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Papageorgiou L, Papakonstantinou E, Diakou I, Pierouli K, Dragoumani K, Bacopoulou F, Chrousos GP, Eliopoulos E, Vlachakis D. Semantic and Population Analysis of the Genetic Targets Related to COVID-19 and Its Association with Genes and Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:59-78. [PMID: 37525033 DOI: 10.1007/978-3-031-31978-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
SARS-CoV-2 is a coronavirus responsible for one of the most serious, modern worldwide pandemics, with lasting and multifaceted effects. By late 2021, SARS-CoV-2 has infected more than 180 million people and has killed more than 3 million. The virus gains entrance to human cells through binding to ACE2 via its surface spike protein and causes a complex disease of the respiratory system, termed COVID-19. Vaccination efforts are being made to hinder the viral spread, and therapeutics are currently under development. Toward this goal, scientific attention is shifting toward variants and SNPs that affect factors of the disease such as susceptibility and severity. This genomic grammar, tightly related to the dark part of our genome, can be explored through the use of modern methods such as natural language processing. We present a semantic analysis of SARS-CoV-2-related publications, which yielded a repertoire of SNPs, genes, and disease ontologies. Population data from the 1000 Genomes Project were subsequently integrated into the pipeline. Data mining approaches of this scale have the potential to elucidate the complex interaction between COVID-19 pathogenesis and host genetic variation; the resulting knowledge can facilitate the management of high-risk groups and aid the efforts toward precision medicine.
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Affiliation(s)
- Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - George P Chrousos
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece.
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece.
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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High prevalence of dengue antibodies and the arginine variant of the FcγRIIa polymorphism in asymptomatic individuals in a population of Minas Gerais State, Southeast Brazil. Immunogenetics 2017; 70:355-362. [DOI: 10.1007/s00251-017-1046-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/12/2017] [Indexed: 12/30/2022]
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Karaca S, Karaca M, Cesuroglu T, Erge S, Polimanti R. GSTM1,GSTP1, andGSTT1genetic variability in Turkish and worldwide populations. Am J Hum Biol 2014; 27:310-6. [DOI: 10.1002/ajhb.22671] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/16/2014] [Accepted: 11/22/2014] [Indexed: 12/22/2022] Open
Affiliation(s)
- Sefayet Karaca
- School of Health Science, Aksaray University; Aksaray Turkey
- GENAR Institute for Public Health and Genomics Research; Ankara Turkey
| | - Mehmet Karaca
- Department of Biology; Faculty of Science and Arts, Aksaray University; Aksaray Turkey
| | - Tomris Cesuroglu
- GENAR Institute for Public Health and Genomics Research; Ankara Turkey
- Department of Social Medicine; Maastricht University; Maastricht the Netherlands
| | - Sema Erge
- GENAR Institute for Public Health and Genomics Research; Ankara Turkey
- Department of Nutrition and Dietetics; Faculty of Health Science, Zirve University; Gaziantep Turkey
| | - Renato Polimanti
- Department of Psychiatry; Yale University School of Medicine; West Haven Connecticut United States
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An abundance of population-specific monomorphic SNPs may or may not be meaningful: a commentary on differences in allele frequencies of familial hypercholesterolemia SNPs in the Malaysian population. J Hum Genet 2012; 57:403-4. [DOI: 10.1038/jhg.2012.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Lin WY, Liu N. Reducing bias of allele frequency estimates by modeling SNP genotype data with informative missingness. Front Genet 2012; 3:107. [PMID: 22719749 PMCID: PMC3376470 DOI: 10.3389/fgene.2012.00107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 05/25/2012] [Indexed: 01/30/2023] Open
Abstract
The presence of missing single-nucleotide polymorphism (SNP) genotypes is common in genetic studies. For studies with low-density SNPs, the most commonly used approach to dealing with genotype missingness is to simply remove the observations with missing genotypes from the analyses. This naïve method is straightforward but is valid only when the missingness is random. However, a given assay often has a different capability in genotyping heterozygotes and homozygotes, causing the phenomenon of "differential dropout" in the sense that the missing rates of heterozygotes and homozygotes are different. In practice, differential dropout among genotypes exists in even carefully designed studies, such as the data from the HapMap project and the Wellcome Trust Case Control Consortium. Under the assumption of Hardy-Weinberg equilibrium and no genotyping error, we here propose a statistical method to model the differential dropout among different genotypes. Compared with the naïve method, our method provides more accurate allele frequency estimates when the differential dropout is present. To demonstrate its practical use, we further apply our method to the HapMap data and a scleroderma data set.
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Affiliation(s)
- Wan-Yu Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University Taipei, Taiwan
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Mattei J, Parnell LD, Lai CQ, Garcia-Bailo B, Adiconis X, Shen J, Arnett D, Demissie S, Tucker KL, Ordovas JM. Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites. BMC Genet 2009; 10:45. [PMID: 19682384 PMCID: PMC2734553 DOI: 10.1186/1471-2156-10-45] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Accepted: 08/14/2009] [Indexed: 12/21/2022] Open
Abstract
Background Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST) can evidence environmental selection pressures. Such genetic information is limited in Puerto Ricans, the second largest Hispanic ethnic group in the US, and a group with high prevalence of chronic disease. We determined allele frequencies and population differentiation for 101 single nucleotide polymorphisms (SNPs) in 30 genes involved in major metabolic and disease-relevant pathways in Puerto Ricans (n = 969, ages 45–75 years) and compared them to similarly aged non-Hispanic whites (NHW) (n = 597). Results Minor allele frequency (MAF) distributions for 45.5% of the SNPs assessed in Puerto Ricans were significantly different from those of NHW. Puerto Ricans carried risk alleles in higher frequency and protective alleles in lower frequency than NHW. Patterns of population differentiation showed that Puerto Ricans had SNPs with exceptional FST values in intronic, non-synonymous and promoter regions. NHW had exceptional FST values in intronic and promoter region SNPs only. Conclusion These observations may serve to explain and broaden studies on the impact of gene polymorphisms on chronic diseases affecting Puerto Ricans.
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Affiliation(s)
- Josiemer Mattei
- Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA.
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Langevin SM, Lin D, Matsuo K, Gao CM, Takezaki T, Stolzenberg-Solomon RZ, Vasavi M, Hasan Q, Taioli E. Review and pooled analysis of studies on MTHFR C677T polymorphism and esophageal cancer. Toxicol Lett 2008; 184:73-80. [PMID: 18840514 DOI: 10.1016/j.toxlet.2008.09.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Revised: 09/03/2008] [Accepted: 09/03/2008] [Indexed: 12/23/2022]
Abstract
Esophageal cancer has been associated with tobacco and alcohol consumption, gastric reflux, exposure to nitrosamines from food or other environmental sources, and diets lacking folate. Susceptibility to esophageal cancer may be modified by functional polymorphisms in genes along the folate metabolic pathway, such as methylenetetrahydrofolate reductase (MTHFR). The C677T polymorphism is the most common functional variant, leading to a reduction in enzyme activity. We report a pooled analysis of 5 studies on the association of MTHFR C677T polymorphism and esophageal cancer, including 725 cases and 1531 controls. A significant association between the MTHFR 677 TT genotype and esophageal cancer was observed (OR=2.63, 95% CI: 1.75-3.94), although there was significant heterogeneity between studies. A sensitivity analysis excluded one study; the association between TT genotype and esophageal cancer was still present, although of reduced magnitude (OR=1.57, 95% CI: 0.96-2.56). A significant interaction between smoking and TT genotype on esophageal cancer risk was observed, while no interaction was observed between alcohol consumption and genotype.
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Affiliation(s)
- S M Langevin
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
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