understanding the microbial diversity in their gut is essential for exploring their ecological contributions.Using Next Generation Sequencing(NGS),we analyzed the mycobiome in the gut of M.peguana.Our findings revealed a high diversity of fungal species,primarily belonging to two major phyla:Ascomycota and Basidiomycota.Ascomycota was the most abundant phylum,comprising 40.1% of the total fungal species identified.A total of 33 distinct fungal species were identified,which underscores the richness of microbial life within the earthworm gut.This study successfully created the first genetic database of the microbial community in M.peguana,providing a foundation for future research in agricultural applications.The microbial species identified,particularly siderophoreproducing fungi,could have significant implications for improving soil fertility and promoting sustainable agricultural practices.The use of NGS technology has enabled comprehensive profiling of microbial communities,allowing for precise identification of fungi that may play essential roles in soil health.Furthermore,the study paves the way for future studies on the potential applications of earthworm gut microbiomes in biotechnology,especially in enhancing soil nutrient availability and plant growth.The findings of this research contribute to the broader understanding of the ecological roles of earthworms and their microbiomes in soil ecosystems.
文摘Cystic echinococcosis (CE) is a prevalent zoonotic disease caused by Echinococcus granulosus, with a cosmopolitan distribution. The parasite is transmitted cyclically between canines and numerous intermediate herbivorous livestock animals. Also, other Taeniid tapeworms could infect domestic dogs and they pose significant veterinary and public health concerns worldwide. This study aimed to develop a sensitive molecular method for detecting Echinococcus spp. DNA in dog fecal samples using next-generation sequencing (NGS). A set of PCR primers targeting conserved regions of Taeniid tapeworms’ 18s rRNA genes was designed and tested for amplifying genomic DNA from various tapeworm species. The PCR system demonstrated high sensitivity, amplifying DNA from all tested tapeworm species, with differences observed in amplified band sizes. The primers were adapted for NGS analysis by adding forward and reverse adapters, enabling the sequencing of amplified DNA fragments. Application of the developed PCR system to dog fecal samples collected from Yatta town, Palestine, revealed the presence of E. granulosus DNA in five out of 50 samples. NGS analysis confirmed the specificity of the amplified DNA fragments, showing 98% - 99% similarity with the 18s rDNA gene of E. granulosus. This study demonstrates the utility of NGS-based molecular methods for accurate and sensitive detection of Echinococcus spp. in dog fecal samples, providing valuable insights for epidemiological surveillance and control programs of echinococcosis in endemic regions.
基金financially supported by the National Natural Science Foundation of China (32161143033, 32272178, and 32001574)National Key Research and Development Program of China (2021YFD1201605)the Agricultural Science and Technology Innovation Project of CAAS。
文摘The improvement of soybean seed carotenoid contents is very important due to the beneficial role of carotenoids in human health and nutrition. However, the genetic architecture underlying soybean carotenoid biosynthesis remains largely unknown. In the present study, we employed next generation sequencing-based bulked-segregant analysis to identify new genomic regions governing seed carotenoids in 1,551 natural soybean accessions. The genomic DNA samples of individual plants with extreme phenotypes were pooled to form two bulks with high(50 accessions) and low(50 accessions) carotenoid contents for Illumina sequencing. A total of 125.09 Gb of clean bases and 89.82% of Q30 were obtained, and the average alignment efficiency was 99.45% with an average coverage depth of 62.20× and 99.75% genome coverage. Based on the G prime statistic algorithm(G') method analysis, 16 candidate genomic loci with a total length 20.41 Mb were found to be related to the trait. Of these loci, the most significant regions displaying the highest elevated G' values were found in chromosome 06 at a position of 18.53–22.67 Mb, and chromosome 19 at genomic region intervals of 8.36–10.94, 12.06–13.79 and 18.45–20.26 Mb. These regions were then used to identify the key candidate genes. In these regions, 250 predicted genes were found and analyzed to obtain 90 significantly enriched(P<0.05) Gene Ontology(GO) terms. Based on ANNOVAR analysis, 50 genes with non-synonymous and stopgained mutations were preferentially selected as potential candidate genes. Of those 50 genes, following their gene annotation functions and high significant haplotype variations in various environments,five genes were identified as the most promising candidate genes regulating soybean seed carotenoid accumulation, and they should be investigated in further functional validation studies. Collectively, understanding the genetic basis of carotenoid pigments and identifying genes underpinning carotenoid accumulation via a bulked-segregant analysis-based sequencing(BSA-seq) approach provide new insights for exploring future molecular breeding efforts to produce soybean cultivars with high carotenoid content.
基金supported by grants from Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer (Grant No. 2017B030314120)General Research Project of Guangzhou Science and Technology Bureau (Grant No. 201607010391)+1 种基金National Key Research and Development Program of China (Grant No. 2016YFC1303800)Guangdong Provincial Applied S&T R&D Program (Grant No. 2016B020237006)
文摘Next-generation sequencing(NGS) technology is capable of sequencing millions or billions of DNA molecules simultaneously.Therefore, it represents a promising tool for the analysis of molecular targets for the initial diagnosis of disease, monitoring of disease progression, and identifying the mechanism of drug resistance. On behalf of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology(CSCO) and the China Actionable Genome Consortium(CAGC), the present expert group hereby proposes advisory guidelines on clinical applications of NGS technology for the analysis of cancer driver genes for precision cancer therapy. This group comprises an assembly of laboratory cancer geneticists, clinical oncologists, bioinformaticians,pathologists, and other professionals. After multiple rounds of discussions and revisions, the expert group has reached a preliminary consensus on the need of NGS in clinical diagnosis, its regulation, and compliance standards in clinical sample collection. Moreover, it has prepared NGS criteria, the sequencing standard operation procedure(SOP), data analysis, report, and NGS platform certification and validation.
基金supported by NINDS/NIH(JZ),Coldwell Foundation(JZ) and TTUHSC(JZ)
文摘This article reviews basic concepts, general applications, and the potential impact of next-generation sequencing （NGS） technologies on genomics, with particular reference to currently available and possible future platforms and bioinformatics. NGS technologies have demon- strated the capacity to sequence DNA at unprecedented speed, thereby enabling previously unimaginable scientific achievements and novel biological applications. But, the massive data produced by NGS also presents a significant challenge for data storage, analyses, and management solutions. Advanced bioinformatic tools are essential for the successful application of NGS technology. As evidenced throughout this review, NGS technologies will have a striking impact on genomic research and the entire biological field. With its ability to tackle the unsolved challenges unconquered by previous genomic technologies, NGS is likely to unravel the complexity of the human genome in terms of genetic variations, some of which may be confined to susceptible loci for some common human conditions. The impact of NGS technologies on genomics will be far reaching and likely change the field for years to come.
基金supported by grants from Scienceand Technology Committee of Shanghai (18411951400)KeyClinical Medical Specialties Project in Shanghai Pudong NewArea (PWZzk2017-22)+1 种基金Science and Technology Action Plan(19495810200)Leading Talent Project in Shanghai Pudong NewArea Health System (PWRl2018-08).
文摘BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of concomitant viral infection on the survival rate of intensive care unit (ICU) sepsis patients.METHODS: A total of 74 ICU patients with sepsis who were admitted to our institution from February1, 2018 to June 30, 2019 were enrolled. Separate blood samples were collected from patients for bloodcultures and metagenomic NGS when the patients’ body temperature was higher than 38 °C. Patients’demographic data, including gender, age, ICU duration, ICU scores, and laboratory results, were recorded.The correlations between pathogen types and sepsis severity and survival rate were evaluated.RESULTS: NGS produced higher positive results (105 of 118;88.98%) than blood cultures(18 of 118;15.25%) over the whole study period. Concomitant viral infection correlated closelywith sepsis severity and had the negative effect on the survival of patients with sepsis. However,correlation analysis indicated that the bacterial variety did not correlate with the severity of sepsis.CONCLUSIONS: Concurrent viral load correlates closely with the severity of sepsis and thesurvival rate of the ICU sepsis patients. This suggests that prophylactic administration of antiviraldrugs combined with antibiotics may be benefi cial to ICU sepsis patients.
文摘Two major types of cancer occur in the esophagus: squamous cell carcinoma, which is associated with chronic smoking and alcohol consumption, and adenocarcinoma, which typically arises in gastric reflux-associated Barrett's esophagus. Although there is increasing incidence of esophageal adenocarcinoma in Western counties, esophageal squamous cell carcinoma(ESCC) accounts for most esophageal malignancies in East Asia, including China and Japan. Technological advances allowing for massively parallel, high-throughput next-generation sequencing(NGS) of DNA have enabled comprehensive characterization of somatic mutations in large numbers of tumor samples. Recently, several studies were published in which whole exome or whole genome sequencing was performed in ESCC tumors and compared with matched normal DNA. Mutations were validated in several genes, including in TP53, CDKN2 A, FAT1, NOTCH1, PIK3 CA, KMT2 D and NFE2L2, which had been previously implicated in ESCC. Several new recurrent alterations have also been identified in ESCC. Combining the clinicopathological characteristics of patients with information obtained from NGS studies may lead to the development of effective diagnostic and therapeutic approaches for ESCC. As this research becomes more prominent, it is important that gastroenterologist become familiar with the various NGS technologies and the results generated using these methods. In the present study, we describe recent research approaches using NGS in ESCC.
基金supported by grants awarded to Yuanqing Yao by the Key Program of the "Twelfth Five-year plan" of People’s liberation Army(No.BWS11J058)the National High Technology Research and Development Program(SS2015AA020402)
文摘Reliable and accurate pre-implantation genetic diagnosis （PGD） of patient＇s embryos by next-generation sequencing （NGS） is dependent on efficient whole genome amplification （WGA） of a representative biopsy sample. However, the performance of the current state of the art WGA methods has not been evaluated for sequencing. Using low template DNA （15 pg） and single cells, we showed that the two PCR-based WGA systems SurePlex and MALBAC are superior to the REPLI-g WGA multiple displacement amplification （MDA） system in terms of consistent and reproducible genome coverage and sequence bias across the 24 chromosomes, allowing better normalization of test to reference sequencing data. When copy number variation sequencing （CNV-Seq） was applied to single cell WGA products derived by either SurePlex or MALBAC amplification, we showed that known disease CNVs in the range of 3-15 Mb could be reliably and accurately detected at the correct genomic positions. These findings indicate that our CNV-Seq pipeline incorporating either SurePlex or MALBAC as the key initial WGA step is a powerful methodology for clinical PGD to identify euploid embryos in a patient＇s cohort for uterine transplantation,
基金supported by the National High Technology Research and Development Program of China(No. 2006AA02A304)Major State Basic Research Development Program of China(No.2007CB512302)
文摘Over the past decade, there has been a growing realization that studying the small RNA transcriptome is essential for understanding the complexity of transcriptional regulation. With an increased throughput and a reduced cost, next-generation sequencing technology has provided an unprecedented opportunity to measure the extent and complexity of small RNA transcriptome. Meanwhile, the large amount of obtained data and varied technology platforms have also posed multiple challenges for effective data analysis and mining. To provide some insight into the small RNA transcriptome investigation, this review describes the major small RNA classes, experimental methods to identify small RNAs, and available bioinformatics tools and databases.
文摘A large proportion of patients with idiopathic spermatogenic failure(SPGF;oligozoospermia or nonobstructive azoospermia[NOA])do not receive a diagnosis despite an extensive diagnostic workup.Recent evidence has shown that the etiology remains undefined in up to 75%of these patients.A number of genes involved in germ-cell proliferation,spermatocyte meiotic divisions,and spermatid development have been called into play in the pathogenesis of idiopathic oligozoospermia or NOA.However,this evidence mainly comes from case reports.Therefore,this study was undertaken to identify the molecular causes of SPGF.To accomplish this,15 genes(USP9Y,NR5A1,KLHL10,ZMYND15,PLK4,TEX15,TEX11,MEIOB,SOHLH1,HSF2,SYCP3,TAF4B,NANOS1,SYCE1,and RHOXF2)involved in idiopathic SPGF were simultaneously analyzed in a cohort of 25 patients with idiopathic oligozoospermia or NOA,accurately selected after a thorough diagnostic workup.After next-generation sequencing(NGS)analysis,we identified the presence of rare variants in the NR5A1 and TEX11 genes with a pathogenic role in 3/25(12.0%)patients.Seventeen other different variants were identified,and among them,13 have never been reported before.Eleven out of 17 variants were likely pathogenic and deserve functional or segregation studies.The genes most frequently mutated were MEIOB,followed by USP9Y,KLHL10,NR5A1,and SOHLH1.No alterations were found in the SYCP3,TAF4B,NANOS1,SYCE1,or RH0XF2 genes.In conclusion,NGS technology,by screening a specific custom-made panel of genes,could help increase the diagnostic rate in patients with idiopathic oligozoospermia or NOA.
基金Supported by Grants-in-Aid for Scientific Research from the Ministry of Education,Culture,Sports,Science and Technology of Japan
文摘Gastric cancer(GC)is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide.There is an increasing understanding of the roles that genetic and epigenetic alterations play in GCs.Recent studies using nextgeneration sequencing(NGS)have revealed a number of potential cancer-driving genes in GC.Whole-exome sequencing of GC has identified recurrent somatic mutations in the chromatin remodeling gene ARID1A and alterations in the cell adhesion gene FAT4,a member of the cadherin gene family.Mutations in chromatin remodeling genes(ARID1A,MLL3 and MLL)have been found in 47%of GCs.Whole-genome sequencing and whole-transcriptome sequencing analyses have also discovered novel alterations in GC.Recent studies of cancer epigenetics have revealed widespread alterations in genes involved in the epigenetic machinery,such as DNA methylation,histone modifications,nucleosome positioning,noncoding RNAs and microRNAs.Recent advances in molecular research on GC have resulted in the introduction of new diagnostic and therapeutic strategies into clinical settings.The antihuman epidermal growth receptor 2(HER2)antibody trastuzumab has led to an era of personalized therapy in GC.In addition,ramucirumab,a monoclonal antibody targeting vascular endothelial growth factor receptor(VEGFR)-2,is the first biological treatment that showed survival benefits as a single-agent therapy in patients with advanced GC who progressed after firstline chemotherapy.Using NGS to systematically identify gene alterations in GC is a promising approach with remarkable potential for investigating the pathogenesis of GC and identifying novel therapeutic targets,as well as useful biomarkers.In this review,we will summarize the recent advances in the understanding of the molecular pathogenesis of GC,focusing on the potential use of these genetic and epigenetic alterations as diagnostic biomarkers and novel therapeutic targets.
