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Recent innovations and in-depth aspects of post-genome wide association study (Post-GWAS) to understand the genetic basis of complex phenotypes. Heredity (Edinb) 2021; 127:485-497. [PMID: 34689168 PMCID: PMC8626474 DOI: 10.1038/s41437-021-00479-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
In the past decade, the high throughput and low cost of sequencing/genotyping approaches have led to the accumulation of a large amount of data from genome-wide association studies (GWASs). The first aim of this review is to highlight how post-GWAS analysis can be used make sense of the obtained associations. Novel directions for integrating GWAS results with other resources, such as somatic mutation, metabolite-transcript, and transcriptomic data, are also discussed; these approaches can help us move beyond each individual data point and provide valuable information about complex trait genetics. In addition, cross-phenotype association tests, when the loci detected by GWASs have significant associations with multiple traits, are reviewed to provide biologically informative results for use in real-time applications. This review also discusses the challenges of identifying interactions between genetic mutations (epistasis) and mutations of loci affecting more than one trait (pleiotropy) as underlying causes of cross-phenotype associations; these challenges can be overcome using post-GWAS analysis. Genetic similarities between phenotypes that can be revealed using post-GWAS analysis are also discussed. In summary, different methodologies of post-GWAS analysis are now available, enhancing the value of information obtained from GWAS results, and facilitating application in both humans and nonhuman species. However, precise methods still need to be developed to overcome challenges in the field and uncover the genetic underpinnings of complex traits.
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Osgood JA, Knight JC. Translating GWAS in rheumatic disease: approaches to establishing mechanism and function for genetic associations with ankylosing spondylitis. Brief Funct Genomics 2019; 17:308-318. [PMID: 29741584 PMCID: PMC6158798 DOI: 10.1093/bfgp/ely015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ankylosing spondylitis (AS) is a highly heritable chronic inflammatory arthritis characterized by osteoproliferation, fusion of affected joints and systemic manifestations. Many disease associations for AS have been reported through genome-wide association studies; however, identifying modulated genes and functional mechanism remains challenging. This review summarizes current genetic associations involving AS and describes strategic approaches for functional follow-up of disease-associated variants. Fine mapping using methods leveraging Bayesian approaches are outlined. Evidence highlighting the importance of context specificity for regulatory variants is reviewed, noting current evidence in AS for the relevant cell and tissue type to conduct such analyses. Technological advances for understanding the regulatory landscape within which functional variants may act are discussed using exemplars. Approaches include defining regulatory elements based on chromatin accessibility, effects of variants on genes at a distance through evidence of physical interactions (chromatin conformation capture), expression quantitative trait loci mapping and single-cell methodologies. Opportunities for mechanistic studies to investigate the function of specific variants, regulatory elements and genes enabled by genome editing using clustered regularly interspaced short palindromic repeats/Cas9 are also described. Further progress in our understanding of the genetics of AS through functional genomic and epigenomic approaches offers new opportunities to understand mechanism and develop innovative treatments.
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Affiliation(s)
- Julie A Osgood
- Functional genomics of ankylosing spondylitis, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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Li Z, Zhou C, Tan L, Chen P, Cao Y, Li X, Yan J, Zeng H, Wang DW, Wang DW. A targeted sequencing approach to find novel pathogenic genes associated with sporadic aortic dissection. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1545-1553. [DOI: 10.1007/s11427-018-9382-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/10/2018] [Indexed: 10/28/2022]
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Jenkins MA, Win AK, Templeton AS, Angelakos MS, Buchanan DD, Cotterchio M, Figueiredo JC, Thibodeau SN, Baron JA, Potter JD, Hopper JL, Casey G, Gallinger S, Le Marchand L, Lindor NM, Newcomb PA, Haile RW. Cohort Profile: The Colon Cancer Family Registry Cohort (CCFRC). Int J Epidemiol 2018; 47:387-388i. [PMID: 29490034 PMCID: PMC5913593 DOI: 10.1093/ije/dyy006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/19/2017] [Accepted: 01/15/2018] [Indexed: 01/02/2023] Open
Affiliation(s)
- Mark A Jenkins
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
- Genetic Medicine, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Allyson S Templeton
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Maggie S Angelakos
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
- Genetic Medicine, Royal Melbourne Hospital, Parkville, VIC, Australia
- Colorectal Oncogenomics Group, University of Melbourne, Parkville, VIC, Australia
| | | | - Jane C Figueiredo
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - John A Baron
- Department of Medicine, University of North Carolina School of Medicine, and Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | | | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - Robert W Haile
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Cheng Y, Wang C, Zhu M, Dai J, Wang Y, Geng L, Li Z, Zhang J, Ma H, Jin G, Lin D, Hu Z, Shen H. Targeted sequencing of chromosome 15q25 identified novel variants associated with risk of lung cancer and smoking behavior in Chinese. Carcinogenesis 2017; 38:552-558. [DOI: 10.1093/carcin/bgx025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/25/2017] [Indexed: 01/15/2023] Open
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Variants of genes encoding collagens and matrix metalloproteinase system increased the risk of aortic dissection. SCIENCE CHINA-LIFE SCIENCES 2016; 60:57-65. [PMID: 27975164 DOI: 10.1007/s11427-016-0333-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 11/01/2016] [Indexed: 10/20/2022]
Abstract
Aortic dissection (AD) is a devastating, heterogeneous condition of aorta. The homeostasis between collagens and matrix metalloproteases (MMPs)/tissue inhibitors of MMPs (TIMPs) system in the extracellular matrix plays an important role for structure and functions of aorta. However, our knowledge on association between variants of genes in this system and pathogenesis of AD is very limited. We analyzed all yet known coding human genes of collagens (45 genes), MMPs/TIMPs (27 genes) in 702 sporadic AD patients and in 163 matched healthy controls, by using massively targeted next-generation and Sanger sequencing. To define the pathogenesis of potential disease-causing candidate genes, we performed transcriptome sequencing and pedigree co-segregation analysis in some genes and generated Col5a2 knockout rats. We identified 257 pathogenic or likely pathogenic variants which involved 88.89% (64/72) genes in collagens-MMPs/TIMPs system and accounted for 31.05% (218/702) sporadic AD patients. In them, 84.86% patients (185/218) carried one variant, 12.84% two variants and 2.30% more than two variants. Importantly, we identified 52 novel probably pathogenic loss-of-function (LOF) variants (20 nonsense, 16 frameshift, 14 splice sites, one stop-loss, one initiation codon) in 11.06% (50/452) AD patients, which were absent in 163 controls (P=2.5×10-5). Transcriptome sequencing revealed that identified variants induced dyshomeostasis in expression of collagens-TIMPs/MMPs systems. The Col5a2 -/- rats manifested growth retardation and aortic dysplasia. Our study provides a first comprehensive map of genetic alterations in collagens-MMPs/TIMPs system in sporadic AD patients and suggests that variants of these genes contribute largely to AD pathogenesis.
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