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Zhang W, Zhang H, Yang H, Li M, Xie Z, Li W. Computational resources associating diseases with genotypes, phenotypes and exposures. Brief Bioinform 2020; 20:2098-2115. [PMID: 30102366 PMCID: PMC6954426 DOI: 10.1093/bib/bby071] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/01/2018] [Indexed: 12/16/2022] Open
Abstract
The causes of a disease and its therapies are not only related to genotypes, but also associated with other factors, including phenotypes, environmental exposures, drugs and chemical molecules. Distinguishing disease-related factors from many neutral factors is critical as well as difficult. Over the past two decades, bioinformaticians have developed many computational resources to integrate the omics data and discover associations among these factors. However, researchers and clinicians are experiencing difficulties in choosing appropriate resources from hundreds of relevant databases and software tools. Here, in order to assist the researchers and clinicians, we systematically review the public computational resources of human diseases related to genotypes, phenotypes, environment factors, drugs and chemical exposures. We briefly describe the development history of these computational resources, followed by the details of the relevant databases and software tools. We finally conclude with a discussion of current challenges and future opportunities as well as prospects on this topic.
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Affiliation(s)
- Wenliang Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Haiyue Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Huan Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhi Xie
- State Key Lab of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 500040, China
| | - Weizhong Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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Mock A, Murphy S, Morris J, Marass F, Rosenfeld N, Massie C. CVE: an R package for interactive variant prioritisation in precision oncology. BMC Med Genomics 2017; 10:37. [PMID: 28545463 PMCID: PMC5445311 DOI: 10.1186/s12920-017-0261-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 04/20/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND An increasing number of precision oncology programmes are being launched world-wide. To support this development, we present the Cancer Variant Explorer (CVE), an R package with an interactive Shiny web browser interface. RESULTS Leveraging Oncotator and the Drug Gene Interaction Database, CVE offers exploration of variants within single or multiple tumour exomes to identify drivers, resistance mechanisms and to assess druggability. We present example applications including the analysis of an individual patient and a cohort-wide study, and provide a first extension of CVE by adding a tumour-specific co-expression network. CONCLUSIONS The CVE package allows interactive variant prioritisation to expedite the analysis of cancer sequencing studies. Our framework also includes the prioritisation of druggable targets, allows exploratory analysis of tissue specific networks and is extendable for specific applications by virtue of its modular design. We encourage the use of CVE within translational research studies and molecular tumour boards. The CVE package is available via Bioconductor ( http://bioconductor.org/packages/CVE/ ).
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Affiliation(s)
- Andreas Mock
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
| | - Suzanne Murphy
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
| | - James Morris
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
| | - Francesco Marass
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
| | - Charlie Massie
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
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Oud MM, Lamers IJC, Arts HH. Ciliopathies: Genetics in Pediatric Medicine. J Pediatr Genet 2016; 6:18-29. [PMID: 28180024 DOI: 10.1055/s-0036-1593841] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/08/2016] [Indexed: 12/15/2022]
Abstract
Ciliary disorders, which are also referred to as ciliopathies, are a group of hereditary disorders that result from dysfunctional cilia. The latter are cellular organelles that stick up from the apical plasma membrane. Cilia have important roles in signal transduction and facilitate communications between cells and their surroundings. Ciliary disruption can result in a wide variety of clinically and genetically heterogeneous disorders with overlapping phenotypes. Because cilia occur widespread in our bodies many organs and sensory systems can be affected when they are dysfunctional. Ciliary disorders may be isolated or syndromic, and common features are cystic liver and/or kidney disease, blindness, neural tube defects, brain anomalies and intellectual disability, skeletal abnormalities ranging from polydactyly to abnormally short ribs and limbs, ectodermal defects, obesity, situs inversus, infertility, and recurrent respiratory tract infections. In this review, we summarize the features, frequency, morbidity, and mortality of each of the different ciliopathies that occur in pediatrics. The importance of genetics and the occurrence of genotype-phenotype correlations are indicated, and advances in gene identification are discussed. The use of next-generation sequencing by which a gene panel or all genes can be screened in a single experiment is highlighted as this technology significantly lowered costs and time of the mutation detection process in the past. We discuss the challenges of this new technology and briefly touch upon the use of whole-exome sequencing as a diagnostic test for ciliary disorders. Finally, a perspective on the future of genetics in the context of ciliary disorders is provided.
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Affiliation(s)
- Machteld M Oud
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ideke J C Lamers
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heleen H Arts
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
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Tan PPC, Rogic S, Zoubarev A, McDonald C, Lui F, Charathsandran G, Jacobson M, Belmadani M, Leong J, Van Rossum T, Portales-Casamar E, Qiao Y, Calli K, Liu X, Hudson M, Rajcan-Separovic E, Lewis MES, Pavlidis P. Interactive Exploration, Analysis, and Visualization of Complex Phenome-Genome Datasets with ASPIREdb. Hum Mutat 2016; 37:719-26. [PMID: 27158917 PMCID: PMC4940263 DOI: 10.1002/humu.23011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/28/2016] [Indexed: 11/10/2022]
Abstract
Identifying variants causal for complex genetic disorders is challenging. With the advent of whole-exome and whole-genome sequencing, computational tools are needed to explore and analyze the list of variants for further validation. Correlating genetic variants with subject phenotype is crucial for the interpretation of the disease-causing mutations. Often such work is done by teams of researchers who need to share information and coordinate activities. To this end, we have developed a powerful, easy to use Web application, ASPIREdb, which allows researchers to search, organize, analyze, and visualize variants and phenotypes associated with a set of human subjects. Investigators can annotate variants using publicly available reference databases and build powerful queries to identify subjects or variants of interest. Functional information and phenotypic associations of these genes are made accessible as well. Burden analysis and additional reporting tools allow investigation of variant properties and phenotype characteristics. Projects can be shared, allowing researchers to work collaboratively to build queries and annotate the data. We demonstrate ASPIREdb's functionality using publicly available data sets, showing how the software can be used to accomplish goals that might otherwise require specialized bioinformatics expertise. ASPIREdb is available at http://aspiredb.chibi.ubc.ca.
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Affiliation(s)
- Powell Patrick Cheng Tan
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Sanja Rogic
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Anton Zoubarev
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Cameron McDonald
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Frances Lui
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Gayathiri Charathsandran
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Jacobson
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Manuel Belmadani
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Justin Leong
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Thea Van Rossum
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Elodie Portales-Casamar
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Ying Qiao
- Department of Pathology, BC Child and Family Research Institute, University of British Columbia (UBC), 950 West 28th, Room 3060, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics, BC Child and Family Research Institute, UBC, Vancouver, BC V6H 3N1, Canada
| | - Kristina Calli
- Department of Medical Genetics, BC Child and Family Research Institute, UBC, Vancouver, BC V6H 3N1, Canada
| | - Xudong Liu
- Department of Psychiatry, Queen's University, Kingston, Ontario K7L 3N6 Canada
- Ongwanada Resource Cente, Kingston, Ontario K7L 3N6 Canada
| | - Melissa Hudson
- Department of Psychiatry, Queen's University, Kingston, Ontario K7L 3N6 Canada
| | - Evica Rajcan-Separovic
- Department of Pathology, BC Child and Family Research Institute, University of British Columbia (UBC), 950 West 28th, Room 3060, Vancouver, BC V5Z 4H4, Canada
| | - ME Suzanne Lewis
- Department of Medical Genetics, BC Child and Family Research Institute, UBC, Vancouver, BC V6H 3N1, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
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Gasc C, Peyretaillade E, Peyret P. Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms. Nucleic Acids Res 2016; 44:4504-18. [PMID: 27105841 PMCID: PMC4889952 DOI: 10.1093/nar/gkw309] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/07/2016] [Accepted: 04/12/2016] [Indexed: 12/25/2022] Open
Abstract
The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology.
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Affiliation(s)
- Cyrielle Gasc
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
| | | | - Pierre Peyret
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
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