The understanding of how genetic and epigenetic factors influence tumorigenesis, progression and invasion, is vastly growing since new technologies allow the analysis of the functional genome namely the exome, the tra...The understanding of how genetic and epigenetic factors influence tumorigenesis, progression and invasion, is vastly growing since new technologies allow the analysis of the functional genome namely the exome, the transcriptome and the epigenome, besides enabling genome-wide assessment of genetic variations. With the advent of new drugs that are indicated tissue agnostic, depending on certain mutations, there is a growing demand for fast and cost-effective genetic diagnosis. The method in focus that already became an indispensable tool in viral diagnosis is next-generation sequencing (NGS). This approach allows sequencing of literally every DNA molecule in the sample and can either be used to assess numerous genetic markers of one patient at a time, or to assess fewer markers of many patients in parallel, which reduces costs. We submitted 23 samples of different tumor entities to four diagnostic companies with different analysis profiles. The results as disclosed and discussed in this report indicate that so far, the main application of NGS is rather in cancer research than in diagnosis, as none of the reports had a real impact on the therapeutic scheme. We are perfectly aware that such a small cohort cannot be generalized, but considering the costs vs. benefits, NGS should be engaged upon a very stringent evaluation only. However, in cases where obtaining a tissue biopsy is impossible or unfavorable, analysis of liquid biopsy by NGS provides a vital alternative.展开更多
Next generation sequencing is currently a cornerstone of genetic testing in routine diagnostics,allowing for the detection of sequence variants with so far unprecedented large scale,mainly in genetically heterogenous ...Next generation sequencing is currently a cornerstone of genetic testing in routine diagnostics,allowing for the detection of sequence variants with so far unprecedented large scale,mainly in genetically heterogenous diseases,such as neurological disorders.It is a fast-moving field,where new wet enrichment protocols and bioinformatics tools are constantly being developed to overcome initial limitations.Despite the as yet undiscussed advantages,however,there are still some challenges in data analysis and the interpretation of variants.In this review,we address the current state of next generation sequencing diagnostic testing for inherited human disorders,particularly giving an overview of the available high-throughput sequencing approaches;including targeted,whole-exome and whole-genome sequencing;and discussing the main critical aspects of the bioinformatic process,from raw data analysis to molecular diagnosis.展开更多
BACKGROUND Colorectal cancer(CRC)is one of the most common malignancies worldwide.Given its insidious onset,the condition often already progresses to advanced stage when symptoms occur.Thus,early diagnosis is of great...BACKGROUND Colorectal cancer(CRC)is one of the most common malignancies worldwide.Given its insidious onset,the condition often already progresses to advanced stage when symptoms occur.Thus,early diagnosis is of great significance for timely clinical intervention,efficacy enhancement,and prognostic improvement.Featuring high throughput,fastness,and rich information,next generation sequencing(NGS)can greatly shorten the detection time,which is a widely used detection technique at present.AIM To screen specific genes or gene combinations in fecal DNA that are suitable for diagnosis and prognostic prediction of CRC,and to establish a technological platform for CRC screening,diagnosis,and efficacy monitoring through fecal DNA detection.METHODS NGS was used to sequence the stool DNA of patients with CRC,which were then compared with the genetic testing results of the stool samples of normal controls and patients with benign intestinal disease,as well as the tumor tissues of CRC patients.Specific genes or gene combinations in fecal DNA suitable for diagnosis and prognostic prediction of CRC were screened,and their significances in diagnosing CRC and predicting patients'prognosis were comprehensively evaluated.RESULTS High mutation frequencies of TP53,APC,and KRAS were detected in the stools and tumor tissues of CRC patients prior to surgery.Contrastively,no pathogenic mutations of the above three genes were noted in the postoperative stools,the normal controls,or the benign intestinal disease group.This indicates that tumor-specific DNA was detectable in the preoperative stools of CRC patients.The preoperative fecal expression of tumor-associated genes can reflect the gene mutations in tumor tissues to some extent.Compared to the postoperative stools and the stools in the two control groups,the pathogenic mutation frequencies of TP53 and KRAS were significantly higher for the preoperative stools(χ^(2)=7.328,P<0.05;χ^(2)=4.219,P<0.05),suggesting that fecal TP53 and KRAS genes can be used for CRC screening,diagnosis,and prognostic prediction.No significant difference in the pathogenic mutation frequency of the APC gene was found from the postoperative stools or the two control groups(χ^(2)=0.878,P>0.05),so further analysis with larger sample size is required.Among CRC patients,the pathogenic mutation sites of TP53 occurred in 16 of 27 preoperative stools,with a true positive rate of 59.26%,while the pathogenic mutation sites of KRAS occurred in 10 stools,with a true positive rate of 37.04%.The sensitivity and negative predictive values of the combined genetic testing of TP53 and KRAS were 66.67%(18/27)and 68.97%,respectively,both of which were higher than those of TP53 or KRAS mutation detection alone,suggesting that the combined genetic testing can improve the CRC detection rate.The mutation sites TP53 exon 4 A84G and EGFR exon 20 I821T(mutation start and stop positions were both 7579436 for the former,while 55249164 for the latter)were found in the preoperative stools and tumor tissues.These"undetected"mutation sites may be new types of mutations occurring during the CRC carcinogenesis and progression,which needs to be confirmed through further research.Some mutations of"unknown clinical significance"were found in such genes as TP53,PTEN,KRAS,BRAF,AKT1,and PIK3CA,whose clinical values is worthy of further exploration.CONCLUSION NGS-based fecal genetic testing can be used as a complementary technique for the CRC diagnosis.Fecal TP53 and KRAS can be used as specific genes for the screening,diagnosis,prognostic prediction,and recurrence monitoring of CRC.Moreover,the combined testing of TP53 and KRAS genes can improve the CRC detection rate.展开更多
Helicobacter pylori(H.pylori)infection is highly prevalent in the human population and may lead to severe gastrointestinal pathology including gastric and duodenal ulcers,mucosa associated tissue lymphoma and gastric ...Helicobacter pylori(H.pylori)infection is highly prevalent in the human population and may lead to severe gastrointestinal pathology including gastric and duodenal ulcers,mucosa associated tissue lymphoma and gastric adenocarcinoma.In recent years,an alarming increase in antimicrobial resistance and subsequently failing empiric H.pylori eradication therapies have been noted worldwide,also in many European countries.Therefore,rapid and accurate determination of H.pylori’s antibiotic susceptibility prior to the administration of eradication regimens becomes ever more important.Traditionally,detection of H.pylori and its antimicrobial resistance is done by culture and phenotypic drug susceptibility testing that are cumbersome with a long turn-around-time.Recent advances in diagnostics provide new tools,like real-time polymerase chain reaction(PCR)and line probe assays,to diagnose H.pylori infection and antimicrobial resistance to certain antibiotics,directly from clinical specimens.Moreover,high-throughput whole genome sequencing technologies allow the rapid analysis of the pathogen’s genome,thereby allowing identification of resistance mutations and associated antibiotic resistance.In the first part of this review,we will give an overview on currently available diagnostic methods for detection of H.pylori and its drug resistance and their implementation in H.pylori management.The second part of the review focusses on the use of next generation sequencing technology in H.pylori research.To this end,we conducted a literature search for original research articles in English using the terms“Helicobacter”,“transcriptomic”,“transcriptome”,“next generation sequencing”and“whole genome sequencing”.This review is aimed to bridge the gap between current diagnostic practice(histology,rapid urease test,H.pylori culture,PCR and line probe assays)and new sequencing technologies and their potential implementation in diagnostic laboratory settings in order to complement the currently recommended H.pylori management guidelines and subsequently improve public health.展开更多
Objective: To investigate immune-related genetic background in bilateral sudden sensorineural hearing loss(SSNHL).Case report and methods: The case is a 45-year-old man presenting with a 7-year history of bilateral pr...Objective: To investigate immune-related genetic background in bilateral sudden sensorineural hearing loss(SSNHL).Case report and methods: The case is a 45-year-old man presenting with a 7-year history of bilateral profound SSNHL. Blood biochemical testing demonstrated increased levels of total cholesterol(5.88 mmol/L). Tests for hepatitis B showed a positive antibody against the hepatitis B core antigen. Complement C3 was below the normal value, and complement C4 and Ig G were in the lower range of normal values. CT images showed a normal inner ear and vestibular aqueduct but round window membranous ossification on both sides. A total number of 232 immuneassociated genes were sequenced using the next generation sequencing technique.Results: Mutations were detected in 5 genes, including the phosphoinositide 3-kinase catalytic subunit delta(PIK3CD), caspase recruitment domain-containing protein 9(CARD9), complement factor H-related(CFHR2), immunoglobulin lambda-like polypeptide 1 Protein(IGLL1),and transmembrane channel-like gene family 8(TMC8). In the PIK3 CD gene, a C896 T substitute in exon 7 was detected. This mutation causes primary immunodeficiency and is an autosomal dominant disease.Conclusion: The PIK3 CD C896T mutation responsible for primary immunodeficiency may contribute to the onset of bilateral SSNHL with subsequent rapid progression.展开更多
BACKGROUND Hereditary spherocytosis(HS)is a hereditary disease of hemolytic anemia that occurs due to the erythrocyte membrane defects.Dubin–Johnson syndrome(DJS),which commonly results in jaundice,is a benign heredi...BACKGROUND Hereditary spherocytosis(HS)is a hereditary disease of hemolytic anemia that occurs due to the erythrocyte membrane defects.Dubin–Johnson syndrome(DJS),which commonly results in jaundice,is a benign hereditary disorder of bilirubin clearance that occurs only rarely.The co-occurrence of HS and DJS is extremely rare.We recently diagnosed and treated a case of co-occurring HS and DJS.CASE SUMMARY A 21-year-old female patient presented to our department because of severe jaundice,severe splenomegaly,and mild anemia since birth.We eventually confirmed the diagnosis of co-occurring DJS and HS by next generation sequencing(NGS).The treatment of ursodeoxycholic acid in combination with phenobarbital successfully increased hemoglobin and reduced total bilirubin and direct bilirubin.CONCLUSION The routine application of NGS can efficiently render a definite diagnosis when inherited disorders are suspected.展开更多
In the last few years,the advent of next generation sequencing(NGS) has revolutionized the approach to genetic studies,making whole-genome sequencing a possible way of obtaining global genomic information.NGS has very...In the last few years,the advent of next generation sequencing(NGS) has revolutionized the approach to genetic studies,making whole-genome sequencing a possible way of obtaining global genomic information.NGS has very recently been shown to be successful in identifying novel causative mutations of rare or common Mendelian disorders.At the present time,it is expected that NGS will be increasingly important in the study of inherited and complex cardiovascular diseases(CVDs).However,the NGS approach to the genetics of CVDs represents a territory which has not been widely investigated.The identification of rare and frequent genetic variants can be very important in clinical practice to detect pathogenic mutations or to establish a profile of risk for the development of pathology.The purpose of this paper is to discuss the recent application of NGS in the study of several CVDs such as inherited cardiomyopathies,channelopathies,coronary artery disease and aortic aneurysm.We also discuss the future utility and challenges related to NGS in studying the genetic basis of CVDs in order to improve diagnosis,prevention,and treatment.展开更多
Type 2 diabetes(T2D)mellitus is a common complex disease that currently affects more than 400 million people worldwide and has become a global health problem.High-throughput sequencing technologies such as whole-genom...Type 2 diabetes(T2D)mellitus is a common complex disease that currently affects more than 400 million people worldwide and has become a global health problem.High-throughput sequencing technologies such as whole-genome and whole-exome sequencing approaches have provided numerous new insights into the molecular bases of T2D.Recent advances in the application of sequencing technologies to T2D research include,but are not limited to:(1)Fine mapping of causal rare and common genetic variants;(2)Identification of confident genelevel associations;(3)Identification of novel candidate genes by specific scoring approaches;(4)Interrogation of disease-relevant genes and pathways by transcriptional profiling and epigenome mapping techniques;and(5)Investigation of microbial community alterations in patients with T2D.In this work we review these advances in application of next-generation sequencing methods for elucidation of T2D pathogenesis,as well as progress and challenges in implementation of this new knowledge about T2D genetics in diagnosis,prevention,and treatment of the disease.展开更多
Objective:To compare the efficacy of platinum-and non-platinum-based regimens as first-line treatment for advanced triple-negative breast cancer(TNBC)and analyze the relationship between their efficacy and BRCA gene s...Objective:To compare the efficacy of platinum-and non-platinum-based regimens as first-line treatment for advanced triple-negative breast cancer(TNBC)and analyze the relationship between their efficacy and BRCA gene status.Methods:Retrospectively analyze clinical data of 220 patients diagnosed pathologically with advanced TNBC and treated at the Department of Breast Oncology,Peking University Cancer Hospital from 2013 to 2018 and evaluate the efficacy of chemotherapy.A total of 114 patients had BRCA1/2 gene tested by next generation sequencing(NGS)using peripheral blood,and we analyzed the correlation between their efficacy and BRCA1/2 gene status.Results:Non-platinum-based chemotherapy(NPCT)was administered to 129 and platinum-based chemotherapy(PBCT)to 91 study patients.The clinical benefit rate(CBR)and median progression-free survival(PFS)were not statistically different between NPCT and PBCT groups.The median overall survival(OS)was 30.0 and 22.5 months for PBCT and NPCT group,respectively[P=0.090,hazard ratios(HR)=0.703].BRCA status was assessed in 114 patients,14 of whom had deleterious germline BRCA1/2(g BRCA)mutations(seven in each group).In PBCT group,the CBR was 85.7%and 35.1%for patients with and without deleterious g BRCA mutations,respectively(P=0.039).The median PFS were 14.9 and 5.3 months and median OS were 26.5 and 15.5 months for patients with and without deleterious g BRCA mutations,respectively(P=0.001,P=0.161,respectively).Patients in PBCT group had significantly greater rates of grade 3-4 anemia(5.5%vs.0%)and thrombocytopenia(8.8%vs.0%),whereas palmar-plantar erythrodysesthesia(12.4%vs.0%)and peripheral neuropathy(8.6%vs.1.1%)occurred more frequently in NPCT group.Conclusions:Platinum-based regimens are more effective in patients with deleterious g BRCA mutations,but no difference in patients without BRCA gene mutations,so non-platinum is an option in patients without BRCA gene mutations considering the toxicity and side effect.And we recommend that patients with advanced TNBC should have BRCA gene test.展开更多
The lung plays a vital role in maintaining homeostasis,as it is responsible for the exchange of oxygen and carbon dioxide.Pulmonary homeostasis is maintained by a network of tissue-resident cells,including epithelial ...The lung plays a vital role in maintaining homeostasis,as it is responsible for the exchange of oxygen and carbon dioxide.Pulmonary homeostasis is maintained by a network of tissue-resident cells,including epithelial cells,endothelial cells and leukocytes.Myeloid cells of the innate immune system and epithelial cells form a critical barrier in the lung.Recently developed unbiased next generation sequencing(NGS)has revealed cell heterogeneity in the lung with respect to physiology and pathology and has reshaped our knowledge.New phenotypes and distinct gene signatures have been identified,and these new findings enhance the diagnosis and treatment of lung diseases.Here,we present a review of the new NGS findings on myeloid cells in lung development,homeostasis,and lung diseases,including acute lung injury(ALI),lung fibrosis,chronic obstructive pulmonary disease(COPD),and lung cancer.展开更多
Perilla frutescens (L.) is an edible, medicinal crop, and most popular in East Asia. Its molecular breeding and research are hampered by the paucity of molecular markers. Simple sequence repeat (SSR) markers are ubiqu...Perilla frutescens (L.) is an edible, medicinal crop, and most popular in East Asia. Its molecular breeding and research are hampered by the paucity of molecular markers. Simple sequence repeat (SSR) markers are ubiquitous and widely used in eukaryotic genomes. EST-SSRs identification of perilla was performed in 116,387 reads generated by Illumina paired-end sequencing technology. In total 25,449 unigenes containing SSR and 33,867 SSR loci were identified, and 19,400 primer pairs were designed. Polymorphism of SSR primers was conducted by searching for insertions and deletions (INDELs), and 1,567 unique SSRs were predicted. Totally, 200 SSR primer pairs were selected for polymorphic validation among 23 perilla accessions. Results showed that 175 primer pairs produced amplicons, and 30 pairs exhibited polymorphism. Polymorphic ratio was higher by using INDEL method than using conventional primers. Phylogenetic analysis showed the 2 distinct groups: P. frutescens var. frutescens and P. frutescens var. crispa. Wrinkled leaf trait and seed trait were distinct between these 2 groups. However, no clear leaf color or geographic relationship was detected. The large scale development and identification of SSR marker in this research laid a foundation for genetic analysis and marker assisted breeding of cultivated perilla.展开更多
Over the past few years, many researchers have attempted to develop non-invasive prenatal testing methods in order to investigate the genetic status of the fetus. The aim is to avoid invasive procedures such as chorio...Over the past few years, many researchers have attempted to develop non-invasive prenatal testing methods in order to investigate the genetic status of the fetus. The aim is to avoid invasive procedures such as chorionic villus and amniotic fluid sampling, which result in a significant risk for pregnancy loss. The discovery of cell free fetal DNA circulating in the maternal blood has great potential for the development of non-invasive prenatal testing(NIPT) methodologies. Such strategies have been successfully applied for the determination of the fetal rhesus status and inherited monogenic disease but the field of fetal aneuploidy investigation seems to be more challenging. The main reason for this is that the maternal cell free DNA in the mother's plasma is far more abundant, and because it is identical to half of the corresponding fetal DNA. Approaches developed are mainly based on next generation sequencing(NGS) technologies and epigenetic genetic modifications, such as fetal-maternal DNA differential methylation. At present, genetic services for non-invasive fetal aneuploidy detection are offered using NGS-based approaches but, for reasons that are presented herein, they still serve as screening tests which are not readily accessed by the majority of couples. Here we discuss the limitations of both strategies for NIPT and the future potential of the methods developed.展开更多
Starfruit (Averrhoa carambola L.) is an important fruit for Malaysian export and great attention has been made to improve starfruit fruit quality at Malaysian Agricultural Research and Development Institute (MARDI). T...Starfruit (Averrhoa carambola L.) is an important fruit for Malaysian export and great attention has been made to improve starfruit fruit quality at Malaysian Agricultural Research and Development Institute (MARDI). The current study used next generation sequencing (NGS) technologies to develop starfruit simple sequence repeat (SSR) from 2 varieties namely B11 and B17 using Illumina HiSeq. The pre-processed reads were de novo assembled to generate approximately 75,000 and 74,000 scaffolds respectively. Total genome size for B11 and B17 were around 345 Mbp and 342 Mbp based on K-mer distribution analysis. In-silico microsatellite mining of each variety has identified more than 17,000 SSR in B11 and B17 respectively. Dinucleotides were the most abundant, accounting for more than 70% of all SSR and repeat motif GA (49%) was most common. A total of 239 SSR primer pairs were designed from contigs larger than 350 nucleotides and tested for amplification. The 30 polymorphic SSRs were used to DNA fingerprint of 12 starfruit hybrids. Polymorphism information content (PIC) ranged from 0.1411 to 0.6838, with an average of 0.3919. The Unweighted Pair-Group Method for Arithmetic Averages (UPGMA) dendrogram clustered 12 starfruit accessions into 2 groups.展开更多
Microsatellites, or simple sequence repeats (SSRs), are highly polymorphic, co-dominant genetic markers commonly used for population genetics analyses although de novo development of species specific microsatellites i...Microsatellites, or simple sequence repeats (SSRs), are highly polymorphic, co-dominant genetic markers commonly used for population genetics analyses although de novo development of species specific microsatellites is cost-and time-intensive. Orchidaceae is one of the most species-rich families of angiosperms with more than 30,000 species estimated. Despite its high species-diversity, microsatellites are available only for a few species and all were developed by only using Sanger sequencing methods. For the first time in orchids, we used 454 GS-FLX sequencing to isolate microsatellites in two species (Cypripedium kentuckiense and Pogonia ophioglossoides), and report preliminary results of the study. From 1/16th plate that was subjected to sequencing, 32,665 reads were generated, from which 15,473 fragments contained at least one SSR. We selected 20,697 SSRs representing di-, tri-, and tetra-nucleotides. While 3,674 microsatellites had flanking regions on both sides, useable primer pairs could be designed for 255 SSRs. The mean numbers of reads, SSRs, and SSR-containing reads useful for primer design estimated for other 15 orchid species using Sanger sequencing method were 166, 78 and 31, respectively. Results demonstrate that the efficiency of microsatellite isolation in orchids is substantially higher with 454 GS-FLX sequencing technique in comparison to the Sanger sequencing methods.展开更多
miRNAs are non-coding RNAs that play a regulatory role in expression of genes and are associated with diseases. Quantitatively measuring expression levels of miRNAs can help understanding the mechanisms of human disea...miRNAs are non-coding RNAs that play a regulatory role in expression of genes and are associated with diseases. Quantitatively measuring expression levels of miRNAs can help understanding the mechanisms of human diseases and discovering new drug targets. There are three major methods that have been used to measure the expression levels of miRNAs: real-time reverse transcription PCR (qRT-PCR), microarray, and the newly introduced next-generation sequencing (NGS). NGS is not only suitable for profiling of known miRNAs that qRT-PCR and microarray can do too but also able to detect unknown miRNAs that the other two methods are incapable. Profiling of miRNAs by NGS has been progressed rapidly and is a promising field for applications in drug development. This paper will review the technical advancement of NGS for profiling miRNAs, including comparative analyses between different platforms and software packages for analyzing NGS data. Examples and future perspectives of applications of NGS profiling miRNAs in drug development will be discussed.展开更多
Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequ...Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequisite step. In this study, 2 independent transgene soybean lines were selected(LB4-AtDCGS-1-20-5-2 and CGS-ZG11) as typical cases. Both lines contained expression cassette of At-DCGS that encoding a feedback-insensitive cystathionine gamma-synthase to produce higher level methionine(Met). LB4-AtDCGS-1-20-5-2 was whole genome sequenced with one paired-end 500 bp library and two mate-paired 1 kb and 2 kb libraries using Illumina HiSeq sequencing platform. CGS-ZG11 was sequenced with only one paired-end 500 bp library. Both genomes were assembled,and 2 scaffold sequences(1 for each line) were screened out by aligning with transgene.Then the transgene insertion and its flanking regions in soybean genome were further identified and confirmed by PCR cloning and Sanger sequencing. Results showed that these 2 transgene lines had single copy of inserted transgene. Their transgene insertion contents were identified, which facilitates further safety assessment. These results indicated that genome assembly using high throughput sequencing is a powerful tool for identifying transgene insertions, even with limited knowledge.展开更多
Hepatocellular carcinoma(HCC)is one of the leading causes of cancer related death in Asia and Africa(1).It reflects the high burden of hepatitis B virus(HBV)infection in these areas.Curative treatments of HCC as radio...Hepatocellular carcinoma(HCC)is one of the leading causes of cancer related death in Asia and Africa(1).It reflects the high burden of hepatitis B virus(HBV)infection in these areas.Curative treatments of HCC as radiofrequency ablation and resection are impaired by a high rate of tumor recurrence.However,most of the time,HCC is frequently diagnosed at advanced stages where展开更多
Objective To evaluate a single-reaction genome amplification method, the multisegment reverse transcription-PCR(M-RTPCR), for its sensitivity to full genome sequencing of influenza A virus, and the ability to differen...Objective To evaluate a single-reaction genome amplification method, the multisegment reverse transcription-PCR(M-RTPCR), for its sensitivity to full genome sequencing of influenza A virus, and the ability to differentiate mix-subtype virus, using the next generation sequencing(NGS) platform. Methods Virus genome copy was quantified and serially diluted to different titers, followed by amplification with the M-RTPCR method and sequencing on the NGS platform. Furthermore, we manually mixed two subtype viruses to different titer rate and amplified the mixed virus with the M-RTPCR protocol, followed by whole genome sequencing on the NGS platform. We also used clinical samples to test the method performance. Results The M-RTPCR method obtained complete genome of testing virus at 125 copies/reaction and determined the virus subtype at titer of 25 copies/reaction. Moreover, the two subtypes in the mixed virus could be discriminated, even though these two virus copies differed by 200-fold using this amplification protocol. The sensitivity of this protocol we detected using virus RNA was also confirmed with clinical samples containing low-titer virus. Conclusion The M-RTPCR is a robust and sensitive amplification method for whole genome sequencing of influenza A virus using NGS platform.展开更多
DNA sequencing is the method of identifying the precise order of DNA nucleotides within a molecule. The information of DNA sequencing is of prime requisite for basic biological research as well as in various clinical ...DNA sequencing is the method of identifying the precise order of DNA nucleotides within a molecule. The information of DNA sequencing is of prime requisite for basic biological research as well as in various clinical specialties.They can be used to determine the individual genetic sequence, larger genetic regions, chromosomes as well as to sequence RNA and proteins. Since the first DNA sequencing in 1970s, there has been tremendous advancements in the technologies aimed to determine the entire human genome. The need for rapid and accurate sequencing of human genome has resulted in the introduction of next generation sequencing(NGS) technology. NGS refers to the secondgeneration DNA sequencing technologies where millions of DNA can be sequenced simultaneously. Some of the next gen sequencing methods employed are Roche/454 life science, Illumina/Solexa, SOLiD system and HeliScope.Application of NGS in decoding the genomic database of various oral diseases may possess therapeutic and prognostic value. This presentation provides an overview of the basics of NGS and their potential applications in oral disease diagnostics.展开更多
BACKGROUND:Prompt pathogen identification can have a substantial impact on the optimization of antimicrobial treatment.The objective of the study was to assess the diagnostic value of next-generation sequencing(NGS)fo...BACKGROUND:Prompt pathogen identification can have a substantial impact on the optimization of antimicrobial treatment.The objective of the study was to assess the diagnostic value of next-generation sequencing(NGS)for identifying pathogen and its clinical impact on antimicrobial intervention in immunocompromised patients with suspected infections.METHODS:This was a retrospective study.Between January and August 2020,47 adult immunocompromised patients underwent NGS testing under the following clinical conditions:1)prolonged fever and negative conventional cultures;2)new-onset fever despite empiric antimicrobial treatment;and 3)afebrile with suspected infections on imaging.Clinical data,including conventional microbial test results and antimicrobial treatment before and after NGS,were collected.Data were analyzed according to documented changes in antimicrobial treatment(escalated,no change,or deescalated)after the NGS results.RESULTS:The median time from hospitalization to NGS sampling was 19 d.Clinically relevant pathogens were detected via NGS in 61.7% of patients(29/47),more than half of whom suffered from fungemia(n=17),resulting in an antimicrobial escalation in 53.2% of patients(25/47)and antimicrobial de-escalation in 0.2% of patients(1/47).Antimicrobial changes were mostly due to the identification of fastidious organisms such as Legionella,Pneumocystis jirovecii,and Candida.In the remaining three cases,NGS detected clinically relevant pathogens also detected by conventional cultures a few days later.The antimicrobial treatment was subsequently adjusted according to the susceptibility test results.Overall,NGS changed antimicrobial management in 55.3%(26/47)of patients,and conventional culture detected clinically relevant pathogens in 14.9% of the patients(7/47).CONCLUSION:With its rapid identification and high sensitivity,NGS could be a promising tool for identifying relevant pathogens and enabling rapid appropriate treatment in immunocompromised patients with suspected infections.展开更多
文摘The understanding of how genetic and epigenetic factors influence tumorigenesis, progression and invasion, is vastly growing since new technologies allow the analysis of the functional genome namely the exome, the transcriptome and the epigenome, besides enabling genome-wide assessment of genetic variations. With the advent of new drugs that are indicated tissue agnostic, depending on certain mutations, there is a growing demand for fast and cost-effective genetic diagnosis. The method in focus that already became an indispensable tool in viral diagnosis is next-generation sequencing (NGS). This approach allows sequencing of literally every DNA molecule in the sample and can either be used to assess numerous genetic markers of one patient at a time, or to assess fewer markers of many patients in parallel, which reduces costs. We submitted 23 samples of different tumor entities to four diagnostic companies with different analysis profiles. The results as disclosed and discussed in this report indicate that so far, the main application of NGS is rather in cancer research than in diagnosis, as none of the reports had a real impact on the therapeutic scheme. We are perfectly aware that such a small cohort cannot be generalized, but considering the costs vs. benefits, NGS should be engaged upon a very stringent evaluation only. However, in cases where obtaining a tissue biopsy is impossible or unfavorable, analysis of liquid biopsy by NGS provides a vital alternative.
文摘Next generation sequencing is currently a cornerstone of genetic testing in routine diagnostics,allowing for the detection of sequence variants with so far unprecedented large scale,mainly in genetically heterogenous diseases,such as neurological disorders.It is a fast-moving field,where new wet enrichment protocols and bioinformatics tools are constantly being developed to overcome initial limitations.Despite the as yet undiscussed advantages,however,there are still some challenges in data analysis and the interpretation of variants.In this review,we address the current state of next generation sequencing diagnostic testing for inherited human disorders,particularly giving an overview of the available high-throughput sequencing approaches;including targeted,whole-exome and whole-genome sequencing;and discussing the main critical aspects of the bioinformatic process,from raw data analysis to molecular diagnosis.
基金Supported by Taizhou Social Development Plan,No.TS202004Natural Science Foundation of Nanjing University of Chinese Medicine China,No.XZR2020093Taizhou People's Hospital Medical Innovation Team Foundation,No.CXTDA201901.
文摘BACKGROUND Colorectal cancer(CRC)is one of the most common malignancies worldwide.Given its insidious onset,the condition often already progresses to advanced stage when symptoms occur.Thus,early diagnosis is of great significance for timely clinical intervention,efficacy enhancement,and prognostic improvement.Featuring high throughput,fastness,and rich information,next generation sequencing(NGS)can greatly shorten the detection time,which is a widely used detection technique at present.AIM To screen specific genes or gene combinations in fecal DNA that are suitable for diagnosis and prognostic prediction of CRC,and to establish a technological platform for CRC screening,diagnosis,and efficacy monitoring through fecal DNA detection.METHODS NGS was used to sequence the stool DNA of patients with CRC,which were then compared with the genetic testing results of the stool samples of normal controls and patients with benign intestinal disease,as well as the tumor tissues of CRC patients.Specific genes or gene combinations in fecal DNA suitable for diagnosis and prognostic prediction of CRC were screened,and their significances in diagnosing CRC and predicting patients'prognosis were comprehensively evaluated.RESULTS High mutation frequencies of TP53,APC,and KRAS were detected in the stools and tumor tissues of CRC patients prior to surgery.Contrastively,no pathogenic mutations of the above three genes were noted in the postoperative stools,the normal controls,or the benign intestinal disease group.This indicates that tumor-specific DNA was detectable in the preoperative stools of CRC patients.The preoperative fecal expression of tumor-associated genes can reflect the gene mutations in tumor tissues to some extent.Compared to the postoperative stools and the stools in the two control groups,the pathogenic mutation frequencies of TP53 and KRAS were significantly higher for the preoperative stools(χ^(2)=7.328,P<0.05;χ^(2)=4.219,P<0.05),suggesting that fecal TP53 and KRAS genes can be used for CRC screening,diagnosis,and prognostic prediction.No significant difference in the pathogenic mutation frequency of the APC gene was found from the postoperative stools or the two control groups(χ^(2)=0.878,P>0.05),so further analysis with larger sample size is required.Among CRC patients,the pathogenic mutation sites of TP53 occurred in 16 of 27 preoperative stools,with a true positive rate of 59.26%,while the pathogenic mutation sites of KRAS occurred in 10 stools,with a true positive rate of 37.04%.The sensitivity and negative predictive values of the combined genetic testing of TP53 and KRAS were 66.67%(18/27)and 68.97%,respectively,both of which were higher than those of TP53 or KRAS mutation detection alone,suggesting that the combined genetic testing can improve the CRC detection rate.The mutation sites TP53 exon 4 A84G and EGFR exon 20 I821T(mutation start and stop positions were both 7579436 for the former,while 55249164 for the latter)were found in the preoperative stools and tumor tissues.These"undetected"mutation sites may be new types of mutations occurring during the CRC carcinogenesis and progression,which needs to be confirmed through further research.Some mutations of"unknown clinical significance"were found in such genes as TP53,PTEN,KRAS,BRAF,AKT1,and PIK3CA,whose clinical values is worthy of further exploration.CONCLUSION NGS-based fecal genetic testing can be used as a complementary technique for the CRC diagnosis.Fecal TP53 and KRAS can be used as specific genes for the screening,diagnosis,prognostic prediction,and recurrence monitoring of CRC.Moreover,the combined testing of TP53 and KRAS genes can improve the CRC detection rate.
文摘Helicobacter pylori(H.pylori)infection is highly prevalent in the human population and may lead to severe gastrointestinal pathology including gastric and duodenal ulcers,mucosa associated tissue lymphoma and gastric adenocarcinoma.In recent years,an alarming increase in antimicrobial resistance and subsequently failing empiric H.pylori eradication therapies have been noted worldwide,also in many European countries.Therefore,rapid and accurate determination of H.pylori’s antibiotic susceptibility prior to the administration of eradication regimens becomes ever more important.Traditionally,detection of H.pylori and its antimicrobial resistance is done by culture and phenotypic drug susceptibility testing that are cumbersome with a long turn-around-time.Recent advances in diagnostics provide new tools,like real-time polymerase chain reaction(PCR)and line probe assays,to diagnose H.pylori infection and antimicrobial resistance to certain antibiotics,directly from clinical specimens.Moreover,high-throughput whole genome sequencing technologies allow the rapid analysis of the pathogen’s genome,thereby allowing identification of resistance mutations and associated antibiotic resistance.In the first part of this review,we will give an overview on currently available diagnostic methods for detection of H.pylori and its drug resistance and their implementation in H.pylori management.The second part of the review focusses on the use of next generation sequencing technology in H.pylori research.To this end,we conducted a literature search for original research articles in English using the terms“Helicobacter”,“transcriptomic”,“transcriptome”,“next generation sequencing”and“whole genome sequencing”.This review is aimed to bridge the gap between current diagnostic practice(histology,rapid urease test,H.pylori culture,PCR and line probe assays)and new sequencing technologies and their potential implementation in diagnostic laboratory settings in order to complement the currently recommended H.pylori management guidelines and subsequently improve public health.
基金supported by the Ministry of Health Fund Industry of China,as part of project"Prevention,Intervention,and Extend Application of Deafness with Birth Defect"(contract#:201202005)the 1255 project of Changhai Hospital,Second Military Medical University,Shanghai,China
文摘Objective: To investigate immune-related genetic background in bilateral sudden sensorineural hearing loss(SSNHL).Case report and methods: The case is a 45-year-old man presenting with a 7-year history of bilateral profound SSNHL. Blood biochemical testing demonstrated increased levels of total cholesterol(5.88 mmol/L). Tests for hepatitis B showed a positive antibody against the hepatitis B core antigen. Complement C3 was below the normal value, and complement C4 and Ig G were in the lower range of normal values. CT images showed a normal inner ear and vestibular aqueduct but round window membranous ossification on both sides. A total number of 232 immuneassociated genes were sequenced using the next generation sequencing technique.Results: Mutations were detected in 5 genes, including the phosphoinositide 3-kinase catalytic subunit delta(PIK3CD), caspase recruitment domain-containing protein 9(CARD9), complement factor H-related(CFHR2), immunoglobulin lambda-like polypeptide 1 Protein(IGLL1),and transmembrane channel-like gene family 8(TMC8). In the PIK3 CD gene, a C896 T substitute in exon 7 was detected. This mutation causes primary immunodeficiency and is an autosomal dominant disease.Conclusion: The PIK3 CD C896T mutation responsible for primary immunodeficiency may contribute to the onset of bilateral SSNHL with subsequent rapid progression.
基金Supported by the National Science and Technology Important and Special Project of China,No.2017ZX09304024
文摘BACKGROUND Hereditary spherocytosis(HS)is a hereditary disease of hemolytic anemia that occurs due to the erythrocyte membrane defects.Dubin–Johnson syndrome(DJS),which commonly results in jaundice,is a benign hereditary disorder of bilirubin clearance that occurs only rarely.The co-occurrence of HS and DJS is extremely rare.We recently diagnosed and treated a case of co-occurring HS and DJS.CASE SUMMARY A 21-year-old female patient presented to our department because of severe jaundice,severe splenomegaly,and mild anemia since birth.We eventually confirmed the diagnosis of co-occurring DJS and HS by next generation sequencing(NGS).The treatment of ursodeoxycholic acid in combination with phenobarbital successfully increased hemoglobin and reduced total bilirubin and direct bilirubin.CONCLUSION The routine application of NGS can efficiently render a definite diagnosis when inherited disorders are suspected.
文摘In the last few years,the advent of next generation sequencing(NGS) has revolutionized the approach to genetic studies,making whole-genome sequencing a possible way of obtaining global genomic information.NGS has very recently been shown to be successful in identifying novel causative mutations of rare or common Mendelian disorders.At the present time,it is expected that NGS will be increasingly important in the study of inherited and complex cardiovascular diseases(CVDs).However,the NGS approach to the genetics of CVDs represents a territory which has not been widely investigated.The identification of rare and frequent genetic variants can be very important in clinical practice to detect pathogenic mutations or to establish a profile of risk for the development of pathology.The purpose of this paper is to discuss the recent application of NGS in the study of several CVDs such as inherited cardiomyopathies,channelopathies,coronary artery disease and aortic aneurysm.We also discuss the future utility and challenges related to NGS in studying the genetic basis of CVDs in order to improve diagnosis,prevention,and treatment.
基金Supported by D.O.Ott Research Institute of Obstetrics,Gynaecology and Reproductology,project 558-2019-0012(АААА-А19-119021290033-1)of FSBSI
文摘Type 2 diabetes(T2D)mellitus is a common complex disease that currently affects more than 400 million people worldwide and has become a global health problem.High-throughput sequencing technologies such as whole-genome and whole-exome sequencing approaches have provided numerous new insights into the molecular bases of T2D.Recent advances in the application of sequencing technologies to T2D research include,but are not limited to:(1)Fine mapping of causal rare and common genetic variants;(2)Identification of confident genelevel associations;(3)Identification of novel candidate genes by specific scoring approaches;(4)Interrogation of disease-relevant genes and pathways by transcriptional profiling and epigenome mapping techniques;and(5)Investigation of microbial community alterations in patients with T2D.In this work we review these advances in application of next-generation sequencing methods for elucidation of T2D pathogenesis,as well as progress and challenges in implementation of this new knowledge about T2D genetics in diagnosis,prevention,and treatment of the disease.
文摘Objective:To compare the efficacy of platinum-and non-platinum-based regimens as first-line treatment for advanced triple-negative breast cancer(TNBC)and analyze the relationship between their efficacy and BRCA gene status.Methods:Retrospectively analyze clinical data of 220 patients diagnosed pathologically with advanced TNBC and treated at the Department of Breast Oncology,Peking University Cancer Hospital from 2013 to 2018 and evaluate the efficacy of chemotherapy.A total of 114 patients had BRCA1/2 gene tested by next generation sequencing(NGS)using peripheral blood,and we analyzed the correlation between their efficacy and BRCA1/2 gene status.Results:Non-platinum-based chemotherapy(NPCT)was administered to 129 and platinum-based chemotherapy(PBCT)to 91 study patients.The clinical benefit rate(CBR)and median progression-free survival(PFS)were not statistically different between NPCT and PBCT groups.The median overall survival(OS)was 30.0 and 22.5 months for PBCT and NPCT group,respectively[P=0.090,hazard ratios(HR)=0.703].BRCA status was assessed in 114 patients,14 of whom had deleterious germline BRCA1/2(g BRCA)mutations(seven in each group).In PBCT group,the CBR was 85.7%and 35.1%for patients with and without deleterious g BRCA mutations,respectively(P=0.039).The median PFS were 14.9 and 5.3 months and median OS were 26.5 and 15.5 months for patients with and without deleterious g BRCA mutations,respectively(P=0.001,P=0.161,respectively).Patients in PBCT group had significantly greater rates of grade 3-4 anemia(5.5%vs.0%)and thrombocytopenia(8.8%vs.0%),whereas palmar-plantar erythrodysesthesia(12.4%vs.0%)and peripheral neuropathy(8.6%vs.1.1%)occurred more frequently in NPCT group.Conclusions:Platinum-based regimens are more effective in patients with deleterious g BRCA mutations,but no difference in patients without BRCA gene mutations,so non-platinum is an option in patients without BRCA gene mutations considering the toxicity and side effect.And we recommend that patients with advanced TNBC should have BRCA gene test.
基金the USA National Institutes of Health Grant R01-HL-079669(J.F.)USA National Institutes of Health Grant R01HL076179(J.F.)+2 种基金USA National Institutes of Health Grant R01HL-139547(J.F.)VA Merit Award 1I01BX002729(J.F.)VA BLR&D Award 1IK6BX004211(J.F.).
文摘The lung plays a vital role in maintaining homeostasis,as it is responsible for the exchange of oxygen and carbon dioxide.Pulmonary homeostasis is maintained by a network of tissue-resident cells,including epithelial cells,endothelial cells and leukocytes.Myeloid cells of the innate immune system and epithelial cells form a critical barrier in the lung.Recently developed unbiased next generation sequencing(NGS)has revealed cell heterogeneity in the lung with respect to physiology and pathology and has reshaped our knowledge.New phenotypes and distinct gene signatures have been identified,and these new findings enhance the diagnosis and treatment of lung diseases.Here,we present a review of the new NGS findings on myeloid cells in lung development,homeostasis,and lung diseases,including acute lung injury(ALI),lung fibrosis,chronic obstructive pulmonary disease(COPD),and lung cancer.
基金support of the National Science Foundation of China (31360067)the Science-Technology Support Projects of Guizhou Province (NY[2016]3052)the Talent base for germplasm resources utilization and innovation of characteristic plant in Guizhou (RCJD2018-14)
文摘Perilla frutescens (L.) is an edible, medicinal crop, and most popular in East Asia. Its molecular breeding and research are hampered by the paucity of molecular markers. Simple sequence repeat (SSR) markers are ubiquitous and widely used in eukaryotic genomes. EST-SSRs identification of perilla was performed in 116,387 reads generated by Illumina paired-end sequencing technology. In total 25,449 unigenes containing SSR and 33,867 SSR loci were identified, and 19,400 primer pairs were designed. Polymorphism of SSR primers was conducted by searching for insertions and deletions (INDELs), and 1,567 unique SSRs were predicted. Totally, 200 SSR primer pairs were selected for polymorphic validation among 23 perilla accessions. Results showed that 175 primer pairs produced amplicons, and 30 pairs exhibited polymorphism. Polymorphic ratio was higher by using INDEL method than using conventional primers. Phylogenetic analysis showed the 2 distinct groups: P. frutescens var. frutescens and P. frutescens var. crispa. Wrinkled leaf trait and seed trait were distinct between these 2 groups. However, no clear leaf color or geographic relationship was detected. The large scale development and identification of SSR marker in this research laid a foundation for genetic analysis and marker assisted breeding of cultivated perilla.
文摘Over the past few years, many researchers have attempted to develop non-invasive prenatal testing methods in order to investigate the genetic status of the fetus. The aim is to avoid invasive procedures such as chorionic villus and amniotic fluid sampling, which result in a significant risk for pregnancy loss. The discovery of cell free fetal DNA circulating in the maternal blood has great potential for the development of non-invasive prenatal testing(NIPT) methodologies. Such strategies have been successfully applied for the determination of the fetal rhesus status and inherited monogenic disease but the field of fetal aneuploidy investigation seems to be more challenging. The main reason for this is that the maternal cell free DNA in the mother's plasma is far more abundant, and because it is identical to half of the corresponding fetal DNA. Approaches developed are mainly based on next generation sequencing(NGS) technologies and epigenetic genetic modifications, such as fetal-maternal DNA differential methylation. At present, genetic services for non-invasive fetal aneuploidy detection are offered using NGS-based approaches but, for reasons that are presented herein, they still serve as screening tests which are not readily accessed by the majority of couples. Here we discuss the limitations of both strategies for NIPT and the future potential of the methods developed.
文摘Starfruit (Averrhoa carambola L.) is an important fruit for Malaysian export and great attention has been made to improve starfruit fruit quality at Malaysian Agricultural Research and Development Institute (MARDI). The current study used next generation sequencing (NGS) technologies to develop starfruit simple sequence repeat (SSR) from 2 varieties namely B11 and B17 using Illumina HiSeq. The pre-processed reads were de novo assembled to generate approximately 75,000 and 74,000 scaffolds respectively. Total genome size for B11 and B17 were around 345 Mbp and 342 Mbp based on K-mer distribution analysis. In-silico microsatellite mining of each variety has identified more than 17,000 SSR in B11 and B17 respectively. Dinucleotides were the most abundant, accounting for more than 70% of all SSR and repeat motif GA (49%) was most common. A total of 239 SSR primer pairs were designed from contigs larger than 350 nucleotides and tested for amplification. The 30 polymorphic SSRs were used to DNA fingerprint of 12 starfruit hybrids. Polymorphism information content (PIC) ranged from 0.1411 to 0.6838, with an average of 0.3919. The Unweighted Pair-Group Method for Arithmetic Averages (UPGMA) dendrogram clustered 12 starfruit accessions into 2 groups.
文摘Microsatellites, or simple sequence repeats (SSRs), are highly polymorphic, co-dominant genetic markers commonly used for population genetics analyses although de novo development of species specific microsatellites is cost-and time-intensive. Orchidaceae is one of the most species-rich families of angiosperms with more than 30,000 species estimated. Despite its high species-diversity, microsatellites are available only for a few species and all were developed by only using Sanger sequencing methods. For the first time in orchids, we used 454 GS-FLX sequencing to isolate microsatellites in two species (Cypripedium kentuckiense and Pogonia ophioglossoides), and report preliminary results of the study. From 1/16th plate that was subjected to sequencing, 32,665 reads were generated, from which 15,473 fragments contained at least one SSR. We selected 20,697 SSRs representing di-, tri-, and tetra-nucleotides. While 3,674 microsatellites had flanking regions on both sides, useable primer pairs could be designed for 255 SSRs. The mean numbers of reads, SSRs, and SSR-containing reads useful for primer design estimated for other 15 orchid species using Sanger sequencing method were 166, 78 and 31, respectively. Results demonstrate that the efficiency of microsatellite isolation in orchids is substantially higher with 454 GS-FLX sequencing technique in comparison to the Sanger sequencing methods.
文摘miRNAs are non-coding RNAs that play a regulatory role in expression of genes and are associated with diseases. Quantitatively measuring expression levels of miRNAs can help understanding the mechanisms of human diseases and discovering new drug targets. There are three major methods that have been used to measure the expression levels of miRNAs: real-time reverse transcription PCR (qRT-PCR), microarray, and the newly introduced next-generation sequencing (NGS). NGS is not only suitable for profiling of known miRNAs that qRT-PCR and microarray can do too but also able to detect unknown miRNAs that the other two methods are incapable. Profiling of miRNAs by NGS has been progressed rapidly and is a promising field for applications in drug development. This paper will review the technical advancement of NGS for profiling miRNAs, including comparative analyses between different platforms and software packages for analyzing NGS data. Examples and future perspectives of applications of NGS profiling miRNAs in drug development will be discussed.
基金supported by the Genetically Modified Organisms Breeding Major Projects of China (2016ZX08011-003)China Agriculture Research System (CARS-04)CAAS Agricultural Science and Technology Innovation Project
文摘Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequisite step. In this study, 2 independent transgene soybean lines were selected(LB4-AtDCGS-1-20-5-2 and CGS-ZG11) as typical cases. Both lines contained expression cassette of At-DCGS that encoding a feedback-insensitive cystathionine gamma-synthase to produce higher level methionine(Met). LB4-AtDCGS-1-20-5-2 was whole genome sequenced with one paired-end 500 bp library and two mate-paired 1 kb and 2 kb libraries using Illumina HiSeq sequencing platform. CGS-ZG11 was sequenced with only one paired-end 500 bp library. Both genomes were assembled,and 2 scaffold sequences(1 for each line) were screened out by aligning with transgene.Then the transgene insertion and its flanking regions in soybean genome were further identified and confirmed by PCR cloning and Sanger sequencing. Results showed that these 2 transgene lines had single copy of inserted transgene. Their transgene insertion contents were identified, which facilitates further safety assessment. These results indicated that genome assembly using high throughput sequencing is a powerful tool for identifying transgene insertions, even with limited knowledge.
基金supported by HECAM (BPI), EBCI, INCa (Wnt HCC project). J-C.N.supported by a fellowship from INCa
文摘Hepatocellular carcinoma(HCC)is one of the leading causes of cancer related death in Asia and Africa(1).It reflects the high burden of hepatitis B virus(HBV)infection in these areas.Curative treatments of HCC as radiofrequency ablation and resection are impaired by a high rate of tumor recurrence.However,most of the time,HCC is frequently diagnosed at advanced stages where
基金funded by a project(2014ZX10004002)of the Chinese National Key Program of Mega Infectious Disease of the National 12th Five-Year Plan
文摘Objective To evaluate a single-reaction genome amplification method, the multisegment reverse transcription-PCR(M-RTPCR), for its sensitivity to full genome sequencing of influenza A virus, and the ability to differentiate mix-subtype virus, using the next generation sequencing(NGS) platform. Methods Virus genome copy was quantified and serially diluted to different titers, followed by amplification with the M-RTPCR method and sequencing on the NGS platform. Furthermore, we manually mixed two subtype viruses to different titer rate and amplified the mixed virus with the M-RTPCR protocol, followed by whole genome sequencing on the NGS platform. We also used clinical samples to test the method performance. Results The M-RTPCR method obtained complete genome of testing virus at 125 copies/reaction and determined the virus subtype at titer of 25 copies/reaction. Moreover, the two subtypes in the mixed virus could be discriminated, even though these two virus copies differed by 200-fold using this amplification protocol. The sensitivity of this protocol we detected using virus RNA was also confirmed with clinical samples containing low-titer virus. Conclusion The M-RTPCR is a robust and sensitive amplification method for whole genome sequencing of influenza A virus using NGS platform.
文摘DNA sequencing is the method of identifying the precise order of DNA nucleotides within a molecule. The information of DNA sequencing is of prime requisite for basic biological research as well as in various clinical specialties.They can be used to determine the individual genetic sequence, larger genetic regions, chromosomes as well as to sequence RNA and proteins. Since the first DNA sequencing in 1970s, there has been tremendous advancements in the technologies aimed to determine the entire human genome. The need for rapid and accurate sequencing of human genome has resulted in the introduction of next generation sequencing(NGS) technology. NGS refers to the secondgeneration DNA sequencing technologies where millions of DNA can be sequenced simultaneously. Some of the next gen sequencing methods employed are Roche/454 life science, Illumina/Solexa, SOLiD system and HeliScope.Application of NGS in decoding the genomic database of various oral diseases may possess therapeutic and prognostic value. This presentation provides an overview of the basics of NGS and their potential applications in oral disease diagnostics.
基金supported by National Natural Science Foundation of China(72274067)。
文摘BACKGROUND:Prompt pathogen identification can have a substantial impact on the optimization of antimicrobial treatment.The objective of the study was to assess the diagnostic value of next-generation sequencing(NGS)for identifying pathogen and its clinical impact on antimicrobial intervention in immunocompromised patients with suspected infections.METHODS:This was a retrospective study.Between January and August 2020,47 adult immunocompromised patients underwent NGS testing under the following clinical conditions:1)prolonged fever and negative conventional cultures;2)new-onset fever despite empiric antimicrobial treatment;and 3)afebrile with suspected infections on imaging.Clinical data,including conventional microbial test results and antimicrobial treatment before and after NGS,were collected.Data were analyzed according to documented changes in antimicrobial treatment(escalated,no change,or deescalated)after the NGS results.RESULTS:The median time from hospitalization to NGS sampling was 19 d.Clinically relevant pathogens were detected via NGS in 61.7% of patients(29/47),more than half of whom suffered from fungemia(n=17),resulting in an antimicrobial escalation in 53.2% of patients(25/47)and antimicrobial de-escalation in 0.2% of patients(1/47).Antimicrobial changes were mostly due to the identification of fastidious organisms such as Legionella,Pneumocystis jirovecii,and Candida.In the remaining three cases,NGS detected clinically relevant pathogens also detected by conventional cultures a few days later.The antimicrobial treatment was subsequently adjusted according to the susceptibility test results.Overall,NGS changed antimicrobial management in 55.3%(26/47)of patients,and conventional culture detected clinically relevant pathogens in 14.9% of the patients(7/47).CONCLUSION:With its rapid identification and high sensitivity,NGS could be a promising tool for identifying relevant pathogens and enabling rapid appropriate treatment in immunocompromised patients with suspected infections.
