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Jin Y, Chen G, Xiao W, Hong H, Xu J, Guo Y, Xiao W, Shi T, Shi L, Tong W, Ning B. Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine. SCIENCE CHINA-LIFE SCIENCES 2019; 62:895-904. [PMID: 31114935 DOI: 10.1007/s11427-018-9479-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/06/2018] [Indexed: 12/26/2022]
Abstract
High-throughput next generation sequencing (NGS) is a shotgun approach applied in a parallel fashion by which the genome is fragmented and sequenced through small pieces and then analyzed either by aligning to a known reference genome or by de novo assembly without reference genome. This technology has led researchers to conduct an explosion of sequencing related projects in multidisciplinary fields of science. However, due to the limitations of sequencing-based chemistry, length of sequencing reads and the complexity of genes, it is difficult to determine the sequences of some portions of the human genome, leaving gaps in genomic data that frustrate further analysis. Particularly, some complex genes are difficult to be accurately sequenced or mapped because they contain high GC-content and/or low complexity regions, and complicated pseudogenes, such as the genes encoding xenobiotic metabolizing enzymes and transporters (XMETs). The genetic variants in XMET genes are critical to predicate inter-individual variability in drug efficacy, drug safety and susceptibility to environmental toxicity. We summarized and discussed challenges, wet-lab methods, and bioinformatics algorithms in sequencing "complex" XMET genes, which may provide insightful information in the application of NGS technology for implementation in toxicogenomics and pharmacogenomics.
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Affiliation(s)
- Yaqiong Jin
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Geng Chen
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wenming Xiao
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Joshua Xu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wenzhong Xiao
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Cancer Center; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200433, China
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Baitang Ning
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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Precision or Personalized Medicine for Cancer Chemotherapy: Is there a Role for Herbal Medicine. Molecules 2016; 21:molecules21070889. [PMID: 27399658 PMCID: PMC6273869 DOI: 10.3390/molecules21070889] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/26/2016] [Accepted: 07/01/2016] [Indexed: 12/15/2022] Open
Abstract
Although over 100 chemotherapeutic agents are currently available for the treatment of cancer patients, the overall long term clinical benefit is disappointing due to the lack of effectiveness or severe side effects from these agents. In order to improve the therapeutic outcome, a new approach called precision medicine or personalized medicine has been proposed and initiated by the U.S. National Institutes of Health. However, the limited availability of effective medications and the high cost are still the major barriers for many cancer patients. Thus alternative approaches such as herbal medicines could be a feasible and less costly option. Unfortunately, scientific evidence for the efficacy of a majority of herbal medicines is still lacking and their development to meet FDA approval or other regulatory agencies is a big challenge. However, herbal medicines may be able to play an important role in precision medicine or personalized medicine. This review will focus on the existing and future technologies that could speed the development of herbal products for treatment of resistant cancer in individual patients. Specifically, it will concentrate on reviewing the phenotypic (activity based) rather than genotypic (mechanism based) approach to develop herbal medicine useful for personalized cancer chemotherapy.
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Li P, Liu Y, Wang H, He Y, Wang X, He Y, Lv F, Chen H, Pang X, Liu M, Shi T, Yi Z. PubAngioGen: a database and knowledge for angiogenesis and related diseases. Nucleic Acids Res 2014; 43:D963-7. [PMID: 25392416 PMCID: PMC4383947 DOI: 10.1093/nar/gku1139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Angiogenesis is the process of generating new blood vessels based on existing ones, which is involved in many diseases including cancers, cardiovascular diseases and diabetes mellitus. Recently, great efforts have been made to explore the mechanisms of angiogenesis in various diseases and many angiogenic factors have been discovered as therapeutic targets in anti- or pro-angiogenic drug development. However, the resulted information is sparsely distributed and no systematical summarization has been made. In order to integrate these related results and facilitate the researches for the community, we conducted manual text-mining from published literature and built a database named as PubAngioGen (http://www.megabionet.org/aspd/). Our online application displays a comprehensive network for exploring the connection between angiogenesis and diseases at multilevels including protein–protein interaction, drug-target, disease-gene and signaling pathways among various cells and animal models recorded through text-mining. To enlarge the scope of the PubAngioGen application, our database also links to other common resources including STRING, DrugBank and OMIM databases, which will facilitate understanding the underlying molecular mechanisms of angiogenesis and drug development in clinical therapy.
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Affiliation(s)
- Peng Li
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yongrui Liu
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Huan Wang
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yuan He
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xue Wang
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yundong He
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Fang Lv
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Huaqing Chen
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Pang
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Mingyao Liu
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China Center for Cancer and Stem Cell Biology, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Tieliu Shi
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhengfang Yi
- The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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Abstract
Hereditary neurological disorders (HNDs) are relatively common in children compared to those occurring in adulthood. Recognising clinical manifestations of HNDs is important for the selection of genetic testing, genetic testing results interpretation, and genetic consultation. Meanwhile, advances in next generation sequencing (NGS) technologies have significantly enabled the discovery of genetic causes of HNDs and also challenge paediatricians on applying genetic investigation. Combination of both clinical information and advanced technologies will enhance the genetic test yields in clinical setting. This review summarises the clinical presentations as well as genetic causes of paediatric neurological disorders in four major areas including movement disorders, neuropsychiatric disorders, neuron peripheral disorders and epilepsy. The aim of this review is to help paediatric neurologists not only to see the clinical features but also the complex genetic aspect of HNDs in order to utilise genetic investigation confidently in their clinical practice. A smooth transition from research based to clinical use of comprehensive genetic testing in HNDs in children could be foreseen in the near future while genetic testing, genetic counselling and genetic data interpretation are in place appropriately.
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Affiliation(s)
- Yue Huang
- 1 Neuroscience Research Australia & the University of New South Wales, NSW, 2031, Australia ; 2 Department of Genetic Medicine, SA Pathology at Women's and Children's Hospital, North Adelaide, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, South Australia, Australia ; 3 Cytogenetics Department, Western Sydney Genetics Program, Children's Hospital at Westmead, NSW, 2145, Australia ; 4 Department of Neurology, Xiangya Hospital, Central South University & National Laboratory of Medical Genetics of China, Changsha 410000, China
| | - Sui Yu
- 1 Neuroscience Research Australia & the University of New South Wales, NSW, 2031, Australia ; 2 Department of Genetic Medicine, SA Pathology at Women's and Children's Hospital, North Adelaide, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, South Australia, Australia ; 3 Cytogenetics Department, Western Sydney Genetics Program, Children's Hospital at Westmead, NSW, 2145, Australia ; 4 Department of Neurology, Xiangya Hospital, Central South University & National Laboratory of Medical Genetics of China, Changsha 410000, China
| | - Zhanhe Wu
- 1 Neuroscience Research Australia & the University of New South Wales, NSW, 2031, Australia ; 2 Department of Genetic Medicine, SA Pathology at Women's and Children's Hospital, North Adelaide, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, South Australia, Australia ; 3 Cytogenetics Department, Western Sydney Genetics Program, Children's Hospital at Westmead, NSW, 2145, Australia ; 4 Department of Neurology, Xiangya Hospital, Central South University & National Laboratory of Medical Genetics of China, Changsha 410000, China
| | - Beisha Tang
- 1 Neuroscience Research Australia & the University of New South Wales, NSW, 2031, Australia ; 2 Department of Genetic Medicine, SA Pathology at Women's and Children's Hospital, North Adelaide, School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, South Australia, Australia ; 3 Cytogenetics Department, Western Sydney Genetics Program, Children's Hospital at Westmead, NSW, 2145, Australia ; 4 Department of Neurology, Xiangya Hospital, Central South University & National Laboratory of Medical Genetics of China, Changsha 410000, China
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