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Tripathi P, Singh J, Lal JA, Tripathi V. Next-Generation Sequencing: An Emerging Tool for Drug Designing. Curr Pharm Des 2020; 25:3350-3357. [PMID: 31544713 DOI: 10.2174/1381612825666190911155508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. METHOD In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. DISCUSSIONS The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. CONCLUSION Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.
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Affiliation(s)
- Pooja Tripathi
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India
| | - Jyotsna Singh
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India
| | - Jonathan A Lal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India.,Institute for Public Health Genomics, Maastricht University, Maastricht, Netherlands
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India
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Explaining cancer type specific mutations with transcriptomic and epigenomic features in normal tissues. Sci Rep 2018; 8:11456. [PMID: 30061703 PMCID: PMC6065413 DOI: 10.1038/s41598-018-29861-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/17/2018] [Indexed: 12/20/2022] Open
Abstract
Most cancer driver genes are involved in generic cellular processes such as DNA repair, cell proliferation and cell adhesion, yet their mutations are often confined to specific cancer types. To resolve this paradox, we explained mutation frequencies of selected genes across tumor types with four features in the corresponding normal tissues from cancer-free subjects: mRNA expression and chromatin accessibility of mutated genes, mRNA expressions of their neighbors in curated pathways and the protein-protein interaction network. Encouragingly, these transcriptomic/epigenomic features in normal tissues were closely associated with mutational/functional characteristics in tumors. First, chromatin accessibility was a necessary but not sufficient condition for frequent mutations. Second, variations of mutation frequencies in selected genes across tissue types were significantly associated with all four features. Third, the genes possessing significant associations between mutation frequency variations and pathway gene expression were enriched with documented cancer genes. We further proposed a novel bivariate gene set enrichment analysis and confirmed that the pathway gene expression was the dominant factor in cancer gene enrichment. These findings shed lights on the functional roles of genes in normal tissues in shaping the mutational landscape during tumor genome evolution.
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Kumar G, Chaudhary KK, Misra K, Tripathi A. Next-Generation Sequencing for Drug Designing and Development: An Omics Approach for Cancer Treatment. INT J PHARMACOL 2017. [DOI: 10.3923/ijp.2017.709.723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Mao Q, Qiu M, Dong G, Xia W, Zhang S, Xu Y, Wang J, Rong Y, Xu L, Jiang F. CAG repeat polymorphisms in the androgen receptor and breast cancer risk in women: a meta-analysis of 17 studies. Onco Targets Ther 2015; 8:2111-20. [PMID: 26316780 PMCID: PMC4540135 DOI: 10.2147/ott.s85130] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The association between polymorphic CAG repeats in the androgen receptor gene in women and breast cancer susceptibility has been studied extensively. However, the conclusions regarding this relationship remain conflicting. The purpose of this meta-analysis was to identify whether androgen receptor CAG repeat lengths were related to breast cancer susceptibility. The MEDLINE, PubMed, and EMBASE databases were searched through to December 2014 to identify eligible studies. Data and study quality were rigorously assessed by two investigators according to the Newcastle-Ottawa Quality Assessment Scale. The publication bias was assessed by the Begg’s test. Seventeen eligible studies were included in this meta-analysis. The overall analysis suggested no association between CAG polymorphisms and breast cancer risk (odds ratio [OR] 1.031, 95% confidence interval [CI] 0.855–1.245). However, in the subgroup analysis, we observed that long CAG repeats significantly increased the risk of breast cancer in the Caucasian population (OR 1.447, 95% CI 1.089–1.992). Additionally, the risk was significantly increased in Caucasian women carrying two alleles with CAG repeats ≥22 units compared with those with two shorter alleles (OR 1.315, 95% CI 1.014–1.707). These findings suggest that long CAG repeats increase the risk of breast cancer in Caucasian women. However, larger scale case-control studies are needed to validate our results.
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Affiliation(s)
- Qixing Mao
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China ; Fourth Clinical College of Nanjing Medical University, Nanjing, People's Republic of China ; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People's Republic of China
| | - Mantang Qiu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China ; Fourth Clinical College of Nanjing Medical University, Nanjing, People's Republic of China ; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People's Republic of China
| | - Gaochao Dong
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People's Republic of China
| | - Wenjie Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China ; Fourth Clinical College of Nanjing Medical University, Nanjing, People's Republic of China ; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People's Republic of China
| | - Shuai Zhang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China ; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People's Republic of China
| | - Youtao Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China ; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People's Republic of China
| | - Jie Wang
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People's Republic of China
| | - Yin Rong
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China ; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People's Republic of China
| | - Lin Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China ; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People's Republic of China
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Institute of Jiangsu Province, Nanjing, People's Republic of China ; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People's Republic of China
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Altinoz MA, Tunalı NE. Trinucleotide repeat expansions in human breast cancer-susceptibility genes: relevant targets for aspirin chemoprevention? Clin Transl Oncol 2015. [PMID: 26199016 DOI: 10.1007/s12094-015-1356-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE Defining novel molecular mechanisms pertinent to aspirin chemoprevention of breast cancer (BC) and to explain controversial epidemiological results in this regard. METHODS Literature search in relevant databases with the following key words; aspirin, nucleotide repeat expansions, breast cancer. Human genome contains nucleotide repeat expansions and exon-1 of the androgen receptor gene AR contains a CAG string with an average of 20 repeats. Longer AR CAG repeats associate with lower AR protein functioning leading relatively higher estrogen receptor signals and higher risk of hormone receptor-positive BC. Nucleotide repeat expansions also exist in E2F4 and POLG genes in BC. In cell culture models, aspirin reduces CAG.CTG expansions in kidney cells and restores myogenic differentiation in cells obtained from tissues with myotonic dystrophy, a disorder caused by large CTG expansions. CONCLUSIONS We hypothesize that aspirin reduction of trinucleotide repeat expansions in breast cancer-susceptibility genes may be one of the relevant mechanisms of its chemopreventive effects.
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Affiliation(s)
- M A Altinoz
- Department of Immunology, Experimental Medicine Research Institute - DETAE, Istanbul University, Istanbul, Turkey.
| | - N E Tunalı
- Department of Molecular Biology and Genetics, Halic University, Istanbul, Turkey
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Shen T, Pajaro-Van de Stadt SH, Yeat NC, Lin JCH. Clinical applications of next generation sequencing in cancer: from panels, to exomes, to genomes. Front Genet 2015; 6:215. [PMID: 26136771 PMCID: PMC4469892 DOI: 10.3389/fgene.2015.00215] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/02/2015] [Indexed: 01/08/2023] Open
Abstract
This article will review recent impact of massively parallel next-generation sequencing (NGS) in our understanding and treatment of cancer. While whole exome sequencing (WES) remains popular and effective as a method of genetically profiling different cancers, advances in sequencing technology has enabled an increasing number of whole-genome based studies. Clinically, NGS has been used or is being developed for genetic screening, diagnostics, and clinical assessment. Though challenges remain, clinicians are in the early stages of using genetic data to make treatment decisions for cancer patients. As the integration of NGS in the study and treatment of cancer continues to mature, we believe that the field of cancer genomics will need to move toward more complete 100% genome sequencing. Current technologies and methods are largely limited to coding regions of the genome. A number of recent studies have demonstrated that mutations in non-coding regions may have direct tumorigenic effects or lead to genetic instability. Non-coding regions represent an important frontier in cancer genomics.
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Affiliation(s)
- Tony Shen
- Rare Genomics InstituteBethesda, MD, USA
- School of Medicine, Washington UniversitySaint Louis, MO, USA
| | | | - Nai Chien Yeat
- Rare Genomics InstituteBethesda, MD, USA
- School of Medicine, Washington UniversitySaint Louis, MO, USA
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Gottlieb B, Beitel LK, Trifiro M. Changing genetic paradigms: creating next-generation genetic databases as tools to understand the emerging complexities of genotype/phenotype relationships. Hum Genomics 2014; 8:9. [PMID: 24885908 PMCID: PMC4040485 DOI: 10.1186/1479-7364-8-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 04/25/2014] [Indexed: 12/18/2022] Open
Abstract
Understanding genotype/phenotype relationships has become more complicated as increasing amounts of inter- and intra-tissue genetic heterogeneity have been revealed through next-generation sequencing and evidence showing that factors such as epigenetic modifications, non-coding RNAs and RNA editing can play an important role in determining phenotype. Such findings have challenged a number of classic genetic assumptions including (i) analysis of genomic sequence obtained from blood is an accurate reflection of the genotype responsible for phenotype expression in an individual; (ii) that significant genetic alterations will be found only in diseased individuals, in germline tissues in inherited diseases, or in specific diseased tissues in somatic diseases such as cancer; and (iii) that mutation rates in putative disease-associated genes solely determine disease phenotypes. With the breakdown of our traditional understanding of genotype to phenotype relationships, it is becoming increasingly apparent that new analytical tools will be required to determine the relationship between genotype and phenotypic expression. To this end, we are proposing that next-generation genetic database (NGDB) platforms be created that include new bioinformatics tools based on algorithms that can evaluate genetic heterogeneity, as well as powerful systems biology analysis tools to actively process and evaluate the vast amounts of both genomic and genomic-modifying information required to reveal the true relationships between genotype and phenotype.
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Affiliation(s)
- Bruce Gottlieb
- Lady Davis Institute for Medical Research, 3755 Côte Ste Catherine Road, Montreal, QC H3T 1E2, Canada
- Segal Cancer Centre, Jewish General Hospital, 3755 Côte Ste Catherine Road, Montreal, QC H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Lenore K Beitel
- Lady Davis Institute for Medical Research, 3755 Côte Ste Catherine Road, Montreal, QC H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Mark Trifiro
- Lady Davis Institute for Medical Research, 3755 Côte Ste Catherine Road, Montreal, QC H3T 1E2, Canada
- Segal Cancer Centre, Jewish General Hospital, 3755 Côte Ste Catherine Road, Montreal, QC H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
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