|
1
|
Palmer DS, Zhou W, Abbott L, Wigdor EM, Baya N, Churchhouse C, Seed C, Poterba T, King D, Kanai M, Bloemendal A, Neale BM. Analysis of genetic dominance in the UK Biobank. Science 2023; 379:1341-1348. [PMID: 36996212 PMCID: PMC10345642 DOI: 10.1126/science.abn8455] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/15/2023] [Indexed: 04/01/2023]
Abstract
Classical statistical genetics theory defines dominance as any deviation from a purely additive, or dosage, effect of a genotype on a trait, which is known as the dominance deviation. Dominance is well documented in plant and animal breeding. Outside of rare monogenic traits, however, evidence in humans is limited. We systematically examined common genetic variation across 1060 traits in a large population cohort (UK Biobank, N = 361,194 samples analyzed) for evidence of dominance effects. We then developed a computationally efficient method to rapidly assess the aggregate contribution of dominance deviations to heritability. Lastly, observing that dominance associations are inherently less correlated between sites at a genomic locus than their additive counterparts, we explored whether they may be leveraged to identify causal variants more confidently.
Collapse
Affiliation(s)
- Duncan S. Palmer
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wei Zhou
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Liam Abbott
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Nikolas Baya
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claire Churchhouse
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cotton Seed
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tim Poterba
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel King
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Masahiro Kanai
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alex Bloemendal
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin M. Neale
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
|
2
|
Chi X, Wang M, Pan Y, Jiang J, Jiang T, Yan H, Wu R, Wang X, Gao X, Niu J. Inosine triphosphate pyrophosphatase polymorphisms are predictors of anemia in Chinese patients with chronic hepatitis C during therapy with ribavirin and interferon. J Gastroenterol Hepatol 2020; 35:97-103. [PMID: 31359493 DOI: 10.1111/jgh.14812] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/26/2019] [Accepted: 07/21/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIM Polymorphisms of inosine triphosphate pyrophosphatase (rs1127354 and rs6051702) and interferon lambda 4 (IFLN4) (rs12979860) are indicators of anemia and/or sustained virological response (SVR) in patients with chronic hepatitis C on ribavirin/interferon. The study aims to investigate the associations of rs1127354, rs6051702, and rs12979860 with hemoglobin levels and SVR in patients on ribavirin/interferon. METHODS Polymorphisms were detected by pyrosequencing. Levels of hemoglobin and hepatitis C virus (HCV) RNA were measured at weeks 2, 4, 12, 24, 36, 48, and 72 of treatment. RESULTS A total of 351 patients (median age, 50 years; male, 71.2%) were recruited and had HCV genotypes 1b (55.8%) or 2a (37.0%). Vedian baseline hemoglobin and HCV RNA were 155 g/dL and 6.07 log10 IU/mL. Major allele homozygosity was observed in 76.3% for rs1127354 (CC), 70.9% for rs6051702 (AA), and 89.7% for rs12979860 (CC). At 4 weeks of ribavirin/interferon treatment, a more significant reduction in hemoglobin was observed with rs112754 CC than with AC/AA (P < 0.05). A decline ≥3 g/dL was more common in patients with the rs112754 CC than with the other two polymorphisms. No significant change was observed regarding rs6051702 and rs12979860 variants. In the multivariable analysis, rs1127354 AA/AC (vs CC) were independently associated with lower odds of hemoglobin decline of > 3 g/dL at 4 weeks (odds ratio, 0.21; 95% CI, 0.09-0.46; P < 0.0001). In 258 patients with 72-week outcome data available, rs1127354, rs6051702, and rs12979860 were not associated with SVR (all P > 0.05). CONCLUSION rs1127354 polymorphisms are associated with hemoglobin levels in Chinese patients with chronic hepatitis C treated with ribavirin/interferon.
Collapse
Affiliation(s)
- Xiumei Chi
- Department of Hepatology, The First Hospital of Jilin University, Changchun, China
| | - Moli Wang
- Department of Hepatology, The Fourth Hospital of Jilin University, Changchun, China
| | - Yu Pan
- Department of Hepatology, The First Hospital of Jilin University, Changchun, China
| | - Jing Jiang
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Tao Jiang
- Infectious Disease Hospital of Jilin Province, Changchun, China
| | - Hongqing Yan
- Department of Hepatology, The First Hospital of Jilin University, Changchun, China
| | - Ruihong Wu
- Department of Hepatology, The First Hospital of Jilin University, Changchun, China
| | - Xiaomei Wang
- Department of Hepatology, The First Hospital of Jilin University, Changchun, China
| | - Xiuzhu Gao
- Department of Hepatology, The First Hospital of Jilin University, Changchun, China
| | - Junqi Niu
- Department of Hepatology, The First Hospital of Jilin University, Changchun, China
| |
Collapse
|
|
3
|
Nyström K, Waldenström J, Tang KW, Lagging M. Ribavirin: pharmacology, multiple modes of action and possible future perspectives. Future Virol 2019. [DOI: 10.2217/fvl-2018-0166] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribavirin is a unique guanosine analog with broad-spectrum activity against many RNA and DNA viruses. In addition to its mutational properties, ribavirin exerts extensive perturbation of cellular and viral gene expression. Furthermore, recent advances indicate that the impact of ribavirin on divergent cellular and viral pathways may be concentration dependent. This review aims at providing an overview of the pharmacology and multiple modes of action of ribavirin as well as pointing to possible novel future uses.
Collapse
Affiliation(s)
- Kristina Nyström
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Västra Götaland Region, Sweden
| | - Jesper Waldenström
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Västra Götaland Region, Sweden
| | - Ka-Wei Tang
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Västra Götaland Region, Sweden
| | - Martin Lagging
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Västra Götaland Region, Sweden
| |
Collapse
|