• molecular dynamic
• network pharmacology
• pulmonary artery hypertension
• sivelestat

• Animals
• Rats
• Sulfonamides/pharmacology
• Sulfonamides/chemistry
• Sulfonamides/administration & dosage
• Glycine/analogs & derivatives
• Glycine/pharmacology
• Glycine/chemistry
• Glycine/administration & dosage
• Network Pharmacology
• Male
• Rats, Sprague-Dawley
• Pulmonary Arterial Hypertension/drug therapy
• Pulmonary Arterial Hypertension/metabolism
• Cell Proliferation/drug effects
• Dose-Response Relationship, Drug
• Disease Models, Animal
• Cells, Cultured
• Structure-Activity Relationship
• Vascular Remodeling/drug effects
• Molecular Structure

• Sichuan Scientific Research Project Program
• Panzhihua Science and Technology Program

• Humans
• Neoplasms/drug therapy
• Neoplasms/genetics
• Neoplasms/therapy
• Nucleic Acids/therapeutic use
• Tumor Microenvironment/drug effects
• Genetic Therapy/methods
• Nanoparticles/therapeutic use
• Antineoplastic Agents/therapeutic use
• Drug Delivery Systems/methods

• Aphanomyces euteiches
• SNPs
• bulk segregant RNA-seq analysis
• differentially expressed genes (DEGs)
• field pea
• root rot

• Aphanomyces/genetics
• Pisum sativum/genetics
• Pisum sativum/metabolism
• Plant Breeding
• Plant Diseases/genetics
• Quantitative Trait Loci

• # 1000210132 Canadian Agricultural Partnership (CAP) Program

• Clinical oncology
• Next-generation sequencing (NGS)
• Personalized medicine (PM)
• Pharmacogenomics

• Animals
• Biomarkers, Tumor/genetics
• Clinical Decision-Making
• Epigenome
• Epigenomics
• Gene Expression Profiling
• Genetic Predisposition to Disease
• High-Throughput Nucleotide Sequencing
• Humans
• Neoplasms/genetics
• Neoplasms/pathology
• Neoplasms/therapy
• Pharmacogenetics
• Phenotype
• Precision Medicine
• Predictive Value of Tests
• Prognosis
• Transcriptome

• BCFtools
• BWA
• Bowtie2
• SNPs
• STAR
• WES
• variants
• wheat

• Genome, Plant
• Polymorphism, Single Nucleotide
• Polyploidy
• Triticum/genetics
• Exome Sequencing

• cellular signalling networks
• systems analysis

• Gene Regulatory Networks
• Genomics
• Models, Genetic
• Mutation
• Software
• Systems Biology

• big data
• drug delivery
• nanotechnology
• next-generation sequencing

• Animals
• Databases, Factual
• Drug Delivery Systems
• High-Throughput Nucleotide Sequencing
• Humans
• Nanotechnology/methods

• T32 EB021962 NIBIB NIH HHS
• T32 GM008433 NIGMS NIH HHS
• PDF-JFA-1860 Parkinson's Disease Foundation

• disease mechanism
• mathematical models
• networks
• signaling pathways
• systems biology
• transcriptomics

• Algorithms
• Humans
• Postmortem Changes
• Signal Transduction
• Systems Biology/methods
• Transcriptome

• Big data
• Fanconi anemia
• Genomics
• Machine learning
• Mathematical models
• Signaling pathways

• Databases, Factual
• Fanconi Anemia/metabolism
• Fanconi Anemia/pathology
• Genomics
• Humans
• Machine Learning
• Phenotype
• Proteins/metabolism
• Signal Transduction

• SAF2017-88908-R MINECO
• PT17/0009/0006 ISCIII
• 813533 H2020 Marie Curie Innovative Training Network
• 676559 H2020
• H2020 Marie Curie Innovative Training Network

Whole exome sequencing (WES) is a cost-effective method that identifies clinical variants but it demands accurate variant caller tools. Currently available tools have variable accuracy in predicting specific clinical variants. But it may be possible to find the best combination of aligner-variant caller tools for detecting accurate single nucleotide variants (SNVs) and small insertion and deletion (InDels) separately. Moreover, many important aspects of InDel detection are overlooked while comparing the performance of tools, particularly its base pair length.

We assessed the performance of variant calling pipelines using the combinations of four variant callers and five aligners on human NA12878 and simulated exome data. We used high confidence variant calls from Genome in a Bottle (GiaB) consortium for validation, and GRCh37 and GRCh38 as the human reference genome. Based on the performance metrics, both BWA and Novoalign aligners performed better with DeepVariant and SAMtools callers for detecting SNVs, and with DeepVariant and GATK for InDels. Furthermore, we obtained similar results on human NA24385 and NA24631 exome data from GiaB.

In this study, DeepVariant with BWA and Novoalign performed best for detecting accurate SNVs and InDels. The accuracy of variant calling was improved by merging the top performing pipelines. The results of our study provide useful recommendations for analysis of WES data in clinical genomics.

The online version of this article (10.1186/s12859-019-2928-9) contains supplementary material, which is available to authorized users.

• Human reference genome
• SNVs and InDels
• Simulated exome data
• Variant calling pipelines
• Whole exome sequencing

• Colorectal cancer
• peritoneal metastasis
• somatic mutations

Noises and artifacts may arise in several steps of the next-generation sequencing (NGS) process. Recently, an NGS library preparation method called SMART, or Switching Mechanism At the 5′ end of the RNA Transcript, is introduced to prepare ChIP-seq (chromatin immunoprecipitation and deep sequencing) libraries from small amount of DNA material, using the DNA SMART ChIP-seq Kit. The protocol adds Ts to the 3′ end of DNA templates, which is subsequently recognized and used by SMART poly(dA) primers for reverse transcription and then addition of PCR primers and sequencing adapters. The poly(dA) primers, however, can anneal to poly(T) sequences in a genome and amplify DNA fragments that are not enriched in the immunoprecipitated DNA templates. This off-target amplification results in false signals in the ChIP-seq data.

Here, we show that the off-target ChIP-seq reads derived from false amplification of poly(T/A) genomic sequences have unique and strand-specific features. Accordingly, we develop a tool (called “SMARTcleaner”) that can exploit these features to remove SMART ChIP-seq artifacts. Application of SMARTcleaner to several SMART ChIP-seq datasets demonstrates that it can remove reads from off-target amplification effectively, leading to significantly improved ChIP-seq peaks and results.

SMARTcleaner could identify and clean the false signals in SMART-based ChIP-seq libraries, leading to improvement in peak calling, and downstream data analysis and interpretation.

The online version of this article (10.1186/s12859-018-2577-4) contains supplementary material, which is available to authorized users.

• ChIP-seq
• False amplification
• False priming
• NGS
• SMART

Cancer can be diagnosed by identifying DNA and microRNA base sequences that have the same base length yet differ in a few base sequences, if the abundance ratios of these slightly deviant base sequences can be determined. However, such quantitative analyses cannot be performed using the current DNA sequencers. Here we determine entire base sequences of four types of DNA corresponding to the let-7 microRNA, which is a 22-base cancer marker. We record the single-molecule conductances of the base molecules using current-tunneling measurements. In addition, we count the numbers of molecules in a solution to determine the abundance ratios of two DNA strands that differ by a single base sequence.

Quality control of high-throughput DNA sequencing data is an important but sometimes laborious task requiring background knowledge of the sequencing protocol used (such as adaptor type, sequencing technology, insert size/stitchability, paired-endedness, etc.). Quality control protocols typically require applying this background knowledge to selecting and executing numerous quality control steps with the appropriate parameters, which is especially difficult when working with public data or data from collaborators who use different protocols. We have created a streamlined quality control pipeline intended to substantially simplify the process of DNA quality control from raw machine output files to actionable sequence data. In contrast to other methods, our proposed pipeline is easy to install and use and attempts to learn the necessary parameters from the data automatically with a single command.

Next-generation sequencing technology is of great importance for many biological disciplines; however, due to technical and biological limitations, the short DNA sequences produced by modern sequencers require numerous quality control (QC) measures to reduce errors, remove technical contaminants, or merge paired-end reads together into longer or higher-quality contigs. Many tools for each step exist, but choosing the appropriate methods and usage parameters can be challenging because the parameterization of each step depends on the particularities of the sequencing technology used, the type of samples being analyzed, and the stochasticity of the instrumentation and sample preparation. Furthermore, end users may not know all of the relevant information about how their data were generated, such as the expected overlap for paired-end sequences or type of adaptors used to make informed choices. This increasing complexity and nuance demand a pipeline that combines existing steps together in a user-friendly way and, when possible, learns reasonable quality parameters from the data automatically. We propose a user-friendly quality control pipeline called SHI7 (canonically pronounced “shizen”), which aims to simplify quality control of short-read data for the end user by predicting presence and/or type of common sequencing adaptors, what quality scores to trim, whether the data set is shotgun or amplicon sequencing, whether reads are paired end or single end, and whether pairs are stitchable, including the expected amount of pair overlap. We hope that SHI7 will make it easier for all researchers, expert and novice alike, to follow reasonable practices for short-read data quality control.

IMPORTANCE Quality control of high-throughput DNA sequencing data is an important but sometimes laborious task requiring background knowledge of the sequencing protocol used (such as adaptor type, sequencing technology, insert size/stitchability, paired-endedness, etc.). Quality control protocols typically require applying this background knowledge to selecting and executing numerous quality control steps with the appropriate parameters, which is especially difficult when working with public data or data from collaborators who use different protocols. We have created a streamlined quality control pipeline intended to substantially simplify the process of DNA quality control from raw machine output files to actionable sequence data. In contrast to other methods, our proposed pipeline is easy to install and use and attempts to learn the necessary parameters from the data automatically with a single command.

• QC
• algorithm
• bioinformatics
• metagenomics
• microbiome
• pipeline
• quality control
• sequencing
• short read

• Bioinformatics
• Biopanning
• In silico analysis
• In vitro selection
• NGS
• Next-generation sequencing

• Broad-spectrum aptamers
• Cell-SELEX
• DNA aptamers
• High-throughput sequencing
• Screening methods

• differentially expressed genes
• expression profile
• gastric cancer
• integrated analysis
• reverse transcription-quantitative polymerase chain reaction

Alternative splicing (AS) regulation is extensive and shapes the functional complexity of higher organisms. However, the contribution of alternative splicing to fungal biology is not well studied.

This study provides sequences of the transcriptomes of the plant wilt pathogen Verticillium dahliae, using two different strains and multiple methods for cDNA library preparations. We identified alternatively spliced mRNA isoforms in over a half of the multi-exonic fungal genes. Over one-thousand isoforms involve TopHat novel splice junction; multiple types of combinatory alternative splicing patterns were identified. We showed that one Verticillium gene could use four different 5′ splice sites and two different 3′ donor sites to produce up to five mature mRNAs, representing one of the most sophisticated alternative splicing model in eukaryotes other than animals. Hundreds of novel intron types involving a pair of new splice sites were identified in the V. dahliae genome. All the types of AS events were validated by using RT-PCR. Functional enrichment analysis showed that AS genes are involved in most known biological functions and enriched in ATP biosynthesis, sexual/asexual reproduction, morphogenesis, signal transduction etc., predicting that the AS regulation modulates mRNA isoform output and shapes the V. dahliae proteome plasticity of the pathogen in response to the environmental and developmental changes.

These findings demonstrate the comprehensive alternative splicing mechanisms in a fungal plant pathogen, which argues the importance of this fungus in developing complicate genome regulation strategies in eukaryotes.

The online version of this article (doi:10.1186/s12864-017-3507-y) contains supplementary material, which is available to authorized users.

• Alternative splicing
• Fungus
• Intron retention
• Verticillium dahliae

• Adenomatous polyposis coli (APC)
• Familial adenomatous polyposis (FAP)
• Tumor suppressor genes (TSGs)

Over the last decade, aptamers have begun to find their way from basic research to diverse commercial applications. The development of diagnostics is even more widespread than clinical applications because aptamers do not have to be extensively modified to enhance their in vivo stability and pharmacokinetics in diagnostic assays. The increasing attention has propelled the technical progress of the in vitro selection technology (SELEX) to enhance the efficiency of developing aptamers for commercially interesting targets. This review highlights recent progress in the technical steps of a SELEX experiment with a focus on high-throughput next-generation sequencing and bioinformatics. Achievements have been made in the optimization of aptamer libraries, separation schemes, amplification of the selected libraries and the identification of aptamer sequences from enriched libraries.

• NGS
• SELEX
• aptamer
• bioinformatics
• microfluidics
• next generation sequencing

• Illumina
• biotinylated baits
• massively parallel sequencing
• next-generation sequencing
• sequence capture
• target enrichment

• Biological Evolution
• Biology/history
• Biology/instrumentation
• Biology/methods
• DNA/chemistry
• DNA/genetics
• DNA/isolation & purification
• Genetic Variation
• Genotyping Techniques/instrumentation
• Genotyping Techniques/methods
• Genotyping Techniques/trends
• High-Throughput Nucleotide Sequencing/instrumentation
• High-Throughput Nucleotide Sequencing/methods
• History, 20th Century
• History, 21st Century
• Nucleic Acid Hybridization/methods
• Specimen Handling/methods

• P20 GM103395 NIGMS NIH HHS

• Bioinformatics
• In silico analysis
• NGS
• Next generation sequencing
• SELEX

We demonstrate a new screening method for obtaining a prostate-specific antigen (PSA) binding aptamer based on an acoustofluidic separation (acoustophoreis) technique. Since acoustophoresis provides simultaneous washing and separation in a continuous flow mode, we efficiently obtained a PSA binding aptamer that shows high affinity without any additional washing step, which is necessary in other screening methods. In addition, next-generation sequencing (NGS) was applied to accelerate the identification of the screened ssDNA pool, improving the selecting process of the aptamer candidate based on the frequency ranking of the sequences. After the 8^th round of the acoustophoretic systematic evolution of ligands by exponential enrichment (SELEX) and following sequence analysis with NGS, 7 PSA binding ssDNA aptamer-candidates were obtained and characterized with surface plasmon resonance (SPR) for affinity and specificity. As a result of the new SELEX method with PSA as the model target protein, the best PSA binding aptamer showed specific binding to PSA with a dissociation constant (K_d) of 0.7 nM.

• Regulation of gene expression
• Student research experiences
• Undergraduate classroom

Stored neonatal dried blood spot (DBS) samples from neonatal screening programmes are a valuable diagnostic and research resource. Combined with information from national health registries they can be used in population-based studies of genetic diseases. DNA extracted from neonatal DBSs can be amplified to obtain micrograms of an otherwise limited resource, referred to as whole-genome amplified DNA (wgaDNA). Here we investigate the robustness of exome sequencing of wgaDNA of neonatal DBS samples. We conducted three pilot studies of seven, eight and seven subjects, respectively. For each subject we analysed a neonatal DBS sample and corresponding adult whole-blood (WB) reference sample. Different DNA sample types were prepared for each of the subjects. Pilot 1: wgaDNA of 2x3.2mm neonatal DBSs (DBS_2x3.2) and raw DNA extract of the WB reference sample (WB_ref). Pilot 2: DBS_2x3.2, WB_ref and a WB_ref replica sharing DNA extract with the WB_ref sample. Pilot 3: DBS_2x3.2, WB_ref, wgaDNA of 2x1.6 mm neonatal DBSs and wgaDNA of the WB reference sample. Following sequencing and data analysis, we compared pairwise variant calls to obtain a measure of similarity—the concordance rate. Concordance rates were slightly lower when comparing DBS vs WB sample types than for any two WB sample types of the same subject before filtering of the variant calls. The overall concordance rates were dependent on the variant type, with SNPs performing best. Post-filtering, the comparisons of DBS vs WB and WB vs WB sample types yielded similar concordance rates, with values close to 100%. WgaDNA of neonatal DBS samples performs with great accuracy and efficiency in exome sequencing. The wgaDNA performed similarly to matched high-quality reference—whole-blood DNA—based on concordance rates calculated from variant calls. No differences were observed substituting 2x3.2 with 2x1.6 mm discs, allowing for additional reduction of sample material in future projects.

• Adult
• Dried Blood Spot Testing
• Exome/genetics
• Genome, Human
• High-Throughput Nucleotide Sequencing/methods
• High-Throughput Nucleotide Sequencing/statistics & numerical data
• Humans
• Infant, Newborn
• Nucleic Acid Amplification Techniques/methods
• Pilot Projects
• Polymorphism, Single Nucleotide
• Reproducibility of Results

• Lundbeckfonden

Butyrate is a nutritional element with strong epigenetic regulatory activity as a histone deacetylase inhibitor. Based on the analysis of differentially expressed genes in the bovine epithelial cells using RNA sequencing technology, a set of unique genes that are activated only after butyrate treatment were revealed. A complementary bioinformatics analysis of the functional category, pathway, and integrated network, using Ingenuity Pathways Analysis, indicated that these genes activated by butyrate treatment are related to major cellular functions, including cell morphological changes, cell cycle arrest, and apoptosis. Our results offered insight into the butyrate-induced transcriptomic changes and will accelerate our discerning of the molecular fundamentals of epigenomic regulation.

• bovine cells
• butyrate
• gene regulation
• histone modification
• transcriptomic

• Algorithms
• Computational Biology/methods
• Computational Biology/statistics & numerical data
• Diabetes Mellitus/genetics
• Gene Expression Profiling
• Gene Regulatory Networks
• Genetic Predisposition to Disease
• Genome-Wide Association Study/statistics & numerical data
• Humans
• Mental Disorders/genetics
• Models, Genetic
• Multifactorial Inheritance
• Transcriptome
• Unsupervised Machine Learning

• MH094267 NIMH NIH HHS
• GM102365 NIGMS NIH HHS
• R01 GM102365 NIGMS NIH HHS
• HL117798 NHLBI NIH HHS
• LM005652 NLM NIH HHS
• U54 HL117798 NHLBI NIH HHS
• R01 LM005652 NLM NIH HHS
• P50 MH094267 NIMH NIH HHS

Traditional modes of investigating influenza nosocomial transmission have entailed a combination of confirmatory molecular diagnostic testing and epidemiological investigation. Common hospital-acquired infections like influenza require a discerning ability to distinguish between viral isolates to accurately identify patient transmission chains. We assessed whether influenza hemagglutinin sequence phylogenies can be used to enrich epidemiological data when investigating the extent of nosocomial transmission over a four-month period within a paediatric Hospital in Cape Town South Africa. Possible transmission chains/channels were initially determined through basic patient admission data combined with Maximum likelihood and time-scaled Bayesian phylogenetic analyses. These analyses suggested that most instances of potential hospital-acquired infections resulted from multiple introductions of Influenza A into the hospital, which included instances where virus hemagglutinin sequences were identical between different patients. Furthermore, a general inability to establish epidemiological transmission linkage of patients/viral isolates implied that identified isolates could have originated from asymptomatic hospital patients, visitors or hospital staff. In contrast, a traditional epidemiological investigation that used no viral phylogenetic analyses, based on patient co-admission into specific wards during a particular time-frame, suggested that multiple hospital acquired infection instances may have stemmed from a limited number of identifiable index viral isolates/patients. This traditional epidemiological analysis by itself could incorrectly suggest linkage between unrelated cases, underestimate the number of unique infections and may overlook the possible diffuse nature of hospital transmission, which was suggested by sequencing data to be caused by multiple unique introductions of influenza A isolates into individual hospital wards. We have demonstrated a functional role for viral sequence data in nosocomial transmission investigation through its ability to enrich traditional, non-molecular observational epidemiological investigation by teasing out possible transmission pathways and working toward more accurately enumerating the number of possible transmission events.

• Base Sequence
• Bayes Theorem
• Child
• Cross Infection/epidemiology
• Cross Infection/transmission
• Cross Infection/virology
• Hospitals, Pediatric
• Humans
• Influenza A Virus, H1N1 Subtype/genetics
• Influenza A Virus, H1N1 Subtype/isolation & purification
• Influenza, Human/epidemiology
• Influenza, Human/transmission
• Influenza, Human/virology
• Molecular Sequence Data
• Phylogeny
• South Africa/epidemiology

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is among the most common congenital malformations. The etiology of NSCL/P remains poorly characterized owing to its complex genetic heterogeneity. The objective of this study was to identify genetic variants that increase susceptibility to NSCL/P.

Whole-exome sequencing (WES) was performed in 8 fetuses with NSCL/P in China. Bioinformatics analysis was performed using commercially available software. Variants detected by WES were validated by Sanger sequencing.

By filtering out synonymous variants in exons, we identified average 8575 nonsynonymous single nucleotide variants (SNVs). We subsequently compared the SNVs against public databases including NCBI dbSNP build 135 and 1000 Genomes Project and obtained an average of 203 SNVs. Total 12 reported candidate genes were verified by Sanger sequencing. Sanger sequencing also confirmed 16 novel SNVs shared by two or more samples.

We have found and confirmed 16 susceptibility genes responsible for NSCL/P, which may play important role in the etiology of NSCL/P. The susceptibility genes identified in this study will not only be useful in revealing the etiology of NSCL/P but also in diagnosis and treatment of the patients with NSCL/P.

Key words:Non-syndromic cleft lip with or without cleft palate, whole-exome sequencing, sanger sequencing, susceptibility gene, single nucleotide variants (SNVs).

• Colorectal adenocarcinoma
• FAP
• HNPCC
• Next generation sequencing

Next-generation sequencing (NGS) is widely used to identify the causative mutations underlying diverse human diseases, including cancers, which can be useful for discovering the diagnostic and therapeutic targets. Currently, a number of single-nucleotide variant (SNV)-calling algorithms are available; however, there is no tool for visualizing the recurrent and phenotype-specific mutations for general researchers. In this study, in order to support defining the recurrent mutations or phenotype-specific mutations from NGS data of a group of cancers with diverse phenotypes, we aimed to develop a user-friendly tool, named mutation arranger for defining phenotype-related SNV (MAP). MAP is a user-friendly program with multiple functions that supports the determination of recurrent or phenotype-specific mutations and provides graphic illustration images to the users. Its operation environment, the Microsoft Windows environment, enables more researchers who cannot operate Linux to define clinically meaningful mutations with NGS data from cancer cohorts.

• cancer
• mutation
• next-generation sequencing (NGS)
• sequence snalysis
• single-nucleotide variant (SNV)
• software

Alternative splicing (AS) is an essential mechanism in post-transcriptional regulation and leads to protein diversity. It has been shown that AS is prevalent in metazoan genomes, and the splicing pattern is dynamically regulated in different tissues and cell types, including embryonic stem cells. These observations suggest that AS may play critical roles in stem cell biology. Since embryonic stem cells and induced pluripotent stem cells have the ability to give rise to all types of cells and tissues, they hold the promise of future cell-based therapy. Many efforts have been devoted to understanding the mechanisms underlying stem cell self-renewal and differentiation. However, most of the studies focused on the expression of a core set of transcription factors and regulatory RNAs. The role of AS in stem cell differentiation was not clear. Recent advances in high-throughput technologies have allowed the profiling of dynamic splicing patterns and cis-motifs that are responsible for AS at a genome-wide scale, and provided novel insights in a number of studies. In this review, we discuss some recent findings involving AS and stem cells. An emerging picture from these findings is that AS is integrated in the transcriptional and post-transcriptional networks and together they control pluripotency maintenance and differentiation of stem cells.

• Alternative splicing
• Stem cell
• Pluripotency
• Differentiation
• Splicing factor

• R00 HL093213 NHLBI NIH HHS

• Amino Acid Substitution/genetics
• Animals
• Aphids/genetics
• Gene Expression Profiling
• Genetic Variation
• Genome, Insect
• Pisum sativum/genetics
• Pisum sativum/parasitology
• Phylogeny
• RNA, Messenger/genetics
• Selection, Genetic
• Sequence Analysis, RNA
• Transcriptome/genetics
• Triticum/genetics
• Triticum/parasitology

• BBS/E/C/00004158 Biotechnology and Biological Sciences Research Council
• BBS/E/C/00004975 Biotechnology and Biological Sciences Research Council

We explored the feasibility of studying loss of heterozygosity (LOH) by using exome sequencing and compared the differences in genetic LOH between primary breast tumors and metastatic lesions. Exome sequencing was conducted to investigate the genetic LOH in the peripheral blood, a primary tumor, and a metastatic lesion from the same patient. LOH was observed in 30 and 48 chromosomal loci of the primary tumor and metastatic lesion, respectively. The incidence of LOH was the highest on chromosome 19, followed by chromosomes 14, 3, and 11 in the metastatic lesion. Among these ‘hot' regions, LOH was observed for multiple genes of the CECAM, MMP and ZNF families. Therefore, the use of exome sequencing for studying LOH is feasible. More members of gene families appeared with LOH in ‘hot' regions, suggesting that these gene families had synergistic effects in tumorigenesis.

• Animals
• Ants/genetics
• DNA, Intergenic/genetics
• Evolution, Molecular
• Gene Rearrangement/genetics
• Genome, Mitochondrial/genetics
• Genomics/methods
• Phylogeny
• RNA, Transfer/genetics
• Ribosomes/genetics
• Transcriptome/genetics

• Aptamers, Nucleotide/chemistry
• Base Sequence
• Cluster Analysis
• High-Throughput Nucleotide Sequencing
• Microscopy, Electron, Transmission

Next generation sequencing (NGS) is being increasingly used for the detection and characterization of pathogens during outbreaks. This technology allows rapid sequencing of pathogen full genomes, useful not only for accurate genotyping and molecular epidemiology, but also for identification of drug resistance and virulence traits.

In this study, an approach based on whole genome sequencing by NGS, comparative genomics, and gene function prediction was set up and retrospectively applied for the investigation of two N. meningitidis serogroup C isolates collected from a cluster of meningococcal disease, characterized by a high fatality rate.

According to conventional molecular typing methods, all the isolates had the same typing results and were classified as outbreak isolates within the same N. meningitidis sequence type ST-11, while full genome sequencing demonstrated subtle genetic differences between the isolates. Looking for these specific regions by means of 9 PCR and cycle sequencing assays in other 7 isolates allowed distinguishing outbreak cases from unrelated cases. Comparative genomics and gene function prediction analyses between outbreak isolates and a set of reference N. meningitidis genomes led to the identification of differences in gene content that could be relevant for pathogenesis. Most genetic changes occurred in the capsule locus and were consistent with recombination and horizontal acquisition of a set of genes involved in capsule biosynthesis.

This study showed the added value given by whole genome sequencing by NGS over conventional sequence-based typing methods in the investigation of an outbreak. Routine application of this technology in clinical microbiology will significantly improve methods for molecular epidemiology and surveillance of infectious disease and provide a bulk of data useful to improve our understanding of pathogens biology.

Like other solid tumors, colorectal cancer (CRC) is a genomic disorder in which various types of genomic alterations, such as point mutations, genomic rearrangements, gene fusions, or chromosomal copy number alterations, can contribute to the initiation and progression of the disease. The advent of a new DNA sequencing technology known as next-generation sequencing (NGS) has revolutionized the speed and throughput of cataloguing such cancer-related genomic alterations. Now the challenge is how to exploit this advanced technology to better understand the underlying molecular mechanism of colorectal carcinogenesis and to identify clinically relevant genetic biomarkers for diagnosis and personalized therapeutics. In this review, we will introduce NGS-based cancer genomics studies focusing on those of CRC, including a recent large-scale report from the Cancer Genome Atlas. We will mainly discuss how NGS-based exome-, whole genome- and methylome-sequencing have extended our understanding of colorectal carcinogenesis. We will also introduce the unique genomic features of CRC discovered by NGS technologies, such as the relationship with bacterial pathogens and the massive genomic rearrangements of chromothripsis. Finally, we will discuss the necessary steps prior to development of a clinical application of NGS-related findings for the advanced management of patients with CRC.

• Next-generation sequencing
• Cancer genomics
• Colorectal cancers
• Personalized medicine
• The cancer genome atlas

• Biomarkers, Tumor/genetics
• Colorectal Neoplasms/diagnosis
• Colorectal Neoplasms/genetics
• Colorectal Neoplasms/therapy
• Gene Expression Regulation, Neoplastic
• Genetic Predisposition to Disease
• Genetic Testing/methods
• High-Throughput Nucleotide Sequencing
• Humans
• Molecular Targeted Therapy
• Patient Selection
• Phenotype
• Precision Medicine
• Predictive Value of Tests
• Prognosis
• Risk Factors

Spinal cord injury (SCI) is a devastating neurological disease without effective treatment. To generate a comprehensive view of the mechanisms involved in SCI pathology, we applied RNA-Sequencing (RNA-Seq) technology to characterize the temporal changes in global gene expression after contusive SCI in mice. We sequenced tissue samples from acute and subacute phases (2 days and 7 days after injury) and systematically characterized the transcriptomes with the goal of identifying pathways and genes critical in SCI pathology. The top enriched functional categories include “inflammation response,” “neurological disease,” “cell death and survival” and “nervous system development.” The top enriched pathways include LXR/RXR Activation and Atherosclerosis Signaling, etc. Furthermore, we developed a systems-based analysis framework in order to identify key determinants in the global gene networks of the acute and sub-acute phases. Some candidate genes that we identified have been shown to play important roles in SCI, which demonstrates the validity of our approach. There are also many genes whose functions in SCI have not been well studied and can be further investigated by future experiments. We have also incorporated pharmacogenomic information into our analyses. Among the genes identified, the ones with existing drug information can be readily tested in SCI animal models. Therefore, in this study we have described an example of how global gene profiling can be translated to identifying genes of interest for functional tests in the future and generating new hypotheses. Additionally, the RNA-Seq enables splicing isoform identification and the estimation of expression levels, thus providing useful information for increasing the specificity of drug design and reducing potential side effect. In summary, these results provide a valuable reference data resource for a better understanding of the SCI process in the acute and sub-acute phases.

• Animals
• Female
• Gene Expression
• Gene Expression Profiling
• Gene Regulatory Networks
• Inflammation/genetics
• Inflammation/metabolism
• Inflammation/pathology
• Mice
• Mice, Inbred C57BL
• Molecular Sequence Annotation
• Oligonucleotide Array Sequence Analysis
• RNA Isoforms/genetics
• RNA Isoforms/metabolism
• RNA Splicing
• RNA, Messenger/genetics
• RNA, Messenger/metabolism
• Sequence Analysis, RNA
• Spinal Cord Injuries/genetics
• Spinal Cord Injuries/metabolism
• Spinal Cord Injuries/pathology
• Transcriptome

• R00 HL093213 NHLBI NIH HHS
• R01 NS061975 NINDS NIH HHS
• NS061975 NINDS NIH HHS

• plasmodium
• deep sequencing
• parasite clearance curves
• mixed infections
• selection differential
• artemisinin

• Animals
• Antimalarials/pharmacology
• Antimalarials/therapeutic use
• Drug Monitoring/methods
• Drug Resistance
• High-Throughput Nucleotide Sequencing
• Humans
• Malaria/drug therapy
• Malaria/parasitology
• Phenotype
• Plasmodium falciparum/drug effects
• Plasmodium falciparum/genetics
• Sequence Analysis, DNA

• U19 AI089676 NIAID NIH HHS
• U19AI089676 NIAID NIH HHS
• R01 AI089819 NIAID NIH HHS
• KL2 TR000160 NCATS NIH HHS
• R01AI089819 NIAID NIH HHS
• UL1 TR000161 NCATS NIH HHS

• diagnostic testing
• medical oncology
• molecular diagnostic techniques
• multiplex assays
• personalized medicine
• technology S-curve
• whole-genome sequencing