简介：AbstractAlthough whole-exome sequencing and whole-genome sequencing has tremendously improved our understanding of the genetic etiology of human disorders, about half of the patients still do not receive a molecular diagnosis. The high fraction of variants with uncertain significance and the challenges of interpretation of noncoding variants have urged scientists to implement RNA sequencing (RNA-seq) in the diagnostic approach as a high throughput assay to complement genomic data with functional evidence. RNA-seq data can be used to identify aberrantly spliced genes, detect allele-specific expression, and identify gene expression outliers. Amongst eight studies utilizing RNA-seq, a mean diagnostic uplift of 15% has been reported. Here, we provide an overview of how RNA-seq has been implemented to aid in identifying the causal variants of Mendelian disorders.

简介：AbstractCell-cell communication is the basis of physiological processes and cell signals. The disease occurs when the cells do not adequately communicate and the messages are blocked. With ligand-receptor interaction databases and single-cell RNA sequencing (scRNA-seq) databases, we can detect intercellular signaling and reconstruct the cell-cell communications among different cell types. This review summarized the computational approaches for analyzing the cell-cell communication based on scRNA-seq data and discussed its applications in carcinogenesis and COVID-19. We believe that this review will accelerate the scRNA-seq data deciphering and facilitate the cell-cell communication studies for complex physiological processes, such as carcinogenesis and SARS-CoV-2 infection.

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简介：AbstractTargeted sequencing and whole exome sequencing are the most common approaches used to detect causative variants in Mendelian diseases; however, using DNA-based sequencing techniques, the current molecular diagnostic yield is at best 50%. In recent years, RNA sequencing has been shown to be able to provide a genetic diagnosis in patients whose conditions were previously unable to be identified by DNA analysis. RNA sequencing can reveal expression outliers, aberrant splicing events, allele-specific expression, and new pathogenic variants, and as such can complement and expand on the traditional genomic methods used to diagnose Mendelian diseases. Therefore, RNA sequencing is expected to become a routine method for genetic diagnosis in the future. This article reviews the applications and challenges of RNA sequencing in the genetic diagnosis of Mendelian diseases.

简介：AbstractSFTS virus (SFTSV) is a novel bunyavirus, which was discovered as the etiological agent of severe fever with thrombocytopenia syndrome (SFTS) in China in 2009, and was now prevalent in at least 25 provinces in China. SFTS was subsequently identified in South Korea and Japan in 2012. To explore the molecular evolution and genetic characteristics of this newly identified pathogen, we reported 72 whole genome sequences of SFTSV, and built a dataset of SFTSV genome sequences containing 292 L-segment, 302 M-segment and 502 S-segment. We clearly divided SFTSV into six genotypes, Genotype A-F. It was found that genotype F was the dominant epidemic genotype of Japan, South Korea, and Zhejiang province of China. The coalescent analysis supported that SFTSV originated in the early 18th century from Zhejiang province, and Genotype F was the most primitive one. Henan, Hubei, and Anhui provinces which are located in Dabie Mountain area were mainly epidemic of Genotype A, which emerged relatively late but distributed widely. A total of 37 recombination events were identified, making SFTSV with a high recombination frequency (L segment 5.1%, M segment 3.6%, S segment 0.8%) among negative-strand segmented RNA viruses. It was identified that 19 reassortant strains belonged to 12 reassortment forms of SFTSV genome containing 6 newly identified forms. The reassortment virus and recombination in tick were both found for the first time. We also found many of genotype-specific mutation sites, 7 of which could be considered as potential molecular marker for genotype classification. This study promoted a more comprehensive understanding of the phylogeny and origin, and the genetic diversity of SFTSV, and it could help the studies of other newly discovered tick-borne bunyavirus as reference data and research ideas.

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简介：Inordertostudythefunctionalstructureofthetranscriptionterminatorsandthemechanismoftemination,asurveyofthechromatinstructure,includingthelocationofDNaseIhypersensitivesitesandthenucleosomearrangement,ofyeastADH1andFLPterminatorswasmade.TheresultsshowthatthereisnorelationshipbetweenthefunctionoftheterminatorsandtheexistenceofDNaseIhypersensitivesites.However,itisfoundthatthereisalwaysanucleosmoeattheimmediateupstreamofthetranscriptionalterminationsites.Asacontrol,thechromatinstructuresofthepBR322DNAfragmentsontheyeastshuttervectorsarealsoinvestigatedatthesametime.TherandomnucleosomearrangementonthebacterialDNAinyesastagreeswiththepublishedreports.Anewhypothesis,aboutthemechanismoftranscriptionalterminationisputforwardandthereasonofdifferentnucleosomearrengementontheDNAswhichareoriginallyfromdifferentspeciesinyeastisdiscussed.

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简介：Inordertostudythefunctionalstructureofthetranscriptionterminatorsandthemechanismoftermination,asurveyofthechromatinstructure,includingthelocationofDNaseIhypersensitivesitesandthenucleosomearrangement,ofyeastADH1andFLPterminatorswasmade.TheresultsshowthatthereisnorelationshipbetweenthefunctionoftheterminatorsandtheexistenceofDNaseIhypersensitivesites.However,itisfoundthatthereisalwaysanucleosomeattheimmediateupstreamofthetranscrip-tionalterminationsites.Asacontrol,thechromatinstructuresofthepBR322DNAfragmentsontheyeastshuttervectorsarealsoinvestigatedatthesametime.TherandomnucleosomearrangementonthebacterialDNAinyeastagreeswiththepublishedreports.Anewhypothesis,aboutthemechanismoftranscriptionalterminationisputforwardandthereasonofdifferentnucleosomearrangementontheDNAswhichareori-ginallyfromdifferentspeciesinyeastisdiscussed.

简介：Saccharina是最重要的无热水设备生活水兵褐之一海藻的类。在这研究，我们分析了S的transcriptome。装饰用的梨树，它属于1000植物(OneKP)工程，由使用定序技术的下一代的高产量的DNA。未加工的数据的大约5.16GB被产生，并且有454bp的平均长度的65536脚手架与肥皂denovo汇编方法被装配。总共，19040unigenes被强风识别；25734脚手架被聚类进37基因本体论功能的组；6760脚手架被分类进25个轮牙范畴，以及被分到306条KEGG小径的2665脚手架。unigenes的多数比另外的cyanobacteria，海洋的硅藻，和植物包括棕色的水藻和硅藻展出了更多的类似到水藻。Saccharina装饰用的梨树有突出的能力积累象Br那样的卤素，我从海水经由halogenation处理。我们在S获得了42不同钒依赖者haloperoxidases(vHPO)。装饰用的梨树transcriptome数据，包括钒依赖者iodoperoxidase(vIPO)的5个片断和钒依赖者bromoperoxidase(vBPO)的37个片断。识别fulllengthS的复杂分析。装饰用的梨树vBPO1和S。装饰用的梨树vBPO2在在海洋的海藻的vBPOs和vIPOs之间的棕色的水藻和强壮的关系的种类之中揭示了vBPO的重要性。这研究将提高我们生物特征的理解和S的经济价值。装饰用的梨树种类。

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简介：AbstractBackground:Rectal cancer (RC) is a malignant tumor that seriously threatens human health. Long non-coding RNAs (lncRNAs) play a vital role in tumor regulation. Nevertheless, their exact expression features and functions remain obscure, and therefore was the aim of the current study.Methods:We utilized the Affymetrix human GeneChip to screen differentially expressed profiles of lncRNAs and mRNAs from the cancer tissues and matched paracancer tissues of 6 RC patients. Gene Ontology (GO) and pathway enrichment analyses identified crucial functions and pathways of the aberrantly expressed mRNAs. We used quantitative real-time polymerase chain reaction to verify the significant expression differences of 11 candidate lncRNAs between the cancer and paracancer tissues. LncRNA-mRNA coexpression networks were built by calculating the Pearson correlation value to identify significant correlation pairs. Online bioinformatics tools GEPIA2, ONCOMINE, and PROGgeneV2 were used to mine the expression and prognosis of three crucial mRNAs and six verified lncRNAs. Competing endogenous RNA networks were constructed by predicting microRNA response elements and calculating free energy.Results:We found 1658 differentially expressed lncRNAs (778 up-regulated and 880 down-regulated) and 1783 aberrantly expressed mRNAs (909 up-regulated and 874 down-regulated). GO and pathway enrichment analyses revealed the vital functions of the differentially expressed mRNAs, including cell proliferation, cell migration, angiogenesis, and cellular response to zinc ion. The canonical signaling pathways mainly included the interleukin-17, cell cycle, Wnt, and mineral absorption signaling pathways. Six lncRNAs including AC017002.2 (P= 0.039), cancer susceptibility 19 (CASC19) (P= 0.021), LINC00152 (P= 0.013), NONHSAT058834 (P= 0.007), NONHSAT007692 (P= 0.045), and ENST00000415991.1 (P= 0.045) showed significant differences in expression levels between the cancer tissue and paracancer tissue groups. AC017002.2, NONHSAT058834, NONHSAT007692, and ENST00000415991.1 have not yet been reported in RC. The crucial mRNAs myelocytomatosis viral oncogene (MYC), transforming growth factor beta induced (TGFBI), and solute carrier family 7 member 5 (SLC7A5) were selected. AC017002.2 and LINC00152 were positively correlated with MYC, TGFBI, and cytochrome P450 family 2 sub-family B member 6 (All r > 0.900, P < 0.050). NONHSAT058834 was positively associated with MYC (r = 0.930, P < 0.001), and CASC19 was positively correlated with SLC7A5 (r= 0.922, P < 0.001).Conclusion:This study offers convincing evidence of differentially expressed lncRNAs and mRNAs as potential biomarkers in RC.

简介：18SribosomalDNA基因(18SrDNA)序列(近似在长度的1300bp)从从与线虫大批从Qingdao海岸的内部潮汐的沉积收集的免费生活的海洋的线虫提取的DNA被放大特定的教材。PCR产品被克隆，重新放大，与Rsa消化了我和Hin6我限制endonucleases和分开的inagarose胶化。在17种限制碎片长度类型之中，打1，2和6盖住61.2%，分别地，当时，克隆的14.4%and9.3%分析了留下14仅仅盖住21克隆，它说明了15.1%总数。24代表性的克隆andphylogenetically被定序由指在RDP和GenBank数据库当前可得到的那些分析了。尽管它是难的由于已知的海洋的免费生活的线虫的18SrDNA顺序数据的缺乏把这些序列分到已知的种类或类，获得的序列被分到Adenophorea的线虫。在他们之中，12个序列接近了PontonemavulgareandAdoncholaimussp，四到Daptonemaprocerus并且二(相同)到Enoplusbrevis。我们的结果证明免费生活的海洋的线虫差异能被检索的PCR决定，18SrDNA的分析定序，仅当免费生活的海洋的线虫的18SrDNA序列被积累到某程度，一个18SrDNA序列能被分到种或一个类。

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简介：Next-generationsequencing(NGS)isanewtechnologyusedforDNAandRNAsequencingandvariant/mutationdetection.NGScansequencehundredsandthousandsofgenesorwholegenomeinashortperiodoftime.Thesequencevariants/mutationsdetectedbyNGShavebeenwidelyusedfordiseasediagnosis,prognosis,therapeuticdecision,andfollowupofpatients.Thecapacityofitsmassiveparallelsequencingoffersnewopportunitiesforpersonalizedprecisionmedicine.

简介：六不同治疗在与变形阉割抵抗的前列腺癌症(mCRPC)指向到病人的阶段III试用表明了改进幸存。为mCRPC的前线的治疗学的选择包括docetaxel，sipuleucel-T，abiraterone和radium-223。Post-docetaxel选择包括cabazitaxel，abiraterone，enzalutamide和radium-223。尽管有最近的年里的许多进步，多是还未知的，争论发生在最佳的治疗选择和序列上。任何一个新代理人都没与对方相比，因此，在今天的实践的医生必须基于非使随机化的比较，毒性考虑和各种各样的假设做选择。Abiraterone现在正在移动直到给最近的规章的赞同的前面线mCRPC空间，enzalutamide将很快列在后面。当时，两个神经质的代理人有更少的毒性与化学疗法的选择和这两个神经质的代理人相比被期望向前在年里在mCRPC病人的一个可观的数字被过去常。很少数据都不为post-abiraterone或post-enzalutamide背景是可得到的。在这评论，当前可得到的定序数据被总结并且解释。生气抵抗是在各种各样的治疗之间的一个潜在的问题，现在是清楚的，特别指向雄激素轴的那些代理人。这评论加亮需要让另外的研究为这些病人优化当前的治疗。

简介：TheproblemofpicksequencingintherotaryrackS/Rsystem(PPS-RRS)isinvestigatedwiththeobjectiveofminimizingtheexecutiontime.TherotaryrackS/RsystemconsistsofoneS/Rmachineandmultiplelevelsofcarouselsthatcanrotateindependentlyinbi-directions.Theroutingpolicy,namelythedecisiononthestorageorretrievalsequence,dominatestheefficiencyandthethroughputforsuchS/Rsystems,duetothecomplicatedrelationshipbetweenalllevelsofcarouselsandtheS/Rmachine.ForthepurposeofoptimizingthePPS-RRS,acomputationalmodelisdevelopedintermsofexecutiontimeforpickingmultipleitemsinonetrip.CharacteristicsofthePPS-RRSareanalyzedandalocalsearchheuristicbasedonanewlyproposedneighborhoodispresented.Integratedwiththeproposedlocalsearchprocedureanewhybridgeneticalgorithmisdeveloped.Experimentalresultsdemonstratethestructurecharacteristicsofgoodsequenceandtheefficiencyandeffectivenessoftheproposedsequencingalgorithms.

简介：技术显著地改进了定序产量并且减少的下一代的定序的出现(NGS)花费。然而，短读的长度，副本读并且数据的巨大的体积使处理的数据比归化为美国人的定序技术更困难、复杂。尽管有包裹开发了估计数据质量的某软件，那些包裹任何一个不对用户容易可得到或要求生物信息学技巧和计算机资源。而且，当前可得到的几乎所有优秀评价软件当在NGS数据处理副本评价时，考虑定序的错误。这里，我们在场一个新用户友好的优秀评价软件包裹叫了BIGpre，它为Illumina和454个平台工作。BIGpre包含另外的优秀评价软件的所有函数，例如关联在之间前面、反向读，读GC内容分发，和基础N质量。更重要地，BIGpre合并联系程序检测并且搬迁副本在订定序错误进报道并且整修低质量以后读也从未加工的数据读。BIGpre首先在Perl被写并且从统计包裹R集成图形的能力。这个包裹为从Illumina和454个平台定序数据集生产数据质量的平坦、图形的摘要。处理几百百万在分钟以内读，这个包裹提供立即的诊断信息让用户操作为下游的分析定序数据。BIGpre在http://bigpre.sourceforge.net是自由地可得到的。

简介：ThispapermakesabriefanalysisontheErrorAnalysis,anditishopedtobehelpfutotheEnglishteachers.

简介：AbstractDrug resistance via drug-resistant mutations in the human immunodeficiency virus (HIV) genome is the primary cause of antiviral therapy failure. Consequently, HIV drug resistance genotyping has become a critical approach in HIV prevention and control. Compared to the Sanger sequencing technology, high-throughput sequencing (HTS) technology has superior sensitivity and timeliness, with strong detection capabilities for low-frequency mutations. With the continued advancement of HTS technologies, their prominence in HIV drug resistance detection techniques has increased accordingly. This article will review the latest developments in HTS technology and its applications in HIV drug resistance testing.