Next Generation Sequencing: Potential and Application in Drug Discovery

Yadav, Navneet Kumar; Shukla, Pooja; Omer, Ankur; Pareek, Shalini; Rajender, Singh

doi:10.1155/2014/802437

Cited by 15 publications

(12 citation statements)

References 46 publications

(51 reference statements)

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“…The most extensively applied techniques of studying miRNA profiles are microarray, real-time PCR-based methods, as well as sequencing and in situ hybridization (ISH) (Weng et al, 2010;Xie et al, 2011). Next Generation Sequencing (NGS) added a new layer of accuracy as new method for miRNA expression measurement and normalization and provided new knowledge of changes in genome and relevant disease for translational studies (Yadav et al, 2014).…”

Section: Cancer Diagnosismentioning

confidence: 99%

MicroRNAs in Colorectal Cancer: from Diagnosis to Targeted Therapy

Orang¹,

Barzegari²

2014

Asian Pacific Journal of Cancer Prevention

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Colorectal cancer (CRC) is one of the major healthcare problems worldwide and its processes of genesis include a sequence of molecular pathways from adenoma to carcinoma. The discovery of microRNAs, a subset of regulatory non-coding RNAs, has added new insights into CRC diagnosis and management. Together with several causes of colorectal neoplasia, aberrant expression of oncomiRs (oncogenic and tumor suppressor miRNAs) in cancer cells was found to be indirectly result in up-or down-regulation of targeted mRNAs specific to tumor promoter or inhibitor genes. The study of miRNAs as CRC biomarkers utilizes expression profiling methods from traditional tissue samples along with newly introduced non-invasive samples of faeces and body fluids. In addition, miRNAs could be employed to predict chemo-and radio-therapy responses and be manipulated in order to alleviate CRC characteristics. The scope of this article is to provide a comprehensive review of scientific literature describing aberrantly expressed miRNAs, and consequently dysregulation of targeted mRNAs along with the potential role of miRNAs in CRC diagnosis and prognosis, as well as to summarize the recent findings on miRNA-based manipulation methods with the aim of advancing in anti-CRC therapies.

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Section: Cancer Diagnosismentioning

confidence: 99%

MicroRNAs in Colorectal Cancer: from Diagnosis to Targeted Therapy

Orang¹,

Barzegari²

2014

Asian Pacific Journal of Cancer Prevention

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“…RNA-Seq, as one of NGS applications, enables high-throughput transcriptomic analysis of gene expression profiles at the tissue level (Metzker 2010) and can be applied to various species and sources of RNA/DNA. The main advantages of RNA-Seq include high detection sensitivity, accuracy, increased automation and relatively low cost (Yadav et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic characterization of culture-associated changes in murine and human precision-cut tissue slices

et al. 2019

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Our knowledge of complex pathological mechanisms underlying organ fibrosis is predominantly derived from animal studies. However, relevance of animal models for human disease is limited; therefore, an ex vivo model of human precision-cut tissue slices (PCTS) might become an indispensable tool in fibrosis research and drug development by bridging the animal-human translational gap. This study, presented as two parts, provides comprehensive characterization of the dynamic transcriptional changes in PCTS during culture by RNA sequencing. Part I investigates the differences in culture-induced responses in murine and human PCTS derived from healthy liver, kidney and gut. Part II delineates the molecular processes in cultured human PCTS generated from diseased liver, kidney and ileum. We demonstrated that culture was associated with extensive transcriptional changes and impacted PCTS in a universal way across the organs and two species by triggering an inflammatory response and fibrosis-related extracellular matrix (ECM) remodelling. All PCTS shared mRNA upregulation of IL-11 and ECM-degrading enzymes MMP3 and MMP10. Slice preparation and culturing activated numerous pathways across all PCTS, especially those involved in inflammation (IL-6, IL-8 and HMGB1 signalling) and tissue remodelling (osteoarthritis pathway and integrin signalling). Despite the converging effects of culture, PCTS display species-, organ-and pathologyspecific differences in the regulation of genes and canonical pathways. The underlying pathology in human diseased PCTS endures and influences biological processes like cytokine release. Our study reinforces the use of PCTS as an ex vivo fibrosis model and supports future studies towards its validation as a preclinical tool for drug development.

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“…The substantial decrease in the cost of NGS techniques in the past decade has dramatically reshaped the biomedical research and has led to its rapid adoption in biological research and drug development [3,4]. Nowadays, massive amount of data, targeting a variety of biological questions, can be generated quickly using NGS platforms.…”

Section: Resultsmentioning

confidence: 99%

“…High-throughput next-generation sequencing (NGS) technologies have evolved rapidly and are reshaping the scope of genomics research [1,2] and drug development [3,4]. The significant advances in NGS technologies, and consequently, the exponential expansion of biological data have created a huge gap between the computer capabilities and sequencing throughput [5,6].…”

Section: Introductionmentioning

confidence: 99%

Cloud Computing for Next-Generation Sequencing Data Analysis

Zhao¹,

Watrous²,

Zhang³

et al. 2017

Cloud Computing - Architecture and Applications

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High-throughput next-generation sequencing (NGS) technologies have evolved rapidly and are reshaping the scope of genomics research. The substantial decrease in the cost of NGS techniques in the past decade has led to its rapid adoption in biological research and drug development. Genomics studies of large populations are producing a huge amount of data, giving rise to computational issues around the storage, transfer, and analysis of the data. Fortunately, cloud computing has recently emerged as a viable option to quickly and easily acquire the computational resources for large-scale NGS data analyses. Some cloud-based applications and resources have been developed specifically to address the computational challenges of working with very large volumes of data generated by NGS technology. In this chapter, we will review some cloud-based systems and solutions for NGS data analysis, discuss the practical hurdles and limitations in cloud computing, including data transfer and security, and share the lessons we learned from the implementation of Rainbow, a cloud-based tool for large-scale genome sequencing data analysis.

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Next Generation Sequencing: Potential and Application in Drug Discovery

Cited by 15 publications

References 46 publications

MicroRNAs in Colorectal Cancer: from Diagnosis to Targeted Therapy

MicroRNAs in Colorectal Cancer: from Diagnosis to Targeted Therapy

Transcriptomic characterization of culture-associated changes in murine and human precision-cut tissue slices

Cloud Computing for Next-Generation Sequencing Data Analysis

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