The next generation sequencing （NGS） is an important process which assures inexpen- sive organization of vast size of raw sequence dataset over any traditional sequencing systems or methods. Various aspects of NGS s...The next generation sequencing （NGS） is an important process which assures inexpen- sive organization of vast size of raw sequence dataset over any traditional sequencing systems or methods. Various aspects of NGS such as template preparation, sequencing imaging and genome alignment and assembly outline the genome sequencing and align- ment. Consequently, de Bruijn graph （dBG） is an important mathematical tool that graphically analyzes how the orientations are constructed in groups of nucleotides. Basi- cally, dBG describes the formation of the genome segments in circular iterative fashions. Some pivotal dBG-based de novo algorithms and software packages such as T-IDBA, Oases, IDBA-tran, Euler, Velvet, ABYSS, AllPaths, SOAPde novo and SOAPde novo2 are illustrated in this paper. Consequently, overlap layout consensus （OLC） graph-based algorithms also play vital role in NGS assembly. Some important OLC-based algorithms such as MIRA3, CABOG, Newbler, Edena, Mosaik and SHORTY are portrayed in this paper. It has been experimented that greedy graph-based algorithms and software pack- ages are also vital for proper genome dataset assembly. A few algorithms named SSAKE, SHARCGS and VCAKE help to perform proper genome sequencing.展开更多
As a relatively uncommon orphan tumor with high mortality,biliary tract cancer(BTC)presents an aggressive course and heterogeneous clinical features[1].BTC patients present with advanced manifestations[2].Unfortunatel...As a relatively uncommon orphan tumor with high mortality,biliary tract cancer(BTC)presents an aggressive course and heterogeneous clinical features[1].BTC patients present with advanced manifestations[2].Unfortunately,there has been little progress in the management of BTC.Most patients have inoperable lesions and must receive palliative therapy.Gemcitabine-based chemotherapy has been the only widely accepted first-line treatment for advanced BTC[3].Nevertheless,BTCs are often refractory to chemotherapeutic regimens,leading to a poor clinical outcome in these patients.Recently,with the rapid development of next generation sequencing(NGS)technologies,some actionable mutations such as those in IDH1,FGFR2,BRAF,HER2 genes,and unique molecular subsets in BTCs have been identified[4],and related targeted therapy against actionable mutations has been introduced into clinical practice as a promising therapeutic strategy[5].展开更多
Rice blast caused by Magnaporthe oryzae （M. oryzae） is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among...Rice blast caused by Magnaporthe oryzae （M. oryzae） is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among different isolates of M. oryzae in nature, we re-sequenced the genomes of two field isolates, CH43 and Zhong-10-8-14, which showed distinct pathogenecity on most of the rice cultivars. Genome-wide genetic variation analysis reveals that ZHONG-10-8-14 exhibits higher sequence variations than CH43. Structural variations （SVs） detection shows that the sequence variations primarily occur in exons and intergenic regions. Bioinformatics analysis for gene variations reveals that many pathogenecity-related pathways are enriched. In addition, 193 candidate effectors with various DNA polymorphisms were identified, including two known effectors AVR-Pik and AVR-Pital. Comparative polymorphism analysis of thirteen randomly selected effectors suggests that the genetic variations of effectors are under positive selection. The expression pattern analysis of several pathogenecity-related variant genes indicates that these genes are differentially regulated in two isolates, with much higher expression levels in Zhong-10-8-14 than CH43. Our data demonstrate that the genetic variations of effectors and pathogenecity-related genes are under positive selection, resulting in the distinct pathogeuicities of CH43 and Zhong- 10-8-14 on rice.展开更多
HLA-A＊02 is the most prevalent and polymorphic major histocompatibility complex （MHC） allele family in humans. Functional differences have been revealed among subtypes, demanding further subtyping of HLA-A＊02 in b...HLA-A＊02 is the most prevalent and polymorphic major histocompatibility complex （MHC） allele family in humans. Functional differences have been revealed among subtypes, demanding further subtyping of HLA-A＊02 in basic and clinical settings. However, the fast growing polymorphisms render traditional primeror probe-based typing methods impractical and result in increasing ambiguities in direct sequence-based typing. In this study, we combined group-specific amplification and mono-allelic sequencing to design and validate a simple scheme for the complete screening and accurate subtyping of all 540 reported HLA-A＊02 alleles. This scheme could be performed in routine labs to facilitate studies with an interest in HLA-A＊02.展开更多
Cyanobacterial harmful algal blooms are a major threat to freshwater eco-systems globally. To deal with this threat, researches into the cyanobacteria bloom in fresh water lakes and rivers have been carried out all ov...Cyanobacterial harmful algal blooms are a major threat to freshwater eco-systems globally. To deal with this threat, researches into the cyanobacteria bloom in fresh water lakes and rivers have been carried out all over the world. This review presents an overlook of studies on cyanobacteria blooms. Conventional studies mainly focus on investigating the environmental factors influencing the blooms, with their limitation in lack of viewing the microbial community structures. Metagenomics study provides insight into the internal community structure of the cyanobacteria at the blooming, and there are researchers reported that sequence data was a better predictor than environmental factors. This further manifests the significance of the metagenomic study. However, large number of the latter appears to be confined only to present snapshoot of the microbial community diversity and structure. This type of investigation has been valuable and important, whilst an effort to integrate and coordinate the conventional approaches that largely focus on the environmental factors control, and the Metagenomics approaches that reveals the microbial community structure and diversity, implemented through machine learning techniques, for a holistic and more comprehensive insight into the cause and control of Cyanobacteria blooms, appear to be a trend and challenge of the study of this field.展开更多
Plant genetic resources collection and utilization had made a huge impact in balancing the genetic diversity of the existing crop plant species and their application in genome based studies had also increased widely. ...Plant genetic resources collection and utilization had made a huge impact in balancing the genetic diversity of the existing crop plant species and their application in genome based studies had also increased widely. Primarily studies were based on model species, although it now enhances the transferability of information to crops and related species. With the tremendous outbreak of new high-throughput technologies like next-generation sequencing (NGS) and reduction in their costs are bringing many more plants within the range of genome and transcriptome level analysis. The completion of reference genome sequences for many important crops and the ability to perform high-throughput resequencing are providing opportunities for improving our understanding of the crop plant genetic resources to accelerate crop improvement. The future of crop improvement will be centred on comparisons of individual crop plant genomes, and some of the best opportunities may lie in using combinations of new genetic mapping strategies and evolutionary analyses to direct and optimize the discovery and use of genetic variation. Here I review the importance of crop plant genetic resources and insights that have been emerged in recent years.展开更多
Common variable immunodeficiency disorders(CVID),a heterogeneous group of inborn errors of immunity,is the most common symptomatic primary immunodeficiency disorder.Patients with CVID have highly variable clinical pre...Common variable immunodeficiency disorders(CVID),a heterogeneous group of inborn errors of immunity,is the most common symptomatic primary immunodeficiency disorder.Patients with CVID have highly variable clinical presentation.With the advent of whole genome sequencing and genome wide association studies(GWAS),there has been a remarkable improvement in understanding the genetics of CVID.This has also helped in understanding the pathogenesis of CVID and has drastically improved the management of these patients.A multiomics approach integrating the DNA sequencing along with RNA sequencing,proteomics,epigenetic and metabolomics profile is the need of the hour to unravel specific CVID associated disease pathways and novel therapeutic targets.In this review,we elaborate various techniques that have helped in understanding the genetics of CVID.展开更多
Mutations might challenge the paternity index calculation in forensic identification.While many studies have focussed on the autosomal short tandem repeats(A-STR),the mutation status of sex chromosomes and single nucl...Mutations might challenge the paternity index calculation in forensic identification.While many studies have focussed on the autosomal short tandem repeats(A-STR),the mutation status of sex chromosomes and single nucleotide polymorphism(SNP)remain blank.Next generation sequencing(NGS),known as high throughput and large sequence polymorphism,is a promising tool for forensic genetics.To describe the mutation landscapes in the paternity cases with genetic inconsistencies,a total of 63 parentage confirmed paternity cases contained at least one mismatched locus have been collected.The mutations were subsequently evaluated using Verogen’s MPSForenSeqTM DNASignature Kit and a microsatellite instability(MSI)detection kit.The result showed 98.41%(62/63)of the cases had no additional autosomal mutations even when the number of A-STRs increased to 27.As for the sex chromosomes,about 11.11%(7/63)of the cases exhibited either X-STR or Y-STR mutations.D2S1338,FGAand Penta Ewere the most frequent altered STRs,which suggested they might be the mutation hotspots.In addition,a male with sex chromosome abnormality was observed accidently,whose genotype might be 47,XXY,rather than MSI.Nearly 56.90%of the STR loci possessed isoalleles,which might result in higher STR polymorphisms.No Mendelian incompatibility was detected among the SNP markers,which indicated that SNP was a more reliable genetic marker in the genetic-inconsistent paternity cases.展开更多
Laboratory medicine is an essential part of the diagnostic process,supporting clinical decisions,guiding and addressing therapy.The recent COVID-19 pandemic illustrated well the key role of laboratory medicine in the ...Laboratory medicine is an essential part of the diagnostic process,supporting clinical decisions,guiding and addressing therapy.The recent COVID-19 pandemic illustrated well the key role of laboratory medicine in the diagnosis,management and prognosis of SARS-CoV-2 infected patients.Technological advances improved the laboratory diagnosis and patients’management and others appear very promising as clustered regularly interspaced short palindromic repeats(CRISPR)or artificial intelligence(AI).This review describes the current diagnostic assays routinely used in laboratory as well as the novel technologies not in routine yet but that represent future directions and will probably dominate the laboratory in the next years.Serology is important for detecting antibodies and/or antigens of the infectious pathogens or for epidemiological purposes,while real-time PCR with its high sensitivity and specificity has a key role in pathogen detection in different biological matrices and in monitoring the therapy.Nanochip-based technologies make possible delivering a laboratory report at the patient’s bed or in settings where a laboratory-based hospital is not available.Next generation sequencing(NGS)is a massively high throughput parallel sequencing technology that allows the simultaneous sequence of billions of DNA fragments in a short time frame.This technology can be used to detect drug-associated mutations,minority species within an infected patient or for pathogen identification.CRISPR-based technology is a fast and accurate diagnostic method that can be applied to different human diseases including infectious diseases.Artificial intelligence is increasingly used in laboratory medicine.In clinical microbiology,it is used to build up diagnosis analyzing genomic information or mass spectra from isolated bacteria,for predicting antibiotic sensitivity or for processing in a short time a large number of images with meaningful results.Thus,the laboratory is becoming increasingly automated and interwoven with sophisticated software or algorithms that will increase the sensitivity and specificity of diagnoses,besides reducing time to results.展开更多
Objective To determine the nosogenetic factors of a 46,XY female with primary amenorrhea and unilateral mixed germ cell tumor.Methods Eight genes associated with 46,XY gonadal dysgenesis were detected in the patient a...Objective To determine the nosogenetic factors of a 46,XY female with primary amenorrhea and unilateral mixed germ cell tumor.Methods Eight genes associated with 46,XY gonadal dysgenesis were detected in the patient and her parents by target region captured-next generation sequencing.Results An insertion of a single nucleotide（adenine） at the coding site 230（c.230231insA） located in the high mobility group（HMG） domain of SRY was revealed,which led to a truncated protein（p.Lys77 fsX 27）. This mutation was at position 2655414 of the Y chromosome, supported with 127 unique mapped reads, however, this mutation was not found in the in-house dataset of 1 092 controls. Additionally, none of the candidate gene was detected in the patient’s parents, which indicated that it is a de novo mutation.Conclusion A novel SRY sporadic mutation due to a single nucleotide insertion at position 230（c.230231insA） was identified as the cause of the disease in this patient.Target region captured-next generation sequencing was found to be an effective method for the molecular genetic testing of 46,XY complete gonadal dysgenesis（46,XY CGD）.展开更多
文摘The next generation sequencing （NGS） is an important process which assures inexpen- sive organization of vast size of raw sequence dataset over any traditional sequencing systems or methods. Various aspects of NGS such as template preparation, sequencing imaging and genome alignment and assembly outline the genome sequencing and align- ment. Consequently, de Bruijn graph （dBG） is an important mathematical tool that graphically analyzes how the orientations are constructed in groups of nucleotides. Basi- cally, dBG describes the formation of the genome segments in circular iterative fashions. Some pivotal dBG-based de novo algorithms and software packages such as T-IDBA, Oases, IDBA-tran, Euler, Velvet, ABYSS, AllPaths, SOAPde novo and SOAPde novo2 are illustrated in this paper. Consequently, overlap layout consensus （OLC） graph-based algorithms also play vital role in NGS assembly. Some important OLC-based algorithms such as MIRA3, CABOG, Newbler, Edena, Mosaik and SHORTY are portrayed in this paper. It has been experimented that greedy graph-based algorithms and software pack- ages are also vital for proper genome dataset assembly. A few algorithms named SSAKE, SHARCGS and VCAKE help to perform proper genome sequencing.
基金supported by a grant from Department of Education of Zhejiang Province(Y201636437)
文摘As a relatively uncommon orphan tumor with high mortality,biliary tract cancer(BTC)presents an aggressive course and heterogeneous clinical features[1].BTC patients present with advanced manifestations[2].Unfortunately,there has been little progress in the management of BTC.Most patients have inoperable lesions and must receive palliative therapy.Gemcitabine-based chemotherapy has been the only widely accepted first-line treatment for advanced BTC[3].Nevertheless,BTCs are often refractory to chemotherapeutic regimens,leading to a poor clinical outcome in these patients.Recently,with the rapid development of next generation sequencing(NGS)technologies,some actionable mutations such as those in IDH1,FGFR2,BRAF,HER2 genes,and unique molecular subsets in BTCs have been identified[4],and related targeted therapy against actionable mutations has been introduced into clinical practice as a promising therapeutic strategy[5].
基金supported by the Chinese Academy of Sciences(Strategic Priority Research Program XDB11020300)National Natural Science Foundation of China(31570252,31601629)+1 种基金the start-up fund of"One Hundred Talents"program of the Chinese Academy of Sciences and by the grants from the State Key Laboratory of Plant Genomics(O8KF021011)the Key Laboratory of Urban Agriculture(North)of Ministry of Agriculture of China Beijing University of Agriculture(KFK2015001)
文摘Rice blast caused by Magnaporthe oryzae （M. oryzae） is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among different isolates of M. oryzae in nature, we re-sequenced the genomes of two field isolates, CH43 and Zhong-10-8-14, which showed distinct pathogenecity on most of the rice cultivars. Genome-wide genetic variation analysis reveals that ZHONG-10-8-14 exhibits higher sequence variations than CH43. Structural variations （SVs） detection shows that the sequence variations primarily occur in exons and intergenic regions. Bioinformatics analysis for gene variations reveals that many pathogenecity-related pathways are enriched. In addition, 193 candidate effectors with various DNA polymorphisms were identified, including two known effectors AVR-Pik and AVR-Pital. Comparative polymorphism analysis of thirteen randomly selected effectors suggests that the genetic variations of effectors are under positive selection. The expression pattern analysis of several pathogenecity-related variant genes indicates that these genes are differentially regulated in two isolates, with much higher expression levels in Zhong-10-8-14 than CH43. Our data demonstrate that the genetic variations of effectors and pathogenecity-related genes are under positive selection, resulting in the distinct pathogeuicities of CH43 and Zhong- 10-8-14 on rice.
基金The authors would like to thank Jueqin Yang for assistance with sample preparation. The authors would also like to thank the Fred Hutchinson Cancer Research Center IHWG Cell and Gene Bank for providing reference genomic DNA samples. This work was supported through grants from the National Natural Science Foundation of China （NSF-30830093） and the National Key Program （973） for Basic Research of China （2009CB522409） to HJ. Supplementary Information accompanies the paper on Cellular ＆ Molecular Immunology website.
文摘HLA-A＊02 is the most prevalent and polymorphic major histocompatibility complex （MHC） allele family in humans. Functional differences have been revealed among subtypes, demanding further subtyping of HLA-A＊02 in basic and clinical settings. However, the fast growing polymorphisms render traditional primeror probe-based typing methods impractical and result in increasing ambiguities in direct sequence-based typing. In this study, we combined group-specific amplification and mono-allelic sequencing to design and validate a simple scheme for the complete screening and accurate subtyping of all 540 reported HLA-A＊02 alleles. This scheme could be performed in routine labs to facilitate studies with an interest in HLA-A＊02.
文摘Cyanobacterial harmful algal blooms are a major threat to freshwater eco-systems globally. To deal with this threat, researches into the cyanobacteria bloom in fresh water lakes and rivers have been carried out all over the world. This review presents an overlook of studies on cyanobacteria blooms. Conventional studies mainly focus on investigating the environmental factors influencing the blooms, with their limitation in lack of viewing the microbial community structures. Metagenomics study provides insight into the internal community structure of the cyanobacteria at the blooming, and there are researchers reported that sequence data was a better predictor than environmental factors. This further manifests the significance of the metagenomic study. However, large number of the latter appears to be confined only to present snapshoot of the microbial community diversity and structure. This type of investigation has been valuable and important, whilst an effort to integrate and coordinate the conventional approaches that largely focus on the environmental factors control, and the Metagenomics approaches that reveals the microbial community structure and diversity, implemented through machine learning techniques, for a holistic and more comprehensive insight into the cause and control of Cyanobacteria blooms, appear to be a trend and challenge of the study of this field.
文摘Plant genetic resources collection and utilization had made a huge impact in balancing the genetic diversity of the existing crop plant species and their application in genome based studies had also increased widely. Primarily studies were based on model species, although it now enhances the transferability of information to crops and related species. With the tremendous outbreak of new high-throughput technologies like next-generation sequencing (NGS) and reduction in their costs are bringing many more plants within the range of genome and transcriptome level analysis. The completion of reference genome sequences for many important crops and the ability to perform high-throughput resequencing are providing opportunities for improving our understanding of the crop plant genetic resources to accelerate crop improvement. The future of crop improvement will be centred on comparisons of individual crop plant genomes, and some of the best opportunities may lie in using combinations of new genetic mapping strategies and evolutionary analyses to direct and optimize the discovery and use of genetic variation. Here I review the importance of crop plant genetic resources and insights that have been emerged in recent years.
文摘Common variable immunodeficiency disorders(CVID),a heterogeneous group of inborn errors of immunity,is the most common symptomatic primary immunodeficiency disorder.Patients with CVID have highly variable clinical presentation.With the advent of whole genome sequencing and genome wide association studies(GWAS),there has been a remarkable improvement in understanding the genetics of CVID.This has also helped in understanding the pathogenesis of CVID and has drastically improved the management of these patients.A multiomics approach integrating the DNA sequencing along with RNA sequencing,proteomics,epigenetic and metabolomics profile is the need of the hour to unravel specific CVID associated disease pathways and novel therapeutic targets.In this review,we elaborate various techniques that have helped in understanding the genetics of CVID.
基金This study was supported by grants from the National Youth Top-notch Talent of Ten Thousand Program(WRQB2019)the Youth Science and Technology Innovation Leader of Ten Thousand Program(2018RA2102).
文摘Mutations might challenge the paternity index calculation in forensic identification.While many studies have focussed on the autosomal short tandem repeats(A-STR),the mutation status of sex chromosomes and single nucleotide polymorphism(SNP)remain blank.Next generation sequencing(NGS),known as high throughput and large sequence polymorphism,is a promising tool for forensic genetics.To describe the mutation landscapes in the paternity cases with genetic inconsistencies,a total of 63 parentage confirmed paternity cases contained at least one mismatched locus have been collected.The mutations were subsequently evaluated using Verogen’s MPSForenSeqTM DNASignature Kit and a microsatellite instability(MSI)detection kit.The result showed 98.41%(62/63)of the cases had no additional autosomal mutations even when the number of A-STRs increased to 27.As for the sex chromosomes,about 11.11%(7/63)of the cases exhibited either X-STR or Y-STR mutations.D2S1338,FGAand Penta Ewere the most frequent altered STRs,which suggested they might be the mutation hotspots.In addition,a male with sex chromosome abnormality was observed accidently,whose genotype might be 47,XXY,rather than MSI.Nearly 56.90%of the STR loci possessed isoalleles,which might result in higher STR polymorphisms.No Mendelian incompatibility was detected among the SNP markers,which indicated that SNP was a more reliable genetic marker in the genetic-inconsistent paternity cases.
文摘Laboratory medicine is an essential part of the diagnostic process,supporting clinical decisions,guiding and addressing therapy.The recent COVID-19 pandemic illustrated well the key role of laboratory medicine in the diagnosis,management and prognosis of SARS-CoV-2 infected patients.Technological advances improved the laboratory diagnosis and patients’management and others appear very promising as clustered regularly interspaced short palindromic repeats(CRISPR)or artificial intelligence(AI).This review describes the current diagnostic assays routinely used in laboratory as well as the novel technologies not in routine yet but that represent future directions and will probably dominate the laboratory in the next years.Serology is important for detecting antibodies and/or antigens of the infectious pathogens or for epidemiological purposes,while real-time PCR with its high sensitivity and specificity has a key role in pathogen detection in different biological matrices and in monitoring the therapy.Nanochip-based technologies make possible delivering a laboratory report at the patient’s bed or in settings where a laboratory-based hospital is not available.Next generation sequencing(NGS)is a massively high throughput parallel sequencing technology that allows the simultaneous sequence of billions of DNA fragments in a short time frame.This technology can be used to detect drug-associated mutations,minority species within an infected patient or for pathogen identification.CRISPR-based technology is a fast and accurate diagnostic method that can be applied to different human diseases including infectious diseases.Artificial intelligence is increasingly used in laboratory medicine.In clinical microbiology,it is used to build up diagnosis analyzing genomic information or mass spectra from isolated bacteria,for predicting antibiotic sensitivity or for processing in a short time a large number of images with meaningful results.Thus,the laboratory is becoming increasingly automated and interwoven with sophisticated software or algorithms that will increase the sensitivity and specificity of diagnoses,besides reducing time to results.
基金supported by grants of the Tianjin Binhai New Area Science and Technology Commission(No.2011-BK120011)Shenzhen Engineering Laboratory for Clinical Molecular Diagnostic,the Shenzhen Municipal Government of China(No.CXZZ20130517144604091)and China National GeneB ank-Shenzhen
文摘Objective To determine the nosogenetic factors of a 46,XY female with primary amenorrhea and unilateral mixed germ cell tumor.Methods Eight genes associated with 46,XY gonadal dysgenesis were detected in the patient and her parents by target region captured-next generation sequencing.Results An insertion of a single nucleotide（adenine） at the coding site 230（c.230231insA） located in the high mobility group（HMG） domain of SRY was revealed,which led to a truncated protein（p.Lys77 fsX 27）. This mutation was at position 2655414 of the Y chromosome, supported with 127 unique mapped reads, however, this mutation was not found in the in-house dataset of 1 092 controls. Additionally, none of the candidate gene was detected in the patient’s parents, which indicated that it is a de novo mutation.Conclusion A novel SRY sporadic mutation due to a single nucleotide insertion at position 230（c.230231insA） was identified as the cause of the disease in this patient.Target region captured-next generation sequencing was found to be an effective method for the molecular genetic testing of 46,XY complete gonadal dysgenesis（46,XY CGD）.
