Objectives:Intravesical Bacillus Calmette-Guérin(BCG)therapy is a gold standard for patients with high-risk non-muscle invasive bladder cancer(NMIBC).Although a long-lasting therapeutic response is observed in mo...Objectives:Intravesical Bacillus Calmette-Guérin(BCG)therapy is a gold standard for patients with high-risk non-muscle invasive bladder cancer(NMIBC).Although a long-lasting therapeutic response is observed in most patients,BCG failure occurs in 30%–50%of patients and a progression to muscle-invasive disease is found in 10%–15%.Therefore,predicting high-risk patients who might not benefit from BCG treatment is critical.The purpose of this study was to identify,whether the presence of specific oncogenic mutations might be indicative of BCG treatment response.Methods:Nineteen high-grade NMIBC patients who received intravesical BCG were retrospectively enrolled and divided into“responders”and“non-responders”groups.Tissue samples from transurethral resection of bladder cancer were performed before starting therapy and were examined using a multigene sequencing panel.Results:Mutations in TP53,FGFR3,PIK3CA,KRAS,CTNNB1,ALK and DDR2 genes were detected.TP53 and FGFR3 were found to be the most frequently mutated genes in our cohort(31.6%and 26.3%,respectively),followed by PIK3CA(15.8%).In the BCG-responsive patient group,90%of samples were found to have mutated genes,with almost 50%of them showing mutations in tyrosine kinase receptors and CTNNB1 genes.On the other hand,in the BCG-unresponsive group,we found mutations in 44.4%of samples,mainly in TP53 gene.Conclusions:Our findings suggest that a Next-Generation Sequencing(NGS)multigene panel is useful in predicting BCG response in patients with NMIBC.展开更多
Korean freshwater snails of the genus Semisulcospira are widely distributed across East Asia.It has been a very popular nutritional food in Korea,and is an ecologically important water quality indicator because it liv...Korean freshwater snails of the genus Semisulcospira are widely distributed across East Asia.It has been a very popular nutritional food in Korea,and is an ecologically important water quality indicator because it lives only in clean water.However,no microsatellite markers have been generated to study the population genetic diversity of this genus.In the present study,we developed and characterized 18 novel microsatellite loci from Semisulcospira coreana genomic DNA.The microsatellites were isolated using 454 GS-FLX titanium sequencing and 18 markers were used for genotyping in S.coreana.In addition,we also tested the cross-species transferability of the microsatellite markers in four additional Semisulcospira spp.We identified 18 polymorphic loci and the number of alleles per loci,and their polymorphism information content values ranged from 2 to 17 and 0.203 to 0.902,respectively.The observed and expected heterozygosities of the loci ranged from 0.063 to 0.924 and 0.226 to 0.924,respectively.According to the analysis of the cross-species transferability of these markers,four species,S.forticosta,S.gottschei,S.tegulata,and S.libertina,showed a very high transferability(80%–85%).These results show that this set of nuclear markers could be useful for population genetics studies of this species and closely related species.展开更多
Assessments of phytoplankton diversity in Sabah waters,North Borneo,have primarily relied on morphology-based identification,which has inherent biases and can be time-consuming.Next-Generation Sequencing(NGS)technolog...Assessments of phytoplankton diversity in Sabah waters,North Borneo,have primarily relied on morphology-based identification,which has inherent biases and can be time-consuming.Next-Generation Sequencing(NGS)technology has been shown to be capable of overcoming several limitations of morphology-based methods.Samples were collected from the Sepanggar Bay over the course of the year 2018 in different monsoon seasons.Morphology-based identification and NGS sequencing of the V8–V9 region of the 18S LSU rDNA were used to investigate the diversity of the phytoplankton community.Microscopy and NGS showed complementary results with more diatom taxa detected by microscopy whereas NGS detected smaller and rarer taxa.The harmful algal genera in the study site comprised of Skeletonema,Margalefidinium,Pyrodinium,Takayama,and Alexandrium as detected by NGS.This study showed that that an integrative approach of both morphological and molecular techniques could provide more comprehensive information about the phytoplankton community as the approach captured quantitative variability as well as the diversity of phytoplankton species.展开更多
【Background】The application of beneficial-microbial seed soaking prior to sowing represents a novel technology that has not been employed in Lanzhou lily cultivation.We conducted an experiment to explore the impact ...【Background】The application of beneficial-microbial seed soaking prior to sowing represents a novel technology that has not been employed in Lanzhou lily cultivation.We conducted an experiment to explore the impact of this soaking method on the fungal and bacterial community structures using next-generation sequencing technology(NGS).【Methods】Lily bulbs were soaked in a seed treating agent containing beneficial microbes(SP treatment)for 4 hours.Subsequently,they were planted in soil in July and sampled in September to assess plant growth,rhizosphere soil physicochemical properties,and microorganism community structures.In addition,we employed the software PICRUSt and FUNGuild to predict bacterial pathways and fungal functions.【Results】Under SP treatment,there were significant alterations in fungi and bacteria community structures,accompanied by improved soil nutrient status.Notably,the relative abundance of dominant microorganism groups,such as the fungi Basidiomycota,Pseudeurotium,Cladophialophora,Microascus,and Dactylonectria,as well as the bacteria Proteobacteria,Chloroflexi,Ochrobactrium,Lysobacter,and RB41,underwent notable changes.Microorganism function prediction results indicated a reduction in pathotrophic fungi(including plant pathogens)and an increase in endophytic and saprotrophic fungi under SP treatment.Among the top 20 metabolism pathways,80%were upregulated in SP treatment compared to the CK.【Conclusions】Seed soaking with beneficial microbial strain promotes the growth of Lanzhou lily bulbs.The beneficial microorganisms play a crucial role in regulating soil microbial structures,enhancing the accumulation of endophytic fungi,reducing the abundance of pathogens,and improving soil functions.Furthermore,specific microbial groups are found to be involved in maintaining soil health.展开更多
Background:Precision medicine is an emerging approach for treating pediatric cancer due to its ability to target tumor-specific genetic drivers rather than provide broad and aggressive treatments.The study aimed to ou...Background:Precision medicine is an emerging approach for treating pediatric cancer due to its ability to target tumor-specific genetic drivers rather than provide broad and aggressive treatments.The study aimed to outline the establishment and impact of a Precision Medicine Clinic(PMC)in the setting of pediatric oncology,with the objective of offering targeted treatment options within the institution and creating a scalable model for adoption by other healthcare systems to achieve a wider impact.Methods:Recognizing this need for an individualized approach to treating patients,Cook Children’s Medical Center(CCMC)established a multidisciplinary molecular tumor board in 2019,followed by the launch of an official PMC in 2021.Before this,there was no dedicated place to discuss and evaluate genetic sequencing results.Results:In 2022 and 2023,the PMC discussed 69 patients with a wide variety of oncologic diagnoses.Through the clinic’s efforts,133 genetic variants across 101 genes have been identified,spanning oncogenic pathways related to cell cycling,DNA processing,and cell signaling.Of the sequenced patients,four have received targeted therapy according to recommendations from the PMC.Conclusion:While the PMC continues to evaluate patients and their long-term outcomes,the continually growing PMC at CCMC represents the beginning of the advancement of treating pediatric oncology patients through the interpretation of genetic sequencing results,making actionable targeted treatment recommendations,and continuing to follow the patient’s course of care over time.This additionally provides a framework for starting a PMC that can be adapted for specific clinical needs and implemented broadly.展开更多
Non-small cell lung cancer(NSCLC)accounts for the majority of lung cancer cases and remains the leading cause of cancer-related mortality worldwide.Firstly,this review explores the limitations of conventional therapie...Non-small cell lung cancer(NSCLC)accounts for the majority of lung cancer cases and remains the leading cause of cancer-related mortality worldwide.Firstly,this review explores the limitations of conventional therapies,chemotherapy,radiotherapy,and surgery,focusing on the development of drug resistance and significant toxicity that often hinder their efficacy.Thereafter,advancements in targeted therapies,such as immune checkpoint inhibitors(ICIs)and tyrosine kinase inhibitors(TKIs),are discussed,highlighting their impact on improving outcomes for patients with specific genetic mutations,including c-ros oncogene 1 receptor tyrosine kinase(ROS1),anaplastic lymphoma kinase(ALK),and epidermal growth factor receptor(EGFR).Additionally,the emergence of novel immunotherapies and phytochemicals is examined,emphasizing their potential to overcome therapeutic resistance,particularly in advanced-stage diseases.The review also delves into the role of next-generation sequencing(NGS)in enabling personalized treatment approaches and explores the clinical potential of innovative agents,such as bispecific T-cell engagers(BiTEs)and antibody-drug conjugates(ADCs).Finally,we address the socioeconomic barriers that limit the accessibility of these therapies in low-resource settings and propose future research directions aimed at improving the long-term efficacy and accessibility of these treatments.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
To identify the possible quarantine viruses in seven common sunflower varieties imported from the United States of America and the Netherlands, we tested total RNAs extracted from the leaf tissues using next-generatio...To identify the possible quarantine viruses in seven common sunflower varieties imported from the United States of America and the Netherlands, we tested total RNAs extracted from the leaf tissues using next-generation sequencing of small RNAs. After analysis of small RNA sequencing data, no any quarantine virus was found, but a double-stranded RNA（dsRNA） molecule showing typical genomic features of endornavirus was detected in two varieties, X3939 and SH1108. Full-length sequence and phylogenetic analysis showed that it is a novel endornavirus, temporarily named as Helianthus annuus alphaendornavirus（HaEV）. Its full genome corresponds to a 14 662-bp dsRNA segment, including a 21-nt 5′ untranslated region（UTR）, 3＇ UTR ending with the unique sequence CCCCCCCC and lacking a poly（A） tail. An open reading frame（ORF） that encodes a deduced 4 867 amino acids（aa） polyprotein with three domains： RdRP, Hel and UGT（UDP-glycosyltransferase）. HaEV mainly distributed in the cytoplasm but less in the nucleus of leaf cells by fluorescence in situ hybridization（FISH） experiment. This virus has a high seed infection rate in the five varieties, X3907, X3939, A231, SH1108 and SR1320. To our knowledge, this is the first report about the virus of the family Endornaviridae in the common sunflower.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
Precision medicine is revolutionizing global healthcare by enabling personalized diagnostics,disease prediction,and tailored treatment strategies.While the integration of genomics and data science holds immense potent...Precision medicine is revolutionizing global healthcare by enabling personalized diagnostics,disease prediction,and tailored treatment strategies.While the integration of genomics and data science holds immense potential to optimize precision therapeutic outcomes,a critical challenge lies in translating gene sequencing data into actionable insights for in vitro diagnostics.This bottleneck is largely attributed to the limitations of edge-side intelligent processing and automation.Despite advancements in gene sequencing technologies and bioinformatics tools,the workflow from sample collection to diagnostic report generation remains fragmented,inefficient,and lacks of intelligence.To address these challenges,we introduce an embodied LLM NGS sequencer on the edge for real-time,on-site smart genetic diagnostics.This instrument integrates a streamlined and comprehensive pipeline with deep learning networks for primary data analysis,machine learning for secondary data processing,and a large language model(LLM)optimized for tertiary data interpretation.The LLM is enhanced through quantization and compression,facilitating deployment on FPGA/GPU to accelerate diagnostic workflows.Experimental results showcased the superior performance by achieving a 13.72%increase in throughput,a 99.50%Q30%,and enable smart diagnostic on the edge with the performance up to 75 tokens/s.This work enables immediate,on-site DNA analysis,hence dramatically improving precision medicine’s accessibility and efficiency,and significantly advances diagnostic accuracy,automation,establishing a robust platform for AI-driven personalized medicine and setting a new benchmark for the future of healthcare delivery.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
Apis mellifera syriaca exhibits a high degree of tolerance to pests and pathogens including varroa mites. This native honey bee subspecies of Jordan expresses behavioral adaptations to high temperature and dry seasons...Apis mellifera syriaca exhibits a high degree of tolerance to pests and pathogens including varroa mites. This native honey bee subspecies of Jordan expresses behavioral adaptations to high temperature and dry seasons typical of the region. However, persistent honey bee imports of commercial breeder lines are endangering local honey bee population. This study reports the use of next-generation sequencing （NGS） technology to study the A. m. syriaca genome and to identify genetic factors possibly contributing toward mite resistance and other favorable traits. We obtained a total of 46.2 million raw reads by applying the NGS to sequence A. m. syriaca and used extensive bioinformatics approach to identify several candidate genes for Varroa mite resistance, behavioral and immune responses char- acteristic for these bees. As a part of characterizing the functional regulation of molecular genetic pathway, we have mapped the pathway genes potentially involved using information from Drosophila melanogaster and present possible functional changes implicated in responses to Varroa destructor mite infestation toward this. We performed in-depth functional annotation methods to identify -600 candidates that are relevant, genes involved in pathways such as microbial recognition and phagocytosis, peptidoglycan recognition protein family, Gram negative binding protein family, phagocytosis receptors, serpins, Toll signaling pathway, Imd pathway, Tnf, JAK-STAT and MAPK pathway, heamatopioesis and cellular response pathways, antiviral, RNAi pathway, stress factors, etc. were selected. Finally, we have cataloged function-specific polymorphisms between A. mellifera and A. m. syriaca that could give better understanding of varroa mite resistance mechanisms and assist in breeding. We have identified immune related embryonic development （Cactus, Relish, dorsal, Ank2, baz）, Varroa hygiene （NorpA2, Zasp, LanA, gasp, impl3） and Varroa resistance （Pug, pcmt, elk, elf3-s10, Dscam2, Dhc64C, gro, futsch） functional variations genes between A. mellifera and A. m. syriaca that could be used to develop an effective molecular tool for bee conservation and breeding programs to improve locally adapted strains such as syriaca and utilize their advantageous traits for the benefit of apiculture industry.展开更多
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
Porcine epidemic diarrhea virus(PEDV)is the most common diarrhea-causing pathogen in newborn piglets.The clarifications of the overall antibody repertoire and antigen-specific antibody repertoire are essential to prov...Porcine epidemic diarrhea virus(PEDV)is the most common diarrhea-causing pathogen in newborn piglets.The clarifications of the overall antibody repertoire and antigen-specific antibody repertoire are essential to provide important insights into the B-cell response and reshape new vaccines.Here,we applied next-generation sequencing(NGS)technology to investigate immunoglobulin(Ig)variable(V)gene segment usage of swine B-cells from peripheral blood lymphocytes(PBL)and mesenteric lymph node(MLN)cells following PEDV vaccination.We identified the transcripts of all functional Ig V-genes in antibody repertoire.IgHV1 S2,IgKV1-11,and IgLV3-4 were the most prevalent gene segments for heavy,kappa,and lambda chains,respectively,in PBL and MLN.Unlike previous studies,IgKV1,instead of IgKV2,and IgLV3,instead of IgLV8,were the prevalent Ig V-gene families for kappa and lambda light chains,respectively.We further examined the antibody repertoire of PEDV spike-specific B cells by single-cell RT-PCR.In contrast to the overall antibody repertoire,Ig V-gene segments of PEDV spike-specific B cells preferentially adopted IgHV1-4 and IgHV1-14 for heavy chain,IgKV1-11 for kappa chain,and IgLV3-3 for lambda chain.These results represent a comprehensive analysis to characterize the Ig V-gene segment usage in the overall and PEDV spike-specific antibody repertoire in PBL and MLN.展开更多
Oncogenic gene fusions occur across a broad range of cancers and are a defining feature of some cancer types.Cancers driven by gene fusion products tend to respond well to targeted therapies,where available;thus,detec...Oncogenic gene fusions occur across a broad range of cancers and are a defining feature of some cancer types.Cancers driven by gene fusion products tend to respond well to targeted therapies,where available;thus,detection of potentially targetable oncogenic fusions is necessary to select optimal treatment.Detection methods include non-sequencing methods,such as fluorescence in situ hybridization and immunohistochemistry,and sequencing methods,such as DNA-and RNA-based nextgeneration sequencing(NGS).While NGS is an efficient way to analyze multiple genes of interest at once,economic and technical factors may preclude its use in routine care globally,despite several guideline recommendations.The aim of this review is to present a summary of oncogenic gene fusions,with a focus on fusions that affect tyrosine kinase signaling,and to highlight the importance of testing for oncogenic fusions.We present an overview of the identification of oncogenic gene fusions and therapies approved for the treatment of cancers harboring gene fusions,and summarize data regarding treating fusion-positive cancers with no current targeted therapies and clinical studies of fusion-positive cancers.Although treatment options may be limited for patients with rare alterations,healthcare professionals should identify patients most likely to benefit from oncogenic gene fusion testing and initiate the appropriate targeted therapy to achieve optimal treatment outcomes.展开更多
The Human Genome Project marked a milestone in scientific exploration,unraveling the genetic blueprint of humanity.However,expectations of direct gene–disease associations gave way to realizing the complexity of gene...The Human Genome Project marked a milestone in scientific exploration,unraveling the genetic blueprint of humanity.However,expectations of direct gene–disease associations gave way to realizing the complexity of genetic interactions,especially in polygenic diseases.This review explores the legacy of the HGP and subsequent advancements in genomic technologies,particularly next-generation sequencing,which have enabled more profound insights into the non-coding genome's role in gene regulation.While initially dismissed as“junk”DNA,non-coding regions are now officially approved as critical gene expression and genome organization regulators.Through integrative genomics approaches and advanced computational methods,researchers have unveiled the intricate network of enhancers,promoters,and chromatin modifications orchestrating gene expression.High-throughput sequencing techniques and functional assays have identified non-coding variants associated with numerous diseases,challenging the conventional focus on coding sequences in genomic studies.By elucidating the regulatory mechanisms governing gene expression,researchers can advance precision medicine approaches and develop novel diagnostic tools.As genomic research continues to evolve,a vast landscape is waiting to be explored,promising transformative insights into human health and disease.This review provides a comprehensive overview of the non-coding genome's role in gene regulation and its implications for understanding complex diseases and developing targeted therapeutic interventions.展开更多
Background:Liquid biopsy has emerged as a non-invasive method for real-time cancer monitoring especially in genitourinary(GU)oncology.Most current studies utilize a panel-based molecular profiling ranging from 50–600...Background:Liquid biopsy has emerged as a non-invasive method for real-time cancer monitoring especially in genitourinary(GU)oncology.Most current studies utilize a panel-based molecular profiling ranging from 50–600 genes;however,a comprehensive exome-wide profiling of real-world patient samples has been lacking.Methods:Over 2000 liquid biopsy samples were analyzed in this study,including urine samples from early-stage bladder cancer and plasma samples from prostate,lung,breast,esophageal,head and neck cancers,among others.Cell-free DNA(cfDNA)was extracted from these samples and ana-lyzed using PredicineWES+^(TM),a boosted comprehensive whole-exome sequencing(WES)assay with an in-depth coverage of 600 cancer-related genes derived from the PredicineATLAS^(TM)panel.Data analysis was conducted in-house using Predicine's DeepSea bioinformatics software.Results:The PredicineWES+^(TM)assay demonstrated high sensitivity for detecting somatic mutations across the exome and showed comparable tumor mutational burden(TMB)estimates with the PredicineATLAS^(TM)panel.Interestingly,the highest tumor TMB score was observed in bladder cancer among the analyzed cancers,which is consistent with literature using tissue-based genomic profiling.The most common cancer variants include TP53,ERBB2,KRAS,PIK3CA,FGFR3,APC,among others.Conclusion:Liquid biopsy-based genomic profiling across various cancer types provides an in-depth analysis of biomarker discovery for personalized cancer care,setting the foundation for improved cancer diagnosis and per-sonalized treatment strategies for urological diseases.展开更多
Next-generation sequencing data are widely utilised for various downstream applications in bioinformatics and numerous techniques have been developed for PCR-deduplication and error-correction to eliminate bias and er...Next-generation sequencing data are widely utilised for various downstream applications in bioinformatics and numerous techniques have been developed for PCR-deduplication and error-correction to eliminate bias and errors introduced during the sequencing.This study first-time provides a joint overview of recent advances in PCR-deduplication and error-correction on short reads.In particular,we utilise UMI-based PCR-deduplication strategies and sequencing data to assess the performance of the solelycomputational PCR-deduplication approaches and investigate how error correction affects the performance of PCR-deduplication.Our survey and comparative analysis reveal that the deduplicated reads generated by the solely-computational PCR-deduplication and error-correction methods exhibit substantial differences and divergence from the sets of reads obtained by the UMI-based deduplication methods.The existing solelycomputational PCR-deduplication and error-correction tools can eliminate some errors but still leave hundreds of thousands of erroneous reads uncorrected.All the error-correction approaches raise thousands or more new sequences after correction which do not have any benefit to the PCRdeduplication process.Based on our findings,we discuss future research directions and make suggestions for improving existing computational approaches to enhance the quality of short-read sequencing data.展开更多
Transcriptomics is one of the most developed fields in the post-genomic era.Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specif...Transcriptomics is one of the most developed fields in the post-genomic era.Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specific physiological condition,including messenger RNA,transfer RNA,ribosomal RNA,and other non-coding RNAs.Transcriptomics focuses on the gene expression at the RNA level and offers the genome-wide information of gene structure and gene function in order to reveal the molecular mechanisms involved in specific biological processes.With the development of next-generation high-throughput sequencing technology,transcriptome analysis has been progressively improving our understanding of RNA-based gene regulatory network.Here,we discuss the concept,history,and especially the recent advances in this inspiring field of study.展开更多
Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplicati...Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms （SNPs） have become popular tools for genetic mapping, discovery and appli- cation of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs （BWA-mem and Bowtie 2） and variant callers （SAMtools, GATK, and Freebayes）. Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.展开更多
文摘Objectives:Intravesical Bacillus Calmette-Guérin(BCG)therapy is a gold standard for patients with high-risk non-muscle invasive bladder cancer(NMIBC).Although a long-lasting therapeutic response is observed in most patients,BCG failure occurs in 30%–50%of patients and a progression to muscle-invasive disease is found in 10%–15%.Therefore,predicting high-risk patients who might not benefit from BCG treatment is critical.The purpose of this study was to identify,whether the presence of specific oncogenic mutations might be indicative of BCG treatment response.Methods:Nineteen high-grade NMIBC patients who received intravesical BCG were retrospectively enrolled and divided into“responders”and“non-responders”groups.Tissue samples from transurethral resection of bladder cancer were performed before starting therapy and were examined using a multigene sequencing panel.Results:Mutations in TP53,FGFR3,PIK3CA,KRAS,CTNNB1,ALK and DDR2 genes were detected.TP53 and FGFR3 were found to be the most frequently mutated genes in our cohort(31.6%and 26.3%,respectively),followed by PIK3CA(15.8%).In the BCG-responsive patient group,90%of samples were found to have mutated genes,with almost 50%of them showing mutations in tyrosine kinase receptors and CTNNB1 genes.On the other hand,in the BCG-unresponsive group,we found mutations in 44.4%of samples,mainly in TP53 gene.Conclusions:Our findings suggest that a Next-Generation Sequencing(NGS)multigene panel is useful in predicting BCG response in patients with NMIBC.
基金Supported by the National Institute of Fisheries Science of Republic of Korea(Nos.R2019030,R2019033)
文摘Korean freshwater snails of the genus Semisulcospira are widely distributed across East Asia.It has been a very popular nutritional food in Korea,and is an ecologically important water quality indicator because it lives only in clean water.However,no microsatellite markers have been generated to study the population genetic diversity of this genus.In the present study,we developed and characterized 18 novel microsatellite loci from Semisulcospira coreana genomic DNA.The microsatellites were isolated using 454 GS-FLX titanium sequencing and 18 markers were used for genotyping in S.coreana.In addition,we also tested the cross-species transferability of the microsatellite markers in four additional Semisulcospira spp.We identified 18 polymorphic loci and the number of alleles per loci,and their polymorphism information content values ranged from 2 to 17 and 0.203 to 0.902,respectively.The observed and expected heterozygosities of the loci ranged from 0.063 to 0.924 and 0.226 to 0.924,respectively.According to the analysis of the cross-species transferability of these markers,four species,S.forticosta,S.gottschei,S.tegulata,and S.libertina,showed a very high transferability(80%–85%).These results show that this set of nuclear markers could be useful for population genetics studies of this species and closely related species.
基金The Partial Funding from Sandric Leong through the National University of Singaporethe Fundamental Research Grant Scheme of the Ministry of Education,Malaysia under contract No.FRGS/1/2017/WAB09/UMS/02/1.
文摘Assessments of phytoplankton diversity in Sabah waters,North Borneo,have primarily relied on morphology-based identification,which has inherent biases and can be time-consuming.Next-Generation Sequencing(NGS)technology has been shown to be capable of overcoming several limitations of morphology-based methods.Samples were collected from the Sepanggar Bay over the course of the year 2018 in different monsoon seasons.Morphology-based identification and NGS sequencing of the V8–V9 region of the 18S LSU rDNA were used to investigate the diversity of the phytoplankton community.Microscopy and NGS showed complementary results with more diatom taxa detected by microscopy whereas NGS detected smaller and rarer taxa.The harmful algal genera in the study site comprised of Skeletonema,Margalefidinium,Pyrodinium,Takayama,and Alexandrium as detected by NGS.This study showed that that an integrative approach of both morphological and molecular techniques could provide more comprehensive information about the phytoplankton community as the approach captured quantitative variability as well as the diversity of phytoplankton species.
文摘【Background】The application of beneficial-microbial seed soaking prior to sowing represents a novel technology that has not been employed in Lanzhou lily cultivation.We conducted an experiment to explore the impact of this soaking method on the fungal and bacterial community structures using next-generation sequencing technology(NGS).【Methods】Lily bulbs were soaked in a seed treating agent containing beneficial microbes(SP treatment)for 4 hours.Subsequently,they were planted in soil in July and sampled in September to assess plant growth,rhizosphere soil physicochemical properties,and microorganism community structures.In addition,we employed the software PICRUSt and FUNGuild to predict bacterial pathways and fungal functions.【Results】Under SP treatment,there were significant alterations in fungi and bacteria community structures,accompanied by improved soil nutrient status.Notably,the relative abundance of dominant microorganism groups,such as the fungi Basidiomycota,Pseudeurotium,Cladophialophora,Microascus,and Dactylonectria,as well as the bacteria Proteobacteria,Chloroflexi,Ochrobactrium,Lysobacter,and RB41,underwent notable changes.Microorganism function prediction results indicated a reduction in pathotrophic fungi(including plant pathogens)and an increase in endophytic and saprotrophic fungi under SP treatment.Among the top 20 metabolism pathways,80%were upregulated in SP treatment compared to the CK.【Conclusions】Seed soaking with beneficial microbial strain promotes the growth of Lanzhou lily bulbs.The beneficial microorganisms play a crucial role in regulating soil microbial structures,enhancing the accumulation of endophytic fungi,reducing the abundance of pathogens,and improving soil functions.Furthermore,specific microbial groups are found to be involved in maintaining soil health.
文摘Background:Precision medicine is an emerging approach for treating pediatric cancer due to its ability to target tumor-specific genetic drivers rather than provide broad and aggressive treatments.The study aimed to outline the establishment and impact of a Precision Medicine Clinic(PMC)in the setting of pediatric oncology,with the objective of offering targeted treatment options within the institution and creating a scalable model for adoption by other healthcare systems to achieve a wider impact.Methods:Recognizing this need for an individualized approach to treating patients,Cook Children’s Medical Center(CCMC)established a multidisciplinary molecular tumor board in 2019,followed by the launch of an official PMC in 2021.Before this,there was no dedicated place to discuss and evaluate genetic sequencing results.Results:In 2022 and 2023,the PMC discussed 69 patients with a wide variety of oncologic diagnoses.Through the clinic’s efforts,133 genetic variants across 101 genes have been identified,spanning oncogenic pathways related to cell cycling,DNA processing,and cell signaling.Of the sequenced patients,four have received targeted therapy according to recommendations from the PMC.Conclusion:While the PMC continues to evaluate patients and their long-term outcomes,the continually growing PMC at CCMC represents the beginning of the advancement of treating pediatric oncology patients through the interpretation of genetic sequencing results,making actionable targeted treatment recommendations,and continuing to follow the patient’s course of care over time.This additionally provides a framework for starting a PMC that can be adapted for specific clinical needs and implemented broadly.
文摘Non-small cell lung cancer(NSCLC)accounts for the majority of lung cancer cases and remains the leading cause of cancer-related mortality worldwide.Firstly,this review explores the limitations of conventional therapies,chemotherapy,radiotherapy,and surgery,focusing on the development of drug resistance and significant toxicity that often hinder their efficacy.Thereafter,advancements in targeted therapies,such as immune checkpoint inhibitors(ICIs)and tyrosine kinase inhibitors(TKIs),are discussed,highlighting their impact on improving outcomes for patients with specific genetic mutations,including c-ros oncogene 1 receptor tyrosine kinase(ROS1),anaplastic lymphoma kinase(ALK),and epidermal growth factor receptor(EGFR).Additionally,the emergence of novel immunotherapies and phytochemicals is examined,emphasizing their potential to overcome therapeutic resistance,particularly in advanced-stage diseases.The review also delves into the role of next-generation sequencing(NGS)in enabling personalized treatment approaches and explores the clinical potential of innovative agents,such as bispecific T-cell engagers(BiTEs)and antibody-drug conjugates(ADCs).Finally,we address the socioeconomic barriers that limit the accessibility of these therapies in low-resource settings and propose future research directions aimed at improving the long-term efficacy and accessibility of these treatments.
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 Inter-Governmental S&T Cooperation Proposal between China and Czech Republic (2016YFE0131000)the Beijng Nova Program, China (Z171100001117036)
文摘To identify the possible quarantine viruses in seven common sunflower varieties imported from the United States of America and the Netherlands, we tested total RNAs extracted from the leaf tissues using next-generation sequencing of small RNAs. After analysis of small RNA sequencing data, no any quarantine virus was found, but a double-stranded RNA（dsRNA） molecule showing typical genomic features of endornavirus was detected in two varieties, X3939 and SH1108. Full-length sequence and phylogenetic analysis showed that it is a novel endornavirus, temporarily named as Helianthus annuus alphaendornavirus（HaEV）. Its full genome corresponds to a 14 662-bp dsRNA segment, including a 21-nt 5′ untranslated region（UTR）, 3＇ UTR ending with the unique sequence CCCCCCCC and lacking a poly（A） tail. An open reading frame（ORF） that encodes a deduced 4 867 amino acids（aa） polyprotein with three domains： RdRP, Hel and UGT（UDP-glycosyltransferase）. HaEV mainly distributed in the cytoplasm but less in the nucleus of leaf cells by fluorescence in situ hybridization（FISH） experiment. This virus has a high seed infection rate in the five varieties, X3907, X3939, A231, SH1108 and SR1320. To our knowledge, this is the first report about the virus of the family Endornaviridae in the common sunflower.
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）.
基金the Shenzhen Science and Technology Program under Grant KQTD20200820113051096,Grant JCYJ20220818100217038the Science and Technology Innovation Key R&D Program of Chongqing.
文摘Precision medicine is revolutionizing global healthcare by enabling personalized diagnostics,disease prediction,and tailored treatment strategies.While the integration of genomics and data science holds immense potential to optimize precision therapeutic outcomes,a critical challenge lies in translating gene sequencing data into actionable insights for in vitro diagnostics.This bottleneck is largely attributed to the limitations of edge-side intelligent processing and automation.Despite advancements in gene sequencing technologies and bioinformatics tools,the workflow from sample collection to diagnostic report generation remains fragmented,inefficient,and lacks of intelligence.To address these challenges,we introduce an embodied LLM NGS sequencer on the edge for real-time,on-site smart genetic diagnostics.This instrument integrates a streamlined and comprehensive pipeline with deep learning networks for primary data analysis,machine learning for secondary data processing,and a large language model(LLM)optimized for tertiary data interpretation.The LLM is enhanced through quantization and compression,facilitating deployment on FPGA/GPU to accelerate diagnostic workflows.Experimental results showcased the superior performance by achieving a 13.72%increase in throughput,a 99.50%Q30%,and enable smart diagnostic on the edge with the performance up to 75 tokens/s.This work enables immediate,on-site DNA analysis,hence dramatically improving precision medicine’s accessibility and efficiency,and significantly advances diagnostic accuracy,automation,establishing a robust platform for AI-driven personalized medicine and setting a new benchmark for the future of healthcare delivery.
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.
文摘Apis mellifera syriaca exhibits a high degree of tolerance to pests and pathogens including varroa mites. This native honey bee subspecies of Jordan expresses behavioral adaptations to high temperature and dry seasons typical of the region. However, persistent honey bee imports of commercial breeder lines are endangering local honey bee population. This study reports the use of next-generation sequencing （NGS） technology to study the A. m. syriaca genome and to identify genetic factors possibly contributing toward mite resistance and other favorable traits. We obtained a total of 46.2 million raw reads by applying the NGS to sequence A. m. syriaca and used extensive bioinformatics approach to identify several candidate genes for Varroa mite resistance, behavioral and immune responses char- acteristic for these bees. As a part of characterizing the functional regulation of molecular genetic pathway, we have mapped the pathway genes potentially involved using information from Drosophila melanogaster and present possible functional changes implicated in responses to Varroa destructor mite infestation toward this. We performed in-depth functional annotation methods to identify -600 candidates that are relevant, genes involved in pathways such as microbial recognition and phagocytosis, peptidoglycan recognition protein family, Gram negative binding protein family, phagocytosis receptors, serpins, Toll signaling pathway, Imd pathway, Tnf, JAK-STAT and MAPK pathway, heamatopioesis and cellular response pathways, antiviral, RNAi pathway, stress factors, etc. were selected. Finally, we have cataloged function-specific polymorphisms between A. mellifera and A. m. syriaca that could give better understanding of varroa mite resistance mechanisms and assist in breeding. We have identified immune related embryonic development （Cactus, Relish, dorsal, Ank2, baz）, Varroa hygiene （NorpA2, Zasp, LanA, gasp, impl3） and Varroa resistance （Pug, pcmt, elk, elf3-s10, Dscam2, Dhc64C, gro, futsch） functional variations genes between A. mellifera and A. m. syriaca that could be used to develop an effective molecular tool for bee conservation and breeding programs to improve locally adapted strains such as syriaca and utilize their advantageous traits for the benefit of apiculture industry.
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 the National Natural Science Foundation of China(31772718)the Open Research Fund of State Key Laboratory of Veterinary Biotechnology(SKLVBF2018XX)。
文摘Porcine epidemic diarrhea virus(PEDV)is the most common diarrhea-causing pathogen in newborn piglets.The clarifications of the overall antibody repertoire and antigen-specific antibody repertoire are essential to provide important insights into the B-cell response and reshape new vaccines.Here,we applied next-generation sequencing(NGS)technology to investigate immunoglobulin(Ig)variable(V)gene segment usage of swine B-cells from peripheral blood lymphocytes(PBL)and mesenteric lymph node(MLN)cells following PEDV vaccination.We identified the transcripts of all functional Ig V-genes in antibody repertoire.IgHV1 S2,IgKV1-11,and IgLV3-4 were the most prevalent gene segments for heavy,kappa,and lambda chains,respectively,in PBL and MLN.Unlike previous studies,IgKV1,instead of IgKV2,and IgLV3,instead of IgLV8,were the prevalent Ig V-gene families for kappa and lambda light chains,respectively.We further examined the antibody repertoire of PEDV spike-specific B cells by single-cell RT-PCR.In contrast to the overall antibody repertoire,Ig V-gene segments of PEDV spike-specific B cells preferentially adopted IgHV1-4 and IgHV1-14 for heavy chain,IgKV1-11 for kappa chain,and IgLV3-3 for lambda chain.These results represent a comprehensive analysis to characterize the Ig V-gene segment usage in the overall and PEDV spike-specific antibody repertoire in PBL and MLN.
文摘Oncogenic gene fusions occur across a broad range of cancers and are a defining feature of some cancer types.Cancers driven by gene fusion products tend to respond well to targeted therapies,where available;thus,detection of potentially targetable oncogenic fusions is necessary to select optimal treatment.Detection methods include non-sequencing methods,such as fluorescence in situ hybridization and immunohistochemistry,and sequencing methods,such as DNA-and RNA-based nextgeneration sequencing(NGS).While NGS is an efficient way to analyze multiple genes of interest at once,economic and technical factors may preclude its use in routine care globally,despite several guideline recommendations.The aim of this review is to present a summary of oncogenic gene fusions,with a focus on fusions that affect tyrosine kinase signaling,and to highlight the importance of testing for oncogenic fusions.We present an overview of the identification of oncogenic gene fusions and therapies approved for the treatment of cancers harboring gene fusions,and summarize data regarding treating fusion-positive cancers with no current targeted therapies and clinical studies of fusion-positive cancers.Although treatment options may be limited for patients with rare alterations,healthcare professionals should identify patients most likely to benefit from oncogenic gene fusion testing and initiate the appropriate targeted therapy to achieve optimal treatment outcomes.
文摘The Human Genome Project marked a milestone in scientific exploration,unraveling the genetic blueprint of humanity.However,expectations of direct gene–disease associations gave way to realizing the complexity of genetic interactions,especially in polygenic diseases.This review explores the legacy of the HGP and subsequent advancements in genomic technologies,particularly next-generation sequencing,which have enabled more profound insights into the non-coding genome's role in gene regulation.While initially dismissed as“junk”DNA,non-coding regions are now officially approved as critical gene expression and genome organization regulators.Through integrative genomics approaches and advanced computational methods,researchers have unveiled the intricate network of enhancers,promoters,and chromatin modifications orchestrating gene expression.High-throughput sequencing techniques and functional assays have identified non-coding variants associated with numerous diseases,challenging the conventional focus on coding sequences in genomic studies.By elucidating the regulatory mechanisms governing gene expression,researchers can advance precision medicine approaches and develop novel diagnostic tools.As genomic research continues to evolve,a vast landscape is waiting to be explored,promising transformative insights into human health and disease.This review provides a comprehensive overview of the non-coding genome's role in gene regulation and its implications for understanding complex diseases and developing targeted therapeutic interventions.
文摘Background:Liquid biopsy has emerged as a non-invasive method for real-time cancer monitoring especially in genitourinary(GU)oncology.Most current studies utilize a panel-based molecular profiling ranging from 50–600 genes;however,a comprehensive exome-wide profiling of real-world patient samples has been lacking.Methods:Over 2000 liquid biopsy samples were analyzed in this study,including urine samples from early-stage bladder cancer and plasma samples from prostate,lung,breast,esophageal,head and neck cancers,among others.Cell-free DNA(cfDNA)was extracted from these samples and ana-lyzed using PredicineWES+^(TM),a boosted comprehensive whole-exome sequencing(WES)assay with an in-depth coverage of 600 cancer-related genes derived from the PredicineATLAS^(TM)panel.Data analysis was conducted in-house using Predicine's DeepSea bioinformatics software.Results:The PredicineWES+^(TM)assay demonstrated high sensitivity for detecting somatic mutations across the exome and showed comparable tumor mutational burden(TMB)estimates with the PredicineATLAS^(TM)panel.Interestingly,the highest tumor TMB score was observed in bladder cancer among the analyzed cancers,which is consistent with literature using tissue-based genomic profiling.The most common cancer variants include TP53,ERBB2,KRAS,PIK3CA,FGFR3,APC,among others.Conclusion:Liquid biopsy-based genomic profiling across various cancer types provides an in-depth analysis of biomarker discovery for personalized cancer care,setting the foundation for improved cancer diagnosis and per-sonalized treatment strategies for urological diseases.
文摘Next-generation sequencing data are widely utilised for various downstream applications in bioinformatics and numerous techniques have been developed for PCR-deduplication and error-correction to eliminate bias and errors introduced during the sequencing.This study first-time provides a joint overview of recent advances in PCR-deduplication and error-correction on short reads.In particular,we utilise UMI-based PCR-deduplication strategies and sequencing data to assess the performance of the solelycomputational PCR-deduplication approaches and investigate how error correction affects the performance of PCR-deduplication.Our survey and comparative analysis reveal that the deduplicated reads generated by the solely-computational PCR-deduplication and error-correction methods exhibit substantial differences and divergence from the sets of reads obtained by the UMI-based deduplication methods.The existing solelycomputational PCR-deduplication and error-correction tools can eliminate some errors but still leave hundreds of thousands of erroneous reads uncorrected.All the error-correction approaches raise thousands or more new sequences after correction which do not have any benefit to the PCRdeduplication process.Based on our findings,we discuss future research directions and make suggestions for improving existing computational approaches to enhance the quality of short-read sequencing data.
基金supported by grants from the National Natural Science Foundation of China(31271318)Natural Science Foundation of Guangdong(S2012010008912)Foundation of Key Laboratory of Plant Resources Conservation and Sustainable Utilization,South China Botanical Garden,Chinese Academy of Sciences
文摘Transcriptomics is one of the most developed fields in the post-genomic era.Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specific physiological condition,including messenger RNA,transfer RNA,ribosomal RNA,and other non-coding RNAs.Transcriptomics focuses on the gene expression at the RNA level and offers the genome-wide information of gene structure and gene function in order to reveal the molecular mechanisms involved in specific biological processes.With the development of next-generation high-throughput sequencing technology,transcriptome analysis has been progressively improving our understanding of RNA-based gene regulatory network.Here,we discuss the concept,history,and especially the recent advances in this inspiring field of study.
文摘Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole- genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms （SNPs） have become popular tools for genetic mapping, discovery and appli- cation of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs （BWA-mem and Bowtie 2） and variant callers （SAMtools, GATK, and Freebayes）. Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.
