scholarly journals A smart polymer for sequence-selective binding, pulldown, and release of DNA targets

2019 ◽  
Author(s):  
Elisha Krieg ◽  
Krishna Gupta ◽  
Andreas Dahl ◽  
Mathias Lesche ◽  
Susanne Boye ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Low Cost ◽  
Clinical Diagnostics ◽  
Ease Of Use ◽  
Preparative Scale ◽  
Smart Polymer ◽  
Double Stranded Dna ◽  
Next Generation Sequencing Ngs ◽  
Pure Target ◽  
Generation Sequencing

AbstractSelective isolation of DNA is crucial for applications in biology, bionanotechnology, clinical diagnostics and forensics. We herein report a smart methanol-responsive polymer (MeRPy) that can be programmed to bind and separate single- as well as double-stranded DNA targets. Captured targets are quickly isolated and released back into solution by denaturation (sequence-agnostic) or toehold-mediated strand displacement (sequence-selective). The latter mode allows 99.8% efficient removal of unwanted sequences and 79% recovery of highly pure target sequences. We applied MeRPy for the depletion of insulin, glucagon, and transthyretin cDNA from clinical next-generation sequencing (NGS) libraries. This step improved data quality for low-abundance transcripts in expression profiles of pancreatic tissues. Its low cost, scalability, high stability and ease of use make MeRPy suitable for diverse applications in research and clinical laboratories, including enhancement of NGS libraries, extraction of DNA from biological samples, preparative-scale DNA isolations, and sorting of DNA-labeled non-nucleic acid targets.

scholarly journals Characteristics and Clinical Application of Extracellular Vesicle-Derived DNA

Cancers ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 3827
Author(s):  
Jae Young Hur ◽  
Kye Young Lee
Keyword(s):  
Therapeutic Potential ◽  
Extracellular Vesicle ◽  
Clinical Settings ◽  
Biomarker Detection ◽  
Diagnosis And Prognosis ◽  
Double Stranded Dna ◽  
Fundamental Research ◽  
The Stability ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Extracellular vesicles (EVs) carry RNA, proteins, lipids, and diverse biomolecules for intercellular communication. Recent studies have reported that EVs contain double-stranded DNA (dsDNA) and oncogenic mutant DNA. The advantage of EV-derived DNA (EV DNA) over cell-free DNA (cfDNA) is the stability achieved through the encapsulation in the lipid bilayer of EVs, which protects EV DNA from degradation by external factors. The existence of DNA and its stability make EVs a useful source of biomarkers. However, fundamental research on EV DNA remains limited, and many aspects of EV DNA are poorly understood. This review examines the known characteristics of EV DNA, biogenesis of DNA-containing EVs, methylation, and next-generation sequencing (NGS) analysis using EV DNA for biomarker detection. On the basis of this knowledge, this review explores how EV DNA can be incorporated into diagnosis and prognosis in clinical settings, as well as gene transfer of EV DNA and its therapeutic potential.

Machine Learning Perspective in Cancer Research

2021 ◽  
pp. 142-163
Author(s):  
Aman Sharma ◽  
Rinkle Rani
Keyword(s):  
Machine Learning ◽  
Cancer Research ◽  
Expression Profiles ◽  
Genetic Diseases ◽  
Cost Effective ◽  
Healthcare Sector ◽  
Diagnosis And Prognosis ◽  
Cost Effective Approach ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Advancement in genome sequencing technology has empowered researchers to think beyond their imagination. Researchers are trying their hard to fight against various genetic diseases like cancer. Artificial intelligence has empowered research in the healthcare sector. Moreover, the availability of opensource healthcare datasets has motivated the researchers to develop applications which can help in early diagnosis and prognosis of diseases. Further, next-generation sequencing (NGS) has helped to look into detailed intricacies of biological systems. It has provided an efficient and cost-effective approach with higher accuracy. The advent of microRNAs also known as small noncoding genes has begun the paradigm shift in oncological research. We are now able to profile expression profiles of RNAs using RNA-seq data. microRNA profiling has helped in uncovering their relationship in various genetic and biological processes. Here in this chapter, the authors present a review of the machine learning perspective in cancer research.

scholarly journals Discrepancy of Karyotype and CMA /NGS in PGD Patient with Cryptical Complex Chromosomal Rearrangement

2021 ◽  
Author(s):  
TING WANG ◽  
Hanbiao Chen ◽  
Jian Lu ◽  
Weiwei Huang ◽  
Huamei Huang ◽  
...  
Keyword(s):  
Chromosomal Abnormalities ◽  
Low Cost ◽  
Chromosome Rearrangement ◽  
Genetic Diagnosis ◽  
Structural Rearrangement ◽  
Balanced Translocation ◽  
Chromosome 10 ◽  
Next Generation Sequencing Ngs ◽  
High Repeatability ◽  
Generation Sequencing

Abstract Background: Complex chromosome rearrangement (CCR) is a structural rearrangement involving more than two breakpoints. CCR carriers are at high risk for phenotypic abnormalities or reproductive failure, such as chromosomal abnormalities in fetuses and infertility.Methods: We presented a carriers with chromosome (3,18) apparent balanced translocation diagnosed in eleswhere, whose fetus had duplications in chromosome 3 and deletions in chromosome 10 demonstrated by chromosome microarray analysis(CMA). Results: Through the high resolution of GTG-banding, a cryptical translocation in chromosome 10 was found and the karyotype of the carrier was revised as 46,XY,t(3;10;18) (p26.3;q26.1;q21.1).In the cycle of preimplantation genetic diagnosis (PGD),21 oocytes were retrieved, and 15 were fertilized. At last 7 embryos were biospied and sent to diagnosis by next generation sequencing(NGS).Unfortunately, none of the NGS results from the 7 biopsy embryos were normal. Combining previous literature and our results, we assessed the odds of a balanced embryo in a CCR carrier to be about 9.3%(28/302).The transferable embryo rate was approximately 71.4%(20/28) and healthy live born delivery rate was 55%(11/20).Conclusions: NGS and CMA featured high automation, relatively low cost, high throughput, and high repeatability, which made them commonly used during prenatal diagnosis and PGD. The multiple technology combination can provide more accurate diagnosis and better fertility services for CCR patients.

scholarly journals Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum

2015 ◽  
Vol 9 ◽  
pp. BBI.S20751 ◽  
Author(s):  
Stefan Simm ◽  
Sotirios Fragkostefanakis ◽  
Puneet Paul ◽  
Mario Keller ◽  
Jens Einloft ◽  
...  
Keyword(s):  
Solanum Lycopersicum ◽  
Expression Profiling ◽  
Ribosome Biogenesis ◽  
Developmental Stages ◽  
Male Gametophyte ◽  
Expression Profiles ◽  
Transcript Abundance ◽  
Rrna Processing ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Ribosome biogenesis involves a large inventory of proteinaceous and RNA cofactors. More than 250 ribosome biogenesis factors (RBFs) have been described in yeast. These factors are involved in multiple aspects like rRNA processing, folding, and modification as well as in ribosomal protein (RP) assembly. Considering the importance of RBFs for particular developmental processes, we examined the complexity of RBF and RP (co-)orthologs by bioinformatic assignment in 14 different plant species and expression profiling in the model crop Solanum lycopersicum. Assigning (co-)orthologs to each RBF revealed that at least 25% of all predicted RBFs are encoded by more than one gene. At first we realized that the occurrence of multiple RBF co-orthologs is not globally correlated to the existence of multiple RP co-orthologs. The transcript abundance of genes coding for predicted RBFs and RPs in leaves and anthers of S. lycopersicum was determined by next generation sequencing (NGS). In combination with existing expression profiles, we can conclude that co-orthologs of RBFs by large account for a preferential function in different tissue or at distinct developmental stages. This notion is supported by the differential expression of selected RBFs during male gametophyte development. In addition, co-regulated clusters of RBF and RP coding genes have been observed. The relevance of these results is discussed.

scholarly journals Reporting results of diagnostic NGS-based testing - user-centered redesign of the clinical report.

2021 ◽  
Author(s):  
Oleg Agafonov ◽  
Sigrun Vik ◽  
Kaja Kjølås ◽  
Sharmini Alagaratnam
Keyword(s):  
Clinical Diagnostics ◽  
Clinical Genetics ◽  
Clinical Report ◽  
Clinical Genomics ◽  
Therapeutic Decisions ◽  
Hand Off ◽  
Level Of Experience ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

The transition of next-generation sequencing (NGS) from the research environment to clinical diagnostics has proven difficult, with exome and whole genome sequencing at various stages of implementation in Nordic hospitals. The clinical genomics report details key findings from the interpretation of NGS data and represents the core hand-off between specialized clinical genomics laboratories and the broader healthcare community. However, these text-heavy reports can be difficult to read: critical information may be scattered around the report, and vital information such as limitations of the test may not always be present. Misunderstanding of results, limitations or key findings can lead to incorrect therapeutic decisions, directly impacting patient management. We applied the principles of user-centred design to redesign clinical reports to respond to user needs, while also incorporating existing recommendations and guidelines. We performed several rounds of needs gathering, first with producers of clinical genetics reports, then with clinicians with various level of experience in genetic testing. Based on the insights from a workshop and interviews, we created prototypes of reports which were evaluated in comparison to a set of simulated reports representing those currently in clinical production. Our results showed that the majority of evaluators found the redesigned reports to be clearer and easier to process, demonstrating the value of this approach.

scholarly journals CODEC enables 'single duplex' sequencing

2021 ◽  
Author(s):  
Jin H. Bae ◽  
Ruolin Liu ◽  
Erica Nguyen ◽  
Justin Rhoades ◽  
Timothy Blewett ◽  
...  
Keyword(s):  
Single Molecule ◽  
Cancer Diagnostics ◽  
Third Generation ◽  
Aging Research ◽  
Third Generation Sequencing ◽  
Double Stranded Dna ◽  
Duplex Sequencing ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Limited Accuracy

Detecting mutations as rare as a single molecule is crucial in many fields such as cancer diagnostics and aging research but remains challenging. Third generation sequencers can read a double-stranded DNA molecule (a 'single duplex') in whole to identify true mutations on both strands apart from false mutations on either strand but with limited accuracy and throughput. Although next generation sequencing (NGS) can track dissociated strands with Duplex Sequencing, the need to sequence each strand independently severely diminishes its throughput. Here, we developed a hybrid method called Concatenating Original Duplex for Error Correction (CODEC) that combines the massively parallel nature of NGS with the single-molecule capability of third generation sequencing. CODEC physically links both strands to enable NGS to sequence a single duplex with a single read pair. By comparing CODEC and Duplex Sequencing, we showed that CODEC achieved a similar error rate (10-6) with 100 times fewer reads and conferred 'single duplex' resolution to most major NGS workflows.

scholarly journals Environmental Variations in Mycobacterium ulcerans Transcriptome: Absence of Mycolactone Expression in Suboptimal Environments

Toxins ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 146
Author(s):  
Daniel Sanhueza ◽  
Jean-François Guégan ◽  
Heather Jordan ◽  
Christine Chevillon
Keyword(s):  
Culture Medium ◽  
Expression Profiles ◽  
Buruli Ulcer ◽  
Mycobacterium Ulcerans ◽  
Virulence Plasmid ◽  
Genomic Expression ◽  
Environmental Variations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Buruli ulcer is a neglected tropical infectious disease, produced by the environmentally persistent pathogen Mycobacterium ulcerans (MU). Neither the ecological niche nor the exact mode of transmission of MU are completely elucidated. However, some environmental factors, such as the concentration in chitin and pH values, were reported to promote MU growth in vitro. We pursued this research using next generation sequencing (NGS) and mRNA sequencing to investigate potential changes in MU genomic expression profiles across in vitro environmental conditions known to be suitable for MU growth. Supplementing the growth culture medium in either chitin alone, calcium alone, or in both chitin and calcium significantly impacted the MU transcriptome and thus several metabolic pathways, such as, for instance, those involved in DNA synthesis or cell wall production. By contrast, some genes carried by the virulence plasmid and necessary for the production of the mycolactone toxin were expressed neither in control nor in any modified environments. We hypothesized that these genes are only expressed in stressful conditions. Our results describe important environmental determinants playing a role in the pathogenicity of MU, helping the understanding of its complex natural life cycle and encouraging further research using genomic approaches.

A benchmarking of pipelines for detecting ncRNAs from RNA-Seq data

2019 ◽  
Vol 21 (6) ◽  
pp. 1987-1998 ◽  
Author(s):  
Sebastiano Di Bella ◽  
Alessandro La Ferlita ◽  
Giovanni Carapezza ◽  
Salvatore Alaimo ◽  
Antonella Isacchi ◽  
...  
Keyword(s):  
Transcriptome Profiling ◽  
Read Count ◽  
Ease Of Use ◽  
Rna Seq ◽  
Huge Amount ◽  
Key Points ◽  
High Throughput Technology ◽  
Different Populations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Next-Generation Sequencing (NGS) is a high-throughput technology widely applied to genome sequencing and transcriptome profiling. RNA-Seq uses NGS to reveal RNA identities and quantities in a given sample. However, it produces a huge amount of raw data that need to be preprocessed with fast and effective computational methods. RNA-Seq can look at different populations of RNAs, including ncRNAs. Indeed, in the last few years, several ncRNAs pipelines have been developed for ncRNAs analysis from RNA-Seq experiments. In this paper, we analyze eight recent pipelines (iSmaRT, iSRAP, miARma-Seq, Oasis 2, SPORTS1.0, sRNAnalyzer, sRNApipe, sRNA workbench) which allows the analysis not only of single specific classes of ncRNAs but also of more than one ncRNA classes. Our systematic performance evaluation aims at guiding users to select the appropriate pipeline for processing each ncRNA class, focusing on three key points: (i) accuracy in ncRNAs identification, (ii) accuracy in read count estimation and (iii) deployment and ease of use.

scholarly journals Advances in legume research in the genomics era

2019 ◽  
Author(s):  
Ashley N. Egan ◽  
Mohammad Vatanparast
Keyword(s):  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Nitrogen Fixers ◽  
Affected Plant ◽  
Plant Families ◽  
Patterns And Processes ◽  
Next Generation Sequencing Ngs ◽  
Marker Discovery ◽  
Generation Sequencing

Next-generation sequencing (NGS) technologies and applications have enabled numerous critical advances in legume biology, from marker discovery to whole-genome sequencing, and will provide many new avenues for legume research in the future. The past 6 years in particular have seen revolutionary advances in legume science because of the use of high-throughput sequencing, including the development of numerous types of markers and data useful for evolutionary studies above and below the species level that have enabled resolution of relationships that were previously unattainable. Such resolution, in turn, affords opportunities for hypothesis testing and inference to improve our understanding of legume biodiversity and the patterns and processes that have created one of the most diverse plant families on earth. In addition, the genomics era has seen significant advances in our understanding of the ecology of legumes, including their role as nitrogen fixers in global ecosystems. The accumulation of genetic and genomic data in the form of sequenced genomes and gene-expression profiles made possible through NGS platforms has also vastly affected plant-breeding and conservation efforts. Here, we summarise the knowledge gains enabled by NGS methods in legume biology from the perspectives of evolution, ecology, and development of genetic and genomic resources.

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