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Al-Eitan LN, ElMotasem MFM, Khair IY, Alahmad SZ. Vaccinomics: Paving the Way for Personalized Immunization. Curr Pharm Des 2024; 30:1031-1047. [PMID: 38898820 DOI: 10.2174/0113816128280417231204085137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/15/2023] [Indexed: 06/21/2024]
Abstract
Vaccines are one of the most important medical advancements in human history. They have been successfully used to control and limit the spread of many of the lethal diseases that have plagued us, such as smallpox and polio. Previous vaccine design methodologies were based on the model of "isolate-inactivateinject", which amounts to giving the same vaccine dose to everyone susceptible to infection. In recent years, the importance of how the host genetic background alters vaccine response necessitated the introduction of vaccinomics, which is aimed at studying the variability of vaccine efficacy by associating genetic variability and immune response to vaccination. Despite the rapid developments in variant screening, data obtained from association studies is often inconclusive and cannot be used to guide the new generation of vaccines. This review aims to compile the polymorphisms in HLA and immune system genes and examine the link with their immune response to vaccination. The compiled data can be used to guide the development of new strategies for vaccination for vulnerable groups. Overall, the highly polymorphic HLA locus had the highest correlation with vaccine response variability for most of the studied vaccines, and it was linked to variation in multiple stages of the immune response to the vaccines for both humoral and cellular immunity. Designing new vaccine technologies and immunization regiments to accommodate for this variability is an important step for reaching a vaccinomics-based approach to vaccination.
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Affiliation(s)
- Laith Naser Al-Eitan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Moh'd Fahmi Munib ElMotasem
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Iliya Yacoub Khair
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Saif Zuhair Alahmad
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
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Mabhida SE, Muhamed B, Sharma JR, Apalata T, Nomatshila S, Mabasa L, Benjeddou M, Masilela C, Ziqubu K, Shabalala S, Johnson R. Methylenetetrahydrofolate Reductase Polymorphism (rs1801133) and the Risk of Hypertension among African Populations: A Narrative Synthesis of Literature. Genes (Basel) 2022; 13:genes13040631. [PMID: 35456437 PMCID: PMC9027465 DOI: 10.3390/genes13040631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 02/07/2023] Open
Abstract
In this review, we have gathered and analyzed the available genetic evidence on the association between the methylenetetrahydrofolate reductase gene (MTHFR), rs1801133 and the risk of Hypertension (HTN) in African populations, which was further compared to the global data evidence. This review was reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol and Human Genome Epidemiology Network (HuGENet) guidelines. Literature was retrieved through major search databases, including PubMed, Scopus, Web of Science, and African Journal Online. We identified 64 potential studies, of which 4 studies were from the African continent and 60 studies were reported globally. Among the studies conducted in Africa, only two (n = 2) reported a significant association between the MTHFR (rs1801133) and the risk of developing HTN. Only one (n = 1) study population was purely composed of black Africans, while others were of other ethnicities. Among studies conducted in other continents (n = 60), forty-seven (n = 47) studies reported a positive association between MTHFR (rs1801133) and the risk of developing HTN, whereas the remaining studies (n = 14) did not show a significant association. Available literature suggests an apparent association between rs1801133 and HTN in global regions; however, such information is still scarce in Africa, especially in the black African population.
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Affiliation(s)
- Sihle E. Mabhida
- Biomedical Research and Innovation Platform, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (S.E.M.); (J.R.S.); (L.M.); (S.S.)
- Department of Biotechnology, Faculty of Natural Science, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
| | - Babu Muhamed
- Division of Infections Disease, University of Tennessee Health Sciences Center (UTHSC), Memphis, TN 38163, USA;
| | - Jyoti R. Sharma
- Biomedical Research and Innovation Platform, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (S.E.M.); (J.R.S.); (L.M.); (S.S.)
| | - Teke Apalata
- Division of Medical Microbiology, Department of Laboratory-Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University, Mthatha 5100, South Africa;
- National Health Laboratory Services, Mthatha 5100, South Africa
| | - Sibusiso Nomatshila
- Division of Preventive Medicine and Health Behavior, Department of Public Health, Faculty of Health Sciences, Walter Sisulu University, Mthatha 5100, South Africa;
| | - Lawrence Mabasa
- Biomedical Research and Innovation Platform, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (S.E.M.); (J.R.S.); (L.M.); (S.S.)
| | - Mongi Benjeddou
- Department of Biotechnology, Faculty of Natural Science, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
| | - Charity Masilela
- Department of Biochemistry, North-West University, Mafikeng Campus, Mmabatho 2735, South Africa; (C.M.); (K.Z.)
| | - Khanyisani Ziqubu
- Department of Biochemistry, North-West University, Mafikeng Campus, Mmabatho 2735, South Africa; (C.M.); (K.Z.)
| | - Samukelisiwe Shabalala
- Biomedical Research and Innovation Platform, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (S.E.M.); (J.R.S.); (L.M.); (S.S.)
- Division of Medical Microbiology, Department of Laboratory-Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University, Mthatha 5100, South Africa;
- National Health Laboratory Services, Mthatha 5100, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (S.E.M.); (J.R.S.); (L.M.); (S.S.)
- Centre for Cardio-Metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
- Correspondence: ; Tel.: +27-21-938-0866
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KDR polymorphism (1192G/A, 1719A/T) and modulation of ARV drug-induced hepatotoxicity. Microb Pathog 2021; 161:105243. [PMID: 34656700 DOI: 10.1016/j.micpath.2021.105243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 01/16/2023]
Abstract
Kinase insert Domain containing Receptor (KDR)/Vascular Endothelial Growth Factor Receptor (VEGFR-2) participate in endothelial dysfunction, which can lead to chronic liver disease. KDR reflects naturally against the toxicants from the damaged liver cells. Association of KDR polymorphism has been reported with many diseases including liver disease, but its role has not been described in ARV induced hepatotoxicity. Hence, we examined the exonic regions KDR (1192G/A, 1719A/T) polymorphism from 165 HIV-infected individuals (34/165 had ARV induced hepatotoxicity, 131/165 were with no hepatotoxicity) and 160 normal uninfected individuals by PCR-RFLP. In univariate analysis, KDR 1719 TT genotype presented at greater frequency from all HIV positive individuals in contrast with normal uninfected individuals (7.87% vs. 4.4%, OR = 1.72, P = 0.38). Individuals with KDR 1719 TT genotype had a risk for increasing hepatotoxicity and its severity (OR = 1.91, P = 0.38). Individuals with haplotype AT had risk for increasing hepatotoxicity and its severity (OR = 1.60, P = 0.50; OR = 2.35, P = 0.27). Whereas haplotype AA was associated with reduced risk of developing hepatotoxicity (OR = 0.40, P = 0.04). Individuals with KDR 1719 TT genotype were at greater risk of advancement of HIV disease (OR = 2.31, P = 0.23). Individuals with KDR 1719 TT genotype had more vulnerability for developing hepatotoxicity among alcohol users (OR = 2.57, P = 0.23). Individuals with KDR 1719 TT genotype were at higher risk of developing hepatotoxicity and its severity among nevirapine and alcohol consumers (OR = 2.47, P = 0.24; OR = 5.42, P = 0.42). In multivariate analysis, hepatotoxicity patients taking ART inclusive of nevirapine was associated with the severity of hepatotoxicity (OR = 4.82, P = 0.002). In conclusion, KDR 1719 TT genotype and haplotype AT may have a risk for development of hepatotoxicity and its severity. Haplotype AA may have influence to reduce the risk of developing hepatotoxicity.
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Heeney C. Problems and promises: How to tell the story of a Genome Wide Association Study? STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2021; 89:1-10. [PMID: 34284196 DOI: 10.1016/j.shpsa.2021.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
The promise of treatments for common complex diseases (CCDs) is understood as an important force driving large scale genetics research over the last few decades. This paper considers the phenomenon of the Genome Wide Association Study (GWAS) via one high profile example, the Wellcome Trust Case Control Consortium (WTCCC). The WTCCC despite not fulfilling promises of new health interventions is still understood as an important step towards tackling CCDs clinically. The 'sociology of expectations' has considered many examples of failure to fulfil promises and the subsequent negative consequences including disillusionment, disappointment and disinvestment. In order to explore why some domains remain resilient in the face of apparent failure, I employ the concept of the 'problematic' found in the work of Giles Deleuze. This alternative theoretical framework challenges the idea that the failure to reach promised goals results in largely negative outcomes for a given field. I will argue that collective scientific action is motivated not only by hopes for the future but also by the drive to create solutions to the actual setbacks and successes which scientists encounter in their day-to-day work. I draw on eighteen interviews.
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Affiliation(s)
- Catherine Heeney
- Usher Institute, University of Edinburgh, Old Medical School, Teviot Place, Edinburgh, EH8 9AG, UK.
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Unal-Aydin P, Aydin O, Arslan A. Genetic Architecture of Depression: Where Do We Stand Now? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1305:203-230. [PMID: 33834402 DOI: 10.1007/978-981-33-6044-0_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The research of depression genetics has been occupied by historical candidate genes which were tested by candidate gene association studies. However, these studies were mostly not replicable. Thus, genetics of depression have remained elusive for a long time. As research moves from candidate gene association studies to GWAS, the hypothesis-free non-candidate gene association studies in genome-wide level, this trend will likely change. Despite the fact that the earlier GWAS of depression were not successful, the recent GWAS suggest robust findings for depression genetics. These altogether will catalyze a new wave of multidisciplinary research to pin down the neurobiology of depression.
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Affiliation(s)
- Pinar Unal-Aydin
- Psychology Program, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Orkun Aydin
- Psychology Program, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Ayla Arslan
- School of Advanced Studies, University of Tyumen, Tyumen, Russia.
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Singh HO, Jadhav S, Samani D, Dhole TN. Polymorphisms in miRNAs Gene (146a, 149, 196a) and Susceptibility to ARV-associated Hepatotoxicity. Curr Genomics 2019; 20:134-150. [PMID: 31555064 PMCID: PMC6728905 DOI: 10.2174/1389202920666190325161439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 11/26/2022] Open
Abstract
Background: Micro RNAs act as a regulatory layer for pharmacogenomics-related gene ex-pression. It could play a role in the efficacy and toxicity of the drug. The SNPs in miRNA genes are linked with different functional consequences.
Methods: Hence, we examined the miR (146a G/C, 149C/T, and 196aC/T) polymorphisms in 34 pa-tients with hepatotoxicity, 123 patients without hepatotoxicity, and 155 healthy controls using a PCR-RFLP method. Results: In patients with hepatotoxicity, miR196aCT genotype and combined genotype GCT showed a risk for hepatotoxicity severity with borderline significance (OR=2.08, P=0.07; OR=2.88, P=0.06). While comparing between patients with hepatotoxicity and healthy controls, the combined genotypes CCC and GCT have shown a susceptibility to hepatotoxicity severity (OR=2.89, P=0.05; OR=2.60, P=0.09). The miR196TT genotype was associated with the individuals of advanced HIV disease stage (OR=3.68, P=0.04). In HIV patients who consumed alcohol and did not have hepatotoxicity, the miR 196aCT genotype showed susceptibility to acquisition of hepatotoxicity with borderline significance (OR=2.36, P=0.06). Discussion: The miR149TT and 196aTT genotypes showed a risk of acquisition of hepatotoxicity to nevirapine usage among HIV patients without hepatotoxicity (OR=4.19, P=0.07; OR=1.97, P=0.84). In HIV patients with and without hepatotoxicity, the miR 196aCT genotype showed a risk of acquisition of hepatotoxicity and its severity to the combined use of alcohol and nevirapine, respectively (OR=14.18, P=0.08; OR=2.29, P=0.08). In multivariate logistic regression, taking nevirapine, 196aCT genotype had an independent risk factor for hepatotoxicity severity (OR=5.98, P=0.005; OR=2.38, P=0.05). Conclusion: In conclusion, miR196aC/T polymorphism and combined genotypes GCT and CCC may facilitate the risk for acquisition of hepatotoxicity and its severity
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Affiliation(s)
- Hari Om Singh
- 1Department of Molecular Biology, National AIDS Research Institute, Pune, India; 2Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, 226014-Lucknow, India
| | - Sushma Jadhav
- 1Department of Molecular Biology, National AIDS Research Institute, Pune, India; 2Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, 226014-Lucknow, India
| | - Dharmesh Samani
- 1Department of Molecular Biology, National AIDS Research Institute, Pune, India; 2Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, 226014-Lucknow, India
| | - Tapan N Dhole
- 1Department of Molecular Biology, National AIDS Research Institute, Pune, India; 2Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, 226014-Lucknow, India
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Singh H, Samani D, Nain S, Dhole TN. Interleukin-10 polymorphisms and susceptibility to ARV associated hepatotoxicity. Microb Pathog 2019; 133:103544. [PMID: 31121270 DOI: 10.1016/j.micpath.2019.103544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 05/11/2019] [Accepted: 05/17/2019] [Indexed: 12/26/2022]
Abstract
Interleukin-10 (IL-10) is an anti-inflammatory cytokine associated with the inhibition of HIV replication. IL-10 polymorphisms were found to be linked to drug-induced hepatotoxicity. Hence we examined the prevalence of IL-10 (-819C/T,-1082A/G) polymorphisms in a total of 165 HIV patients which included 34 patients with hepatotoxicity, 131 without hepatotoxicity and 155 healthy controls by the PCR-RFLP method. In HIV patients with hepatotoxicity, the IL-10-819TT genotype increased the risk of ARV associated hepatotoxicity severity (OR = 1.61, P = 0.35). IL-10-819TT genotype was overrepresented in patients with hepatotoxicity as compared to healthy controls (26.5% vs. 13.5%, OR = 1.61, P = 0.46). IL-10 -819CT genotype was associated with advance HIV disease stage (OR = 0.49, P = 0.045). In HIV patients without hepatotoxicity, the IL-10-819TT genotype was more prevalent in patients consuming tobacco as compared to non-users (OR = 1.60, P = 0.41). In HIV patients without hepatotoxicity using both alcohol + efavirenz along with IL-10 -819CT genotype resulted in increased risk for the acquisition of ARV associated hepatotoxicity (OR = 4.00, P = 0.36). In multivariate logistic regression, taking nevirapine was associated with the risk hepatotoxicity severity (OR = 0.23, P = 0.005). In conclusion, an insignificant association between IL-10 polymorphisms and susceptibility to ARV associated hepatotoxicity.
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Affiliation(s)
- HariOm Singh
- Department of Molecular Biology, National AIDS Research Institute Pune, 411026, India.
| | - Dharmesh Samani
- Department of Molecular Biology, National AIDS Research Institute Pune, 411026, India
| | - Sumitra Nain
- Department of Pharmacy, University of Banasthali, Banasthali Vidyapith, Jaipur, 302001, India
| | - T N Dhole
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, India
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Toosi A, Fernando RL, Dekkers JCM. Genome-wide mapping of quantitative trait loci in admixed populations using mixed linear model and Bayesian multiple regression analysis. Genet Sel Evol 2018; 50:32. [PMID: 29914353 PMCID: PMC6006859 DOI: 10.1186/s12711-018-0402-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 06/01/2018] [Indexed: 12/18/2022] Open
Abstract
Background Population stratification and cryptic relationships have been the main sources of excessive false-positives and false-negatives in population-based association studies. Many methods have been developed to model these confounding factors and minimize their impact on the results of genome-wide association studies. In most of these methods, a two-stage approach is applied where: (1) methods are used to determine if there is a population structure in the sample dataset and (2) the effects of population structure are corrected either by modeling it or by running a separate analysis within each sub-population. The objective of this study was to evaluate the impact of population structure on the accuracy and power of genome-wide association studies using a Bayesian multiple regression method. Methods We conducted a genome-wide association study in a stochastically simulated admixed population. The genome was composed of six chromosomes, each with 1000 markers. Fifteen segregating quantitative trait loci contributed to the genetic variation of a quantitative trait with heritability of 0.30. The impact of genetic relationships and breed composition (BC) on three analysis methods were evaluated: single marker simple regression (SMR), single marker mixed linear model (MLM) and Bayesian multiple-regression analysis (BMR). Each method was fitted with and without BC. Accuracy, power, false-positive rate and the positive predictive value of each method were calculated and used for comparison. Results SMR and BMR, both without BC, were ranked as the worst and the best performing approaches, respectively. Our results showed that, while explicit modeling of genetic relationships and BC is essential for models SMR and MLM, BMR can disregard them and yet result in a higher power without compromising its false-positive rate. Conclusions This study showed that the Bayesian multiple-regression analysis is robust to population structure and to relationships among study subjects and performs better than a single marker mixed linear model approach.
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Affiliation(s)
- Ali Toosi
- Cobb-Vantress Inc., 4703 US HWY 412 E, Siloam Springs, AR, 72761, USA.
| | - Rohan L Fernando
- Department of Animal Science, Iowa State University, Ames, IA, 50010, USA
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, 50010, USA
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Singh H, Gangakhedkar RR. Occurrence of APOBEC3G variations in West Indian HIV patients. Microb Pathog 2018; 121:325-330. [PMID: 29864532 DOI: 10.1016/j.micpath.2018.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 05/28/2018] [Accepted: 06/01/2018] [Indexed: 12/22/2022]
Abstract
The genetic variations in APOBEC3G gene are correlated with HIV disease progression. These variations differ in different ethnic groups. The prevalence of APOBEC3G (-90C/G, -571G/C) variations have not been studied in Indian population. Hence, we assessed the occurrence of APOBEC3G polymorphisms in HIV patients and its association with acquisition of HIV and disease progression. Polymorphisms in APOBEC3G were genotyped in a total of 153 HIV patients, naïve to ARV and 156 healthy controls by PCR-RFLP method. In single locus model, the frequency of distribution of APOBEC3G -90CG, -571 GC genotypes were higher in HIV patients as compared to healthy controls (57.5% vs. 50.0%, OR = 1.22; 17.0% vs. 12.8%, OR = 1.39). In double locus model, the dominant -571 GC + CC genotype was distributed at a much higher frequency in HIV patients as compared to healthy controls (18.3% vs. 14.1%, OR = 1.50). The frequency of APOBEC3G -571CC and CC + GC genotypes were higher in early HIV disease stage as compared to healthy controls (23.9% vs. 12.8%, OR = 2.23, P = 0.08; 28.3% vs. 14.1%, OR = 2.40, P = 0.04). APOBEC3G-571 GC and GC + CC genotypes were more prevalent in HIV patients consuming tobacco and alcohol as compared to non-users (22.7% vs. 15.3%, OR = 1.71, P = 0.56; 27.3% vs. 16.5%, OR = 1.90, P = 0.39 and 31.6% vs. 13.6%, OR = 2.31, P = 0.08; 36.8% vs14.8%, OR = 2.49, P = 0.04, respectively). In conclusion, APOBEC3G-571G/C polymorphism was associated with the early stage of HIV infection and could potentially influence HIV disease progression in alcohol users. The distribution of APOBEC3G polymorphisms and its haplotypes were not significantly different between HIV patients and healthy controls.
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Affiliation(s)
- HariOm Singh
- Department of Molecular Biology, National AIDS Research Institute, Pune, 411026, India.
| | - R R Gangakhedkar
- Department of Clinical Sciences, National AIDS Research Institute, Pune, 411026, India
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IL-1RN and IL-1 β Polymorphism and ARV-Associated Hepatotoxicity. Mediators Inflamm 2018; 2018:4398150. [PMID: 29849489 PMCID: PMC5911319 DOI: 10.1155/2018/4398150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 02/28/2018] [Accepted: 03/13/2018] [Indexed: 12/28/2022] Open
Abstract
The severity of hepatic injury depends upon cytokines. Previous studies associated IL-1RN allele 2 with IL-1β production. Hence, we examined the association of IL-1 RN and IL-1β polymorphisms with ARV-associated hepatotoxicity. Genotyping of IL-1RN (VNTR), IL-1β (-511C/T) polymorphisms was done in 162 HIV-infected patients, 34 with ARV hepatotoxicity, 128 without hepatotoxicity, and 152 healthy controls using PCR and PCR-RFLP method. The haplotypes 1T and 2C enhanced the risk for severe hepatotoxicity (OR = 1.41, P = 0.25; OR = 1.67, P = 0.31). IL-1β-511TT genotype significantly represented among tobacco using HIV-infected individuals compared to nonusers (OR = 3.74, P = 0.05). IL-1β-511TT genotype among alcohol users increased the risk for hepatotoxicity (OR = 1.80, P = 0.90). IL-1β-511CT and -511TT genotypes overrepresented in alcohol using HIV-infected individuals (OR = 2.29, P = 0.27; OR = 2.64, P = 0.19). IL-RN 2/2 and 1/3 genotypes represented higher in nevirapine using hepatotoxicity patients (OR = 1.42, P = 0.64, OR = 8.79, P = 0.09). IL-1β-511CT and -511 TT genotypes among nevirapine users enhanced the risk for severe hepatotoxicity (OR = 4.29, P = 0.20; OR = 1.95, P = 0.56). IL-1β-511CT and -511TT genotypes were overrepresented in combined nevirapine and alcohol using HIV-infected individuals as compared to nevirapine users and alcohol nonusers (OR = 2.56, P = 0.26; OR = 2.84, P = 0.24). IL-1β-511TT genotype with tobacco, alcohol, and nevirapine usage revealed a trend of risk for the development of ARV-associated hepatotoxicity and its severity.
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Singh H, Samani D, Ghate MV, Gangakhedkar RR. Impact of cellular restriction gene (TRIM5α, BST-2) polymorphisms on the acquisition of HIV-1 and disease progression. J Gene Med 2018; 20:e3004. [PMID: 29282802 DOI: 10.1002/jgm.3004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 11/22/2017] [Accepted: 12/14/2017] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND TRIM5α and BST-2 are cellular restriction factors affecting the HIV-1 infection and its progression. Genetic variability in these genes alters the expression pattern. Hence, we aimed to examine the impact of the TRIM5α (rs10838525, rs7127617 and rs904375) and BST2 (rs3217318 and rs71694748) polymorphisms on the acquisition of HIV-1 and its progression. METHODS Genotyping of TRIM5α and BST-2 polymorphisms was performed in a total of 153 HIV-infected patients and 158 unrelated healthy individuals using a polymerase chain reaction-restriction fragment length polymorphism method. RESULTS No significant differences were found in the genotype frequencies of TRIM5α polymorphisms between HIV patients and healthy controls. BST-2 Δ19/i19 and i19/i19+ Δ19/i19 genotypes appeared more frequently in HIV patients compared to healthy controls (10.4% versus 7.0%, p = 0.20; 11.10% versus 7.6%, p = 0.16). The BST-2 i19 allele was associated with the acquisition of HIV-1 [odds ratio (OR) = 2.76, p = 0.030)]. TRIM5α haplotypes ATG and ACA elevated the risk, whereas haplotype ATA reduced the risk for the acquisition of HIV-1 (OR = 1.92, p = 0.026; OR = 4.88, p = 0.016; OR = 0.31, p = 0.014). BST-2 Δ19/i19 and i19/i19+ Δ19/i19 genotypes were more prevalent in patients with early HIV disease stage compared to healthy controls (15.9% versus 7.0%, p = 0.096; 15.9% versus 7.6%, p = 0.12). The prevalence of TRIM5α rs7127617 CC and BST-2 Δ19/i19 genotypes was observed to be higher in alcohol-using HIV patients compared to non-users (27.8% versus 20.0%, p = 0.35, 22.2% versus 10.0%, p = 0.24). CONCLUSIONS TRIM5α haplotypes and the BST-2 i19 allele may significantly affect the modulation of HIV-1 acquisition and its progression. TRIM5α rs7127617 CC and BST-2 Δ19/i19 genotypes in alcohol-using HIV patients elevated the risk of HIV disease progression.
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Affiliation(s)
- HariOm Singh
- Department of Molecular Biology, National AIDS Research Institute, Pune, India
| | - Dharmesh Samani
- Department of Molecular Biology, National AIDS Research Institute, Pune, India
| | - Manisha V Ghate
- Department of Clinical Sciences, National AIDS Research Institute, Pune, India
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Mukherjee S, Saxena R, Palmer LJ. The genetics of obstructive sleep apnoea. Respirology 2018; 23:18-27. [PMID: 29113020 PMCID: PMC7308164 DOI: 10.1111/resp.13212] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/11/2017] [Accepted: 09/29/2017] [Indexed: 12/19/2022]
Abstract
Obstructive sleep apnoea (OSA) is a common chronic disease and is associated with high social and economic costs. OSA is heritable, and there is evidence of both direct genetic contributions to OSA susceptibility and indirect contributions via 'intermediate' phenotypes such as obesity, craniofacial structure, neurological control of upper airway muscles and of sleep and circadian rhythm. Investigation of the genetics of OSA is an important research area and may lead to improved understanding of disease aetiology, pathogenesis, adverse health consequences and new preventive strategies and treatments. Genetic studies of OSA have lagged behind other chronic diseases; however recent gene discovery efforts have been successful in finding genetic loci contributing to OSA-associated intermediate phenotypes. Nevertheless, many of the seminal questions relating to the genetic epidemiology of OSA and associated factors remain unanswered. This paper reviews the current state of knowledge of the genetics of OSA, with a focus on genomic approaches to understanding sleep apnoea.
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Affiliation(s)
- Sutapa Mukherjee
- Sleep Health Service, Respiratory and Sleep Services, Southern Adelaide Local Health Network, Adelaide, South Australia, Australia
- Adelaide Institute for Sleep Health, Flinders University, Adelaide, South Australia, Australia
| | - Richa Saxena
- Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Lyle J Palmer
- School of Public Health, University of Adelaide, North Terrace, Adelaide, South Australia, Australia
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Kuo KH. Multiple Testing in the Context of Gene Discovery in Sickle Cell Disease Using Genome-Wide Association Studies. GENOMICS INSIGHTS 2017; 10:1178631017721178. [PMID: 28811740 PMCID: PMC5542087 DOI: 10.1177/1178631017721178] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 06/26/2017] [Indexed: 12/25/2022]
Abstract
The issue of multiple testing, also termed multiplicity, is ubiquitous in studies where multiple hypotheses are tested simultaneously. Genome-wide association study (GWAS), a type of genetic association study that has gained popularity in the past decade, is most susceptible to the issue of multiple testing. Different methodologies have been employed to address the issue of multiple testing in GWAS. The purpose of the review is to examine the methodologies employed in dealing with multiple testing in the context of gene discovery using GWAS in sickle cell disease complications.
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Affiliation(s)
- Kevin H.M. Kuo
- Departments of Medical Oncology and Hematology and Medicine, University Health Network, Toronto, ON, Canada
- Division of Hematology, Department of Medicine, University of Toronto, Toronto, ON, Canada
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Precision Radiology: Predicting longevity using feature engineering and deep learning methods in a radiomics framework. Sci Rep 2017; 7:1648. [PMID: 28490744 PMCID: PMC5431941 DOI: 10.1038/s41598-017-01931-w] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/06/2017] [Indexed: 02/06/2023] Open
Abstract
Precision medicine approaches rely on obtaining precise knowledge of the true state of health of an individual patient, which results from a combination of their genetic risks and environmental exposures. This approach is currently limited by the lack of effective and efficient non-invasive medical tests to define the full range of phenotypic variation associated with individual health. Such knowledge is critical for improved early intervention, for better treatment decisions, and for ameliorating the steadily worsening epidemic of chronic disease. We present proof-of-concept experiments to demonstrate how routinely acquired cross-sectional CT imaging may be used to predict patient longevity as a proxy for overall individual health and disease status using computer image analysis techniques. Despite the limitations of a modest dataset and the use of off-the-shelf machine learning methods, our results are comparable to previous 'manual' clinical methods for longevity prediction. This work demonstrates that radiomics techniques can be used to extract biomarkers relevant to one of the most widely used outcomes in epidemiological and clinical research - mortality, and that deep learning with convolutional neural networks can be usefully applied to radiomics research. Computer image analysis applied to routinely collected medical images offers substantial potential to enhance precision medicine initiatives.
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Singh H, Lata S, Nema V, Samani D, Ghate M, Gangakhedkar RR. CYP1A1m1 and CYP2C9*2 and *3 polymorphism and risk to develop ARV-associated hepatotoxicity and its severity. APMIS 2017; 125:523-535. [PMID: 28370504 DOI: 10.1111/apm.12683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 01/22/2017] [Indexed: 11/30/2022]
Abstract
Non-nucleoside reverse transcriptase inhibitors are metabolized in the liver by cytochrome P450 (CYP) isoenzymes. Variations in the genes encoding these enzymes may influence the activity of corresponding metabolizing enzymes. This study aimed at assessing association of CYP2C9*2 430C/T, CYP2C9*31075A/C, and CYP1A1m1 3801T/C polymorphism with risk to develop ARV Antiretroviral-associated hepatotoxicity and its severity. In this case-control study, genotyping of CYP2C9*2, CYP2C9*3, and CYP1A1m1 genes was done in 34 HIV-infected individuals with hepatotoxicity and 131 without hepatotoxicity, and 153 unrelated healthy individuals using PCR-RFLP. CYP1A1m13801CC genotype was likely to be associated with severe ARV-associated hepatotoxicity (OR = 1.78, p = 0.70). CYP1A1m13801CC genotype and combined genotype TC + CC were likely to be associated with development of ARV-associated hepatotoxicity (OR = 2.57, p = 0.08; OR = 1.42, p = 0.17). CYP1A1m1 3801CC genotype among advanced and intermediate HIV disease stage was likely to be associated with advancement of disease (OR = 2.56, p = 0.77; OR = 2.37, p = 0.45). CYP2C9*31075AC genotype among alcohol users was likely to be associated with development of ARV-associated hepatotoxicity (OR = 1.67, p = 0.38). CYP1A1m1 3801TC genotype and combined genotype TC + CC among nevirapine users were likely to be associated with severe ARV-associated hepatotoxicity (OR = 3.68, p = 0.27; OR = 4.91, p = 0.13). Among those who received nevirapine, presence of CYP1A1m1 3801TC genotype was likely to be associated with increased risk of development of ARV-associated hepatotoxicity (OR = 1.50, p = 0.78). CYP1A1m1 3801TC, 3801CC, and CYP2C9*3 1075AC genotypes among combined alcohol + nevirapine users increased the risk of development of ARV-associated hepatotoxicity (OR = 1.41, p = 0.53; OR = 1.49, p = 0.83; OR = 1.78, p = 0.35). In conclusion, individuals with CYP1A1m13801CC and 3801TC genotypes independently and in the presence of alcohol and nevirapine usage is likely to be associated with increased risk of development of ARV-associated hepatotoxicity, its severity, and advancement of disease. CYP2C9*31075AC genotype with combined alcohol and nevirapine usage indicated a risk for development of ARV-associated hepatotoxicity.
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Affiliation(s)
- HariOm Singh
- Department of Molecular Biology, National AIDS Research Institute, Pune, India
| | - Sonam Lata
- Department of Molecular Biology, National AIDS Research Institute, Pune, India
| | - Vijay Nema
- Department of Molecular Biology, National AIDS Research Institute, Pune, India
| | - Dharmesh Samani
- Department of Molecular Biology, National AIDS Research Institute, Pune, India
| | - Manisha Ghate
- Department of Clinical Sciences, National AIDS Research Institute, Pune, India
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16
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Faruque MU, Chen G, Doumatey AP, Zhou J, Huang H, Shriner D, Adeyemo AA, Rotimi CN, Dunston GM. Transferability of genome-wide associated loci for asthma in African Americans. J Asthma 2017; 54:1-8. [PMID: 27177148 PMCID: PMC5300042 DOI: 10.1080/02770903.2016.1188941] [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: 11/13/2015] [Revised: 05/05/2016] [Accepted: 05/08/2016] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Transferability of significantly associated loci or GWAS "hits" adds credibility to genotype-disease associations and provides evidence for generalizability across different ancestral populations. We sought evidence of association of known asthma-associated single nucleotide polymorphisms (SNPs) in an African American population. METHODS Subjects comprised 661 participants (261 asthma cases and 400 controls) from the Howard University Family Study. Forty-eight SNPs previously reported to be associated with asthma by GWAS were selected for testing. We adopted a combined strategy by first adopting an "exact" approach where we looked-up only the reported index SNP. For those index SNPs missing form our dataset, we used a "local" approach that examined all the regional SNPs in LD with the index SNP. RESULTS Out of the 48 SNPs, our cohort had genotype data available for 27, which were examined for exact replication. Of these, two SNPs were found positively associated with asthma. These included: rs10508372 (OR = 1.567 [95%CI, 1.133-2.167], P = 0.0066) and rs2378383 (OR = 2.147 [95%CI, 1.149-4.013], P = 0.0166), located on chromosomal bands 10p14 and 9q21.31, respectively. Local replication of the remaining 21 loci showed association at two chromosomal loci (9p24.1-rs2381413 and 6p21.32-rs3132947; Bonferroni-corrected P values: 0.0033 and 0.0197, respectively). Of note, multiple SNPs in LD with rs2381413 located upstream of IL33 were significantly associated with asthma. CONCLUSIONS This study has successfully transferred four reported asthma-associated loci in an independent African American population. Identification of several asthma-associated SNPs in the upstream of the IL33, a gene previously implicated in allergic inflammation of asthmatic airway, supports the generalizability of this finding.
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Affiliation(s)
- Mezbah U. Faruque
- National Human Genome Center, Howard University College of Medicine, Washington, DC, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ayo P. Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hanxia Huang
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adebowale A. Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Georgia M. Dunston
- National Human Genome Center, Howard University College of Medicine, Washington, DC, USA
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Jepson RE, Warren HR, Syme HM, Elliott J, Munroe PB. Uromodulin gene variants and their association with renal function and blood pressure in cats: a pilot study. J Small Anim Pract 2016; 57:580-588. [DOI: 10.1111/jsap.12582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 07/19/2016] [Accepted: 07/19/2016] [Indexed: 11/28/2022]
Affiliation(s)
- R. E. Jepson
- Department of Clinical Sciences and Services; Royal Veterinary College; Nr Hatfield Herts AL9 7TA
| | - H. R. Warren
- Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London EC1M 6BQ
| | - H. M. Syme
- Department of Clinical Sciences and Services; Royal Veterinary College; Nr Hatfield Herts AL9 7TA
| | - J. Elliott
- Department of Comparative Biomedical Sciences; Royal Veterinary College; London NW1 0TU
| | - P. B. Munroe
- Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London EC1M 6BQ
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Riordan SM, Bittel DC, Le Pichon JB, Gazzin S, Tiribelli C, Watchko JF, Wennberg RP, Shapiro SM. A Hypothesis for Using Pathway Genetic Load Analysis for Understanding Complex Outcomes in Bilirubin Encephalopathy. Front Neurosci 2016; 10:376. [PMID: 27587993 PMCID: PMC4988977 DOI: 10.3389/fnins.2016.00376] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/02/2016] [Indexed: 01/18/2023] Open
Abstract
Genetic-based susceptibility to bilirubin neurotoxicity and chronic bilirubin encephalopathy (kernicterus) is still poorly understood. Neonatal jaundice affects 60–80% of newborns, and considerable effort goes into preventing this relatively benign condition from escalating into the development of kernicterus making the incidence of this potentially devastating condition very rare in more developed countries. The current understanding of the genetic background of kernicterus is largely comprised of mutations related to alterations of bilirubin production, elimination, or both. Less is known about mutations that may predispose or protect against CNS bilirubin neurotoxicity. The lack of a monogenetic source for this risk of bilirubin neurotoxicity suggests that disease progression is dependent upon an overall decrease in the functionality of one or more essential genetically controlled metabolic pathways. In other words, a “load” is placed on key pathways in the form of multiple genetic variants that combine to create a vulnerable phenotype. The idea of epistatic interactions creating a pathway genetic load (PGL) that affects the response to a specific insult has been previously reported as a PGL score. We hypothesize that the PGL score can be used to investigate whether increased susceptibility to bilirubin-induced CNS damage in neonates is due to a mutational load being placed on key genetic pathways important to the central nervous system's response to bilirubin neurotoxicity. We propose a modification of the PGL score method that replaces the use of a canonical pathway with custom gene lists organized into three tiers with descending levels of evidence combined with the utilization of single nucleotide polymorphism (SNP) causality prediction methods. The PGL score has the potential to explain the genetic background of complex bilirubin induced neurological disorders (BIND) such as kernicterus and could be the key to understanding ranges of outcome severity in complex diseases. We anticipate that this method could be useful for improving the care of jaundiced newborns through its use as an at-risk screen. Importantly, this method would also be useful in uncovering basic knowledge about this and other polygenetic diseases whose genetic source is difficult to discern through traditional means such as a genome-wide association study.
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Affiliation(s)
- Sean M Riordan
- Division of Child Neurology, Department of Pediatrics, Children's Mercy HospitalKansas City, MO, USA; Department of Neurology, University of Kansas Medical CenterKansas City, KS, USA
| | - Douglas C Bittel
- Ward Family Heart Center, Children's Mercy HospitalKansas City, MO, USA; Department of Pediatrics, University of Missouri-Kansas City School of MedicineKansas City, MO, USA
| | - Jean-Baptiste Le Pichon
- Division of Child Neurology, Department of Pediatrics, Children's Mercy HospitalKansas City, MO, USA; Department of Neurology, University of Kansas Medical CenterKansas City, KS, USA; Department of Pediatrics, University of Missouri-Kansas City School of MedicineKansas City, MO, USA; Department of Pediatrics, University of Kansas Medical CenterKansas City, KS, USA
| | - Silvia Gazzin
- Italian Liver Foundation, Centro Studi Fegato (CSF) Trieste, Italy
| | - Claudio Tiribelli
- Italian Liver Foundation, Centro Studi Fegato (CSF)Trieste, Italy; Department of Medical Sciences, University of TriesteTrieste, Italy
| | - Jon F Watchko
- Division of Newborn Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine Pittsburgh, PA, USA
| | | | - Steven M Shapiro
- Division of Child Neurology, Department of Pediatrics, Children's Mercy HospitalKansas City, MO, USA; Department of Neurology, University of Kansas Medical CenterKansas City, KS, USA; Department of Pediatrics, University of Missouri-Kansas City School of MedicineKansas City, MO, USA; Department of Pediatrics, University of Kansas Medical CenterKansas City, KS, USA
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Gender bias in individual radiosensitivity and the association with genetic polymorphic variations. Radiother Oncol 2016; 119:236-43. [PMID: 26987471 DOI: 10.1016/j.radonc.2016.02.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 12/08/2015] [Accepted: 02/29/2016] [Indexed: 12/11/2022]
Abstract
PURPOSE To assess the extent of variation in radiosensitivity between individuals, gender-related dissimilarity and impact on the association with single nucleotide polymorphisms (SNPs). MATERIALS AND METHODS Survival curves of 152 fibroblast cell strains derived from both gender were generated. Individual radiosensitivity was characterized by the surviving fraction at 2Gy (SF2). SNPs in 10 radiation responsive genes were genotyped by direct sequencing. RESULTS The wide variation in SF2 (0.12-0.50; mean=0.33) was significantly associated with 3 SNPs: TP53 G72C (P=0.007), XRCC1 G399A (P=0.002) and ATM G1853A (P=0.01). Females and males differed significantly in radiosensitivity (P=0.004) that impacted genetic association where only XRCC1 remained significant in both gender (P<0.05). Meanwhile, discordant association was observed for TP53 that was significant in females (P=0.012) and ATM that was significant in males (P=0.0006). When gender-specific SF2-mean (0.31 and 0.35 for females and males; respectively) was considered, further discordance was observed where XRCC1 turned out not to be associated with radiosensitivity in males (P>0.05). CONCLUSIONS Although the variation in individual radiosensitivity was associated with certain SNPs, gender bias for both endpoints was evident. Therefore, assessing the risk of radiation exposure in females and males should be considered separately in order to achieve the ultimate goal of personalized radiation medicine.
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Mirkovic B, Laurent C, Podlipski MA, Frebourg T, Cohen D, Gerardin P. Genetic Association Studies of Suicidal Behavior: A Review of the Past 10 Years, Progress, Limitations, and Future Directions. Front Psychiatry 2016; 7:158. [PMID: 27721799 PMCID: PMC5034008 DOI: 10.3389/fpsyt.2016.00158] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
Suicidal behaviors (SBs), which range from suicidal ideation to suicide attempts and completed suicide, represent a fatal dimension of mental ill-health. The involvement of genetic risk factors in SB is supported by family, twin, and adoption studies. The aim of this paper is to review recent genetic association studies in SBs including (i) case-control studies, (ii) family-based association studies, and (iii) genome-wide association studies (GWAS). Various studies on genetic associations have tended to suggest that a number of genes [e.g., tryptophan hydroxylase, serotonin receptors and transporters, or brain-derived neurotrophic factors (BDNFs)] are linked to SBs, but these findings are not consistently supported by the results obtained. Although the candidate-gene approach is useful, it is hampered by the present state of knowledge concerning the pathophysiology of diseases. Interpretations of GWAS results are mostly hindered by a lack of annotation describing the functions of most variation throughout the genome. Association studies have addressed a wide range of single-nucleotide polymorphisms in numerous genes. We have included 104 such studies, of which 10 are family-based association studies and 11 are GWAS. Numerous meta-analyses of case-control studies have shown significant associations of SB with variants in the serotonin transporter gene (5-HTT or SLC6A4) and the tryptophan hydroxylase 1 gene (TPH1), but others report contradictory results. The gene encoding BDNF and its receptor (NTRK2) are also promising candidates. Only two of the GWAS showed any significant associations. Several pathways are mentioned in an attempt to understand the lack of reproducibility and the disappointing results. Consequently, we review and discuss here the following aspects: (i) sample characteristics and confounding factors; (ii) statistical limits; (iii) gene-gene interactions; (iv) gene, environment, and by time interactions; and (v) technological and theoretical limits.
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Affiliation(s)
- Bojan Mirkovic
- Department of Child and Adolescent Psychiatry, CHU Charles Nicolle, Rouen, France; INSERM Unit U1079, Genetics of Cancer and Neurogenetics, University of Rouen, Rouen, France; Department of Child and Adolescent Psychiatry, Hôpital Pitié-Salpêtrière, Paris, France
| | - Claudine Laurent
- Department of Child and Adolescent Psychiatry, Hôpital Pitié-Salpêtrière, Paris, France; ICM - Brain and Spine Institute, Hôpital Pitié-Salpêtrière - University Pierre and Marie Curie, Paris, France
| | | | - Thierry Frebourg
- INSERM Unit U1079, Genetics of Cancer and Neurogenetics, University of Rouen, Rouen, France; Department of Genetics, CHU Charles Nicolle, Rouen, France
| | - David Cohen
- Department of Child and Adolescent Psychiatry, Hôpital Pitié-Salpêtrière, Paris, France; UMR 7222, Institute for Intelligent Systems and Robotics, University Pierre and Marie Curie, Paris, France
| | - Priscille Gerardin
- Department of Child and Adolescent Psychiatry, CHU Charles Nicolle, Rouen, France; Laboratoire Psy-NCA-EA-4700, University of Rouen, Rouen, France
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Tai CG, Graff RE, Liu J, Passarelli MN, Mefford JA, Shaw GM, Hoffmann TJ, Witte JS. Detecting gene-environment interactions in human birth defects: Study designs and statistical methods. ACTA ACUST UNITED AC 2015; 103:692-702. [PMID: 26010994 DOI: 10.1002/bdra.23382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/25/2015] [Accepted: 03/30/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND The National Birth Defects Prevention Study (NBDPS) contains a wealth of information on affected and unaffected family triads, and thus provides numerous opportunities to study gene-environment interactions (G×E) in the etiology of birth defect outcomes. Depending on the research objective, several analytic options exist to estimate G×E effects that use varying combinations of individuals drawn from available triads. METHODS In this study, we discuss important considerations in the collection of genetic data and environmental exposures. RESULTS We will also present several population- and family-based approaches that can be applied to data from the NBDPS including case-control, case-only, family-based trio, and maternal versus fetal effects. For each, we describe the data requirements, applicable statistical methods, advantages, and disadvantages. CONCLUSION A range of approaches can be used to evaluate potentially important G×E effects in the NBDPS. Investigators should be aware of the limitations inherent to each approach when choosing a study design and interpreting results.
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Affiliation(s)
- Caroline G Tai
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Jinghua Liu
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Michael N Passarelli
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Joel A Mefford
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.,Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.,Institute for Human Genetics, University of California San Francisco, San Francisco, California.,Department of Urology, University of California San Francisco, San Francisco, California.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
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Fuiano N, Delvecchio M, Incorvaia C. Factors associated with different results of allergy tests in children with dust mite-induced atopic dermatitis. Allergol Immunopathol (Madr) 2015; 43:238-42. [PMID: 25087092 DOI: 10.1016/j.aller.2014.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/09/2014] [Accepted: 02/25/2014] [Indexed: 11/26/2022]
Abstract
BACKGROUND Atopic dermatitis (AD) is a public health problem, with an increasing prevalence worldwide. AD is a chronic inflammatory disease characterised by skin lesions and severe itching. Immunologically, AD has two forms, IgE-mediated and cell-mediated, but it may also be idiopathic. In the pathogenesis of AD, the gene mutations for filaggrin, a filament-aggregating protein present in the epidermis, are of pivotal importance, but other genetic factors are also operating, including those linked to family atopy. METHODS We evaluated the role of family atopy, and of the results of the atopy patch test (APT) in parents, in children with mite-induced AD. 64 children, 38 males and 26 females, mean age 4.97 years, were included for the diagnosis of AD and underwent APT and skin prick test (SPT) with dust mite extracts, with evaluation of atopy and result of APT also in parents. RESULTS A positive family history of atopy was shown for children with positivity to both APT and SPT compared to those with negative or only one positive result to APT or SPT (p=0.08). Significant associations were found concerning APT results in children and parents. In particular, children of a positive-APT parent had an 18-fold higher risk of APT-positivity in comparison with children of negative-APT parents, while the risk was 6.6-fold higher if APT was positive in father. CONCLUSION Family atopy and a positive APT in fathers are risk factors to develop cell-mediated AD, as assessed by the APT, in children.
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Kriszt Á, Losonczy G, Berta A, Vereb G, Takács L. Segregation analysis suggests that keratoconus is a complex non-mendelian disease. Acta Ophthalmol 2014; 92:e562-8. [PMID: 24629050 DOI: 10.1111/aos.12389] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 02/08/2014] [Indexed: 12/17/2022]
Abstract
PURPOSE Complex segregation analysis of 60 unrelated sporadic keratoconus (KC) families was performed to reveal the presumed mode of inheritance in our dataset. METHODS Sixty probands, 212 family members and 212 age and gender matched healthy controls underwent clinical and videokeratographic examination. Family aggregation and distribution of videokeratography parameters were examined. Segregation of KSI, KISA and 6mm Fourier asymmetry alone or in covariate analysis with gender or the presence of Fleischer ring, exploring mendelian and non-mendelian models of inheritance was tested using complex segregation analysis with the S.A.G.E. program package. RESULTS In 145 relatives of probands, the estimated prevalence of manifest KC was 7.6% (95% CI: 3.3-11.9) based on KISA index, indicating strong familial aggregation. All examined videokeratography indices were able to differentiate between KC and non-KC family members as well as normal controls (anova p < 0.001). Hypotheses accepted as most parsimonius models of inheritance (p > 0.1) for all indices indicated the presence of a non-mendelian major gene effect (MG). Inclusion of Fleischer ring as covariate improved the fit of MG models. Mendelian, Sporadic and polygenic models were consistently rejected. CONCLUSIONS Complex segregation analysis indicates a strong genetic contribution to the transmission of keratoconus. Inheritance is most probably due to a non-mendelian major gene effect. Low genotype-phenotype correlation in sporadic KC families can make linkage studies difficult, thus genome wide association studies, epigenetic and pathway analyses may provide more information on disease pathogenesis in non-familial keratoconus.
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Affiliation(s)
- Ágnes Kriszt
- Department of Ophthalmology; University of Debrecen Medical and Health Science Center; Debrecen Hungary
- Department of Biophysics and Cell Biology; University of Debrecen Medical and Health Science Center; Debrecen Hungary
| | - Gergely Losonczy
- Department of Ophthalmology; University of Debrecen Medical and Health Science Center; Debrecen Hungary
| | - András Berta
- Department of Ophthalmology; University of Debrecen Medical and Health Science Center; Debrecen Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology; University of Debrecen Medical and Health Science Center; Debrecen Hungary
| | - Lili Takács
- Department of Ophthalmology; University of Debrecen Medical and Health Science Center; Debrecen Hungary
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Saeki N, Sakamoto H, Yoshida T. Mucin 1 gene (MUC1) and gastric-cancer susceptibility. Int J Mol Sci 2014; 15:7958-73. [PMID: 24810688 PMCID: PMC4057712 DOI: 10.3390/ijms15057958] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/11/2014] [Accepted: 04/21/2014] [Indexed: 12/22/2022] Open
Abstract
Gastric cancer (GC) is one of the major malignant diseases worldwide, especially in Asia. It is classified into intestinal and diffuse types. While the intestinal-type GC (IGC) is almost certainly caused by Helicobacter pylori (HP) infection, its role in the diffuse-type GC (DGC) appears limited. Recently, genome-wide association studies (GWAS) on Japanese and Chinese populations identified chromosome 1q22 as a GC susceptibility locus which harbors mucin 1 gene (MUC1) encoding a cell membrane-bound mucin protein. MUC1 has been known as an oncogene with an anti-apoptotic function in cancer cells; however, in normal gastric mucosa, it is anticipated that the mucin 1 protein has a role in protecting gastric epithelial cells from a variety of external insults which cause inflammation and carcinogenesis. HP infection is the most definite insult leading to GC, and a protective function of mucin 1 protein has been suggested by studies on Muc1 knocked-out mice.
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Affiliation(s)
- Norihisa Saeki
- Division of Genetics, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan.
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan.
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tsukiji 5-1-1, Chuo-ku, Tokyo 104-0045, Japan.
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GeMes, clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease. Am J Hum Genet 2014; 94:485-95. [PMID: 24656863 DOI: 10.1016/j.ajhg.2014.02.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 02/14/2014] [Indexed: 02/04/2023] Open
Abstract
Epigenetic marks such as DNA methylation have generated great interest in the study of human disease. However, studies of DNA methylation have not established population-epigenetics principles to guide design, efficient statistics, or interpretation. Here, we show that the clustering of correlated DNA methylation at CpGs was similar to that of linkage-disequilibrium (LD) correlation in genetic SNP variation but for much shorter distances. Some clustering of methylated CpGs appeared to be genetically driven. Further, a set of correlated methylated CpGs related to a single SNP-based LD block was not always physically contiguous-segments of uncorrelated methylation as long as 300 kb could be interspersed in the cluster. Thus, we denoted these sets of correlated CpGs as GeMes, defined as potentially noncontiguous methylation clusters under the control of one or more methylation quantitative trait loci. This type of correlated methylation structure has implications for both biological functions of DNA methylation and for the design, analysis, and interpretation of epigenome-wide association studies.
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Itariu BK, Stulnig TM. Autoimmune aspects of type 2 diabetes mellitus - a mini-review. Gerontology 2014; 60:189-96. [PMID: 24457898 DOI: 10.1159/000356747] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/14/2013] [Indexed: 11/19/2022] Open
Abstract
Autoimmunity is a well-known pathogenic component in type 1 diabetes (T1DM). The assumption that the pathogenesis of type 2 diabetes (T2DM) also encompasses autoimmune aspects is recognized increasingly, based on the presence of circulating autoantibodies against β cells, self-reactive T cells, but also on the glucose-lowering efficacy of some immunomodulatory therapies in T2DM. The identification of these autoantibodies in elderly patients with slowly progressive manifestation of diabetes led to the introduction of a distinct clinical entity termed latent autoimmune diabetes of the adult (LADA), which combines features of both T1DM and T2DM. The autoantibody cluster differs in patients with LADA from patients with T1DM, but their presence indicates steady progression towards β-cell death and subsequent need for initiation of insulin treatment in a shorter period of time compared to autoantibody-negative T2DM patients. Autoimmune aspects in T2DM are not solely restricted to autoantibodies and thus LADA. They include the self-reactive T cells or defects in regulatory T cells (Tregs), which have been detected in autoantibody-negative T2DM patients as well. One contributor to the autoimmune activation in T2DM seems to be the chronic inflammatory state, characteristic of this disease. Upon inflammation-induced tissue destruction, cryptic 'self' antigens can trigger an autoimmune response, which in turn accelerates β-cell death. Both innate and adaptive immune system components, specifically macrophages and self-reactive T cells, contribute to an increased secretion of inflammatory cytokines involved in inflammatory and autoimmune processes. However, the extent to which inflammation overlaps with autoimmunity is not known. Our review focuses on autoimmune involvement in T2DM, with an emphasis on LADA and the humoral immune response, on the involvement of chronic inflammation in autoimmunity, and specifically the role of B and T cells as links between inflammatory and autoimmune reactions. We will further stress the consequences of autoimmune activation for T2DM patients and present novel therapeutic approaches for T2DM management that rely on immune modulation.
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Affiliation(s)
- Bianca K Itariu
- Christian Doppler Laboratory for Cardio-Metabolic Immunotherapy, Medical University of Vienna, Vienna, Austria
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Kerns SL, Ostrer H, Rosenstein BS. Radiogenomics: using genetics to identify cancer patients at risk for development of adverse effects following radiotherapy. Cancer Discov 2014; 4:155-65. [PMID: 24441285 DOI: 10.1158/2159-8290.cd-13-0197] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
UNLABELLED Normal-tissue adverse effects following radiotherapy are common and significantly affect quality of life. These effects cannot be accounted for by dosimetric, treatment, or demographic factors alone, and evidence suggests that common genetic variants are associated with radiotherapy adverse effects. The field of radiogenomics has evolved to identify such genetic risk factors. Radiogenomics has two goals: (i) to develop an assay to predict which patients with cancer are most likely to develop radiation injuries resulting from radiotherapy, and (ii) to obtain information about the molecular pathways responsible for radiation-induced normal-tissue toxicities. This review summarizes the history of the field and current research. SIGNIFICANCE A single-nucleotide polymorphism–based predictive assay could be used, along with clinical and treatment factors, to estimate the risk that a patient with cancer will develop adverse effects from radiotherapy. Such an assay could be used to personalize therapy and improve quality of life for patients with cancer.
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Affiliation(s)
- Sarah L Kerns
- Departments of 1Radiation Oncology and 2Dermatology, Preventive Medicine and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai; 3Department of Radiation Oncology, New York University School of Medicine, New York; Departments of 4Pathology, and 5Genetics and Pediatrics, Albert Einstein College of Medicine, Bronx, New York
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Expansive marker analysis replicating the association of glaucoma susceptibility with human chromosome loci 1q43 and 10p12.31. Eur J Hum Genet 2013; 22:409-13. [PMID: 23838595 DOI: 10.1038/ejhg.2013.149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 05/18/2013] [Accepted: 06/06/2013] [Indexed: 01/30/2023] Open
Abstract
Three human chromosome loci (1q43, 10p12.31, and 12q21.31) were recently associated with the susceptibility to primary open-angle glaucoma (POAG) in a Japanese population; however, this was not replicated in three subsequent studies using South Indian, Afro-Caribbean, and Chinese populations. To identify genetic markers that are robustly associated across ethnic populations, numerous markers in addition to the six in the three reported loci were examined in this study. A total of 31 single-nucleotide polymorphism (SNP) markers were genotyped for 1115 Korean participants, and many neighboring SNPs were imputed using the Korean HapMap Project genotype data. Each SNP was statistically tested for association with POAG susceptibility by comparisons among 211 POAG patients with 904 unaffected controls. A strong and statistically significant association was found with a previously unreported SNP, rs7098387 (odds ratio, OR=2.0 (1.4-3.0), P=0.00038) at the 10p12.31 locus (where 11 SNPs were typed and 38 imputed) in contrast to the reported rs7081455, which was too poorly correlated with newly associated rs7098387 (r2=0.003, D'=0.40) to show association. Additionally, a modest association was observed with the reported rs693421 (OR=1.4 (1.1-1.7), P=0.0082) and several other SNPs located within and around ZP4 at the 1q43 locus (10 SNPs typed and 14 imputed). However, no association was observed with the reported rs7961953 SNP or any other SNPs at the 12q21.31 locus, upstream of TMTC2 (10 SNPs typed and 29 imputed). Accordingly, POAG susceptibility association was replicated using rs7098387 (C) rather than rs7081455 (T) at the 10p12.31 locus and additionally with rs693421 (T) at the 1q43 locus.
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Similarity in recombination rate and linkage disequilibrium at CYP2C and CYP2D cytochrome P450 gene regions among Europeans indicates signs of selection and no advantage of using tagSNPs in population isolates. Pharmacogenet Genomics 2013; 22:846-57. [PMID: 23089684 DOI: 10.1097/fpc.0b013e32835a3a6d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Linkage disequilibrium (LD) and recombination rate variations are known to vary considerably between human genome regions and populations mostly because of the combined effects of mutation, recombination, and demographic history. Thus, the pattern of LD is a key issue to disentangle variants associated with complex traits. Here, we aim to describe the haplotype structure and LD variation at the pharmacogenetically relevant cytochrome P450 CYP2C and CYP2D gene regions among European populations. METHODS To assess the haplotype structure, LD pattern, and recombination rate variations in the clinically significant CYP2C and CYP2D regions, we genotyped 143 single-nucleotide polymorphisms (SNPs) across these two genome regions in a diverse set of 11 European population samples and one sub-Saharan African sample. RESULTS Our results showed extended patterns of LD and in general a low rate of recombination at these loci, and a low degree of allele differentiation for the two cytochrome P450 regions among Europeans, with the exception of the Sami and the Finns as European outliers. The Sami sample showed reduced haplotype diversity and higher LD for the two cytochrome P450 regions than the other Europeans, a feature that is proposed to enhance the LD mapping of underlying common complex traits. However, recombination hotspots and LD blocks at these two regions showed highly consistent structures across Europeans including Finns and Sami. Moreover, we showed that the CEPH sample has significantly higher tag transferability among Europeans and a more efficient tagging of both the rare CYP2C9 and the common CYP2C19 functional variants than the Sami. Our data set included CYP2C9*3 (rs1057910) and CYP2C19*2 (rs4244285) enzyme activity-altering variants associated in a recent genome-wide study with acenocoumarol-induced and warfarin-induced anticoagulation or to the antiplatelet effect of clopidogrel, respectively. Including these known activity-altering variants, we showed the haplotype variation and high derived allele frequencies of novel recently identified acenocoumarol genome-wide associated SNPs at CYP2C9 (rs4086116) and CYP2C18 (rs12772169, rs1998591, rs2104543, rs1042194) loci in a comprehensive set of 11 European populations. Furthermore, a significant frequency difference of a CYP2C19*2 gene mutation causing variable drug reactions was observed among Europeans. CONCLUSION The CEPH sample representing the general European population as such in the HapMap project seems to be the optimal population sample for the LD mapping of common complex traits among Europeans. Nevertheless, it is still argued that the unique pattern of LD in the Sami may offer an advantage for further association mapping, especially if multiple rare variants play a role in disease etiology. However, besides the activity-altering CYP2C9*3 (rs1057910) and CYP2C19*2 (rs4244285) variants, the high derived allele frequencies of novel recently identified acenocoumarol genome-wide associated SNPs at CYP2C9 (rs4086116) and CYP2C18 (rs12772169, rs1998591, rs2104543, rs1042194) loci variants indicated that the CYP2C region may have been influenced by selection. Thus, this fine-scale haplotype map of the CYP2C and CYP2D regions may help to choose markers for further association mapping of complex pharmacogenetic traits at these loci.
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Gu SJ, Guo ZR, Wu M, Ding Y, Luo WS. Association of Peroxisome Proliferator-Activated Receptor γ Polymorphisms and Haplotypes with Essential Hypertension. Genet Test Mol Biomarkers 2013; 17:418-23. [DOI: 10.1089/gtmb.2012.0425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shu-Jun Gu
- Department of Epidemiology, School of Public Health, Soochow University, Suzhou, China
| | - Zhi-Rong Guo
- Department of Epidemiology, School of Public Health, Soochow University, Suzhou, China
| | - Ming Wu
- Center for Disease Control of Jiangsu Province, Nanjing, China
| | - Yi Ding
- Department of Epidemiology, School of Public Health, Soochow University, Suzhou, China
| | - Wen-Shu Luo
- Department of Epidemiology, School of Public Health, Soochow University, Suzhou, China
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Saeki N, Ono H, Sakamoto H, Yoshida T. Genetic factors related to gastric cancer susceptibility identified using a genome-wide association study. Cancer Sci 2013; 104:1-8. [PMID: 23057512 PMCID: PMC7657243 DOI: 10.1111/cas.12042] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/03/2012] [Accepted: 10/08/2012] [Indexed: 12/11/2022] Open
Abstract
Gastric cancer (GC) is one of the major malignant diseases worldwide, especially in Asia, where Japan and Korea have the highest incidence in the world. Gastric cancer is classified into intestinal and diffuse types. While the former is almost absolutely caused by Helicobacter pylori infection as the initial insult, the latter seems to include cases in which the role of infection is limited, if any, and a contribution of genetic factors is anticipated. Previously, we performed a genome-wide association study (GWAS) on diffuse-type GC by using single nucleotide polymorphisms (SNP) catalogued for Japanese population (JSNP), and identified a prostate stem cell antigen (PSCA) gene encoding a glycosylphosphatidylinositol-anchored cell surface antigen as a GC susceptibility gene. From the second candidate locus identified using the GWAS, 1q22, we found the Mucin 1 (MUC1) gene encoding a cell membrane-bound mucin protein as another gene related to diffuse-type GC. A two-allele analysis based on risk genotypes of the two genes revealed approximately 95% of Japanese population have at least one of the two risk genotypes, and approximately 56% of the population have both risk genotypes. The two-SNP genotype might offer ample room to further stratify a high GC risk subpopulation in Japan and Asia by adding another genetic and/or non-genetic factor. Recently, a GWAS on the Chinese population disclosed an additional three GC susceptibility loci: 3q13.31, 5p13.1 and 10q23.
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Affiliation(s)
- Norihisa Saeki
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan.
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Petersdorf EW, Malkki M, Gooley TA, Spellman SR, Haagenson MD, Horowitz MM, Wang T. MHC-resident variation affects risks after unrelated donor hematopoietic cell transplantation. Sci Transl Med 2012; 4:144ra101. [PMID: 22837536 DOI: 10.1126/scitranslmed.3003974] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Blood malignancies can be cured with hematopoietic cell transplantation from human leukocyte antigen (HLA)-matched unrelated donors; however, acute graft-versus-host disease (GVHD) affects up to 80% of patients and contributes to increased mortality. To test the hypothesis that undetected patient-donor differences for non-HLA genetic variation within the major histocompatibility complex (MHC) could confer risks after HLA-matched transplantation, we conducted a discovery-validation study of 4205 transplants for 1120 MHC region single-nucleotide polymorphisms (SNPs). Two SNPs were identified as markers for disease-free survival and acute GVHD. Among patients with two or more HLA-matched unrelated donors identified on their search, SNP genotyping of patients and their potential donors demonstrated that most patients have a choice of SNP-matched donors. In conclusion, the success of HLA-matched unrelated donor hematopoietic cell transplantation depends on non-HLA MHC region genetic variation. Prospective SNP screening and matching provides an approach for lowering risks to patients.
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Affiliation(s)
- Effie W Petersdorf
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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Relton CL, Davey Smith G. Two-step epigenetic Mendelian randomization: a strategy for establishing the causal role of epigenetic processes in pathways to disease. Int J Epidemiol 2012; 41:161-76. [PMID: 22422451 DOI: 10.1093/ije/dyr233] [Citation(s) in RCA: 327] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The burgeoning interest in the field of epigenetics has precipitated the need to develop approaches to strengthen causal inference when considering the role of epigenetic mediators of environmental exposures on disease risk. Epigenetic markers, like any other molecular biomarker, are vulnerable to confounding and reverse causation. Here, we present a strategy, based on the well-established framework of Mendelian randomization, to interrogate the causal relationships between exposure, DNA methylation and outcome. The two-step approach first uses a genetic proxy for the exposure of interest to assess the causal relationship between exposure and methylation. A second step then utilizes a genetic proxy for DNA methylation to interrogate the causal relationship between DNA methylation and outcome. The rationale, origins, methodology, advantages and limitations of this novel strategy are presented.
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Affiliation(s)
- Caroline L Relton
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.
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Rosenfeld JA, Mason CE, Smith TM. Limitations of the human reference genome for personalized genomics. PLoS One 2012; 7:e40294. [PMID: 22811759 PMCID: PMC3394790 DOI: 10.1371/journal.pone.0040294] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 06/07/2012] [Indexed: 11/19/2022] Open
Abstract
Data from the 1000 genomes project (1KGP) and Complete Genomics (CG) have dramatically increased the numbers of known genetic variants and challenge several assumptions about the reference genome and its uses in both clinical and research settings. Specifically, 34% of published array-based GWAS studies for a variety of diseases utilize probes that overlap unanticipated single nucleotide polymorphisms (SNPs), indels, or structural variants. Linkage disequilibrium (LD) block length depends on the numbers of markers used, and the mean LD block size decreases from 16 kb to 7 kb,when HapMap-based calculations are compared to blocks computed from1KGP data. Additionally, when 1KGP and CG variants are compared, 19% of the single nucleotide variants (SNVs) reported from common genomes are unique to one dataset; likely a result of differences in data collection methodology, alignment of reads to the reference genome, and variant-calling algorithms. Together these observations indicate that current research resources and informatics methods do not adequately account for the high level of variation that already exists in the human population and significant efforts are needed to create resources that can accurately assess personal genomics for health, disease, and predict treatment outcomes.
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Affiliation(s)
- Jeffrey A. Rosenfeld
- Division of High Performance and Research Computing, University of Medicine & Dentistry of New Jersey, Newark, New Jersey, United States of America
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, New York, United States of America
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Todd M. Smith
- PerkinElmer, Seattle, Washington, United States of America
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Fuiano N, Incorvaia C. Dissecting the causes of atopic dermatitis in children: less foods, more mites. Allergol Int 2012; 61:231-43. [PMID: 22361514 DOI: 10.2332/allergolint.11-ra-0371] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 10/07/2011] [Indexed: 12/16/2022] Open
Abstract
Atopic dermatitis (AD) is a common, chronic or chronically relapsing, multifactorial skin disease that mainly occurs in children but affects also adults. AD usually begins early in life and often concerns people with a personal or family history of asthma and allergic rhinitis. AD is characterized by eczematous changes in the epidermis and originates from a late, T-cell mediated reaction associated to the formation and production of memory T-cell of TH2 type, occurrence of homing receptor at skin level and cutaneous lymphocyte-associated (CLA) antigens. Extrinsic or allergic AD, but not intrinsic AD, shows high total serum IgE levels and the presence of specific IgE for environmental and food allergens. A pivotal role in the pathogenesis of AD is played by filaggrin, a protein contained in the granular layer of the epidermis regulating the aggregation of keratin filaments. Mutation in the filaggrin gene causes decreased barrier function of the corny layers of the epidermis. This favours the enter through the skin of environmental allergens, especially the house dust mite, that further facilitates such entering by the proteolytic activity of its major allergen Der p 1. In fact, recent advances suggest that the dust mite, more than foods, is the major cause of allergic AD. As far as the causal diagnosis of AD is concerned, there is notable evidence supporting the capacity of the atopy patch test (APT) to reproduce the pathophysiologic events of AD. This makes APT a valuable diagnostic tool for AD.
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MESH Headings
- Animals
- Antigens, Dermatophagoides/adverse effects
- Antigens, Dermatophagoides/immunology
- Arthropod Proteins/adverse effects
- Arthropod Proteins/immunology
- Child
- Cysteine Endopeptidases/adverse effects
- Cysteine Endopeptidases/immunology
- Dermatitis, Atopic/diagnosis
- Dermatitis, Atopic/etiology
- Dermatitis, Atopic/genetics
- Dermatitis, Atopic/immunology
- Filaggrin Proteins
- Gene-Environment Interaction
- Humans
- Hypersensitivity, Delayed/diagnosis
- Hypersensitivity, Delayed/etiology
- Hypersensitivity, Delayed/genetics
- Hypersensitivity, Delayed/immunology
- Immunologic Memory
- Intermediate Filament Proteins/genetics
- Mutation
- Patch Tests
- Pyroglyphidae/immunology
- Skin/immunology
- Th2 Cells/immunology
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Affiliation(s)
- Nicola Fuiano
- Pediatric Allergy Service, ASL FG, Torremaggiore, Italy.
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Parkinsonism. Neurogenetics 2012. [DOI: 10.1017/cbo9781139087711.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Zhang DF, Pang Z, Li S, Thomassen M, Wang S, Jiang W, Hjelmborg JVB, Kruse TA, Kyvik KO, Christensen K, Tan Q. High-resolution genome-wide linkage mapping identifies susceptibility loci for BMI in the Chinese population. Obesity (Silver Spring) 2012; 20:830-3. [PMID: 21273998 DOI: 10.1038/oby.2010.349] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The genetic loci affecting the commonly used BMI have been intensively investigated using linkage approaches in multiple populations. This study aims at performing the first genome-wide linkage scan on BMI in the Chinese population in mainland China with hypothesis that heterogeneity in genetic linkage could exist in different ethnic populations. BMI was measured from 126 dizygotic twins in Qingdao municipality who were genotyped using high-resolution Affymetrix Genome-Wide Human SNP arrays containing about 1 million single-nucleotide polymorphisms (SNPs). Nonparametric linkage analysis was performed with Merlin software package for linkage analysis using variance components approach for quantitative trait loci mapping. We identified a strong linkage peak at the end of chromosome 7 (7q36 at 186 cM) with a lod score of 4.06 which overlaps with that reported by a large multicenter study in western countries. Multiple loci showing suggestive linkage were found on chromosome 1 (lod score 2.38 at 242 cM), chromosome 8 (2.48 at 95 cM), and chromosome 14 (2.2 at 89.4 cM). The strong linkage identified in the Chinese subjects that is consistent with that found in populations of European origin could suggest the existence of evolutionarily preserved genetic mechanisms for BMI whereas the multiple suggestive loci could represent genetic effect from gene-environment interaction as a result of population-specific environmental adaptation.
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MESH Headings
- Adult
- Asian People/genetics
- Body Mass Index
- China/epidemiology
- Chromosome Mapping
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 14/genetics
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 8/genetics
- Female
- Genetic Predisposition to Disease
- Humans
- Lod Score
- Male
- Middle Aged
- Obesity/epidemiology
- Obesity/genetics
- Phenotype
- Polymorphism, Single Nucleotide
- Quantitative Trait Loci
- Statistics, Nonparametric
- Twins, Dizygotic/genetics
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Affiliation(s)
- Dong Feng Zhang
- Department of Public Health, Qingdao University Medical College, Qingdao, China.
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Dekker MJHJ, Tiemeier H, Luijendijk HJ, Kuningas M, Hofman A, de Jong FH, Stewart PM, Koper JW, Lamberts SWJ. The effect of common genetic variation in 11β-hydroxysteroid dehydrogenase type 1 on hypothalamic-pituitary-adrenal axis activity and incident depression. J Clin Endocrinol Metab 2012; 97:E233-7. [PMID: 22112815 DOI: 10.1210/jc.2011-0601] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
BACKGROUND Accumulating evidence suggests that hyperactivity of the hypothalamic-pituitary-adrenal axis (HPA axis) is involved in depression. 11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) converts inert cortisone to active cortisol and is implicated in HPA axis regulation in animal studies. The aim of our study was to identify polymorphisms in 11β-HSD1 gene (HSD11B1) with consistent associations with increased HPA axis activity and relate those polymorphisms to depression. METHODS Twelve single-nucleotide polymorphisms (SNPs), including 11 tagging SNPs, were selected using the HapMap database and genotyped in 4228 participants of the population-based Rotterdam Study. The outcome measures were salivary cortisol levels after awakening, 30 min later, at 1700 h, at bedtime, and plasma levels of androstenedione (in women only). SNPs that were significantly associated with cortisol as well as androstenedione levels were also related to incident depression. RESULTS rs11119328 was associated with higher cortisol saliva samples collected at bedtime as well as higher androstenedione levels (P value after correction for multiple testing: 0.01 and 0.04, respectively). Carriers of this polymorphism had an increased risk of an incident depression (hazard ratio 1.28, 95% confidence interval 1.03-1.59). Two other SNPs, which were in high linkage disequilibrium with rs11119328, were related to higher cortisol levels but not with androstenedione levels. CONCLUSIONS We identified one SNP, which was associated with increased salivary cortisol levels at nadir as well as higher androstenedione levels. Moreover, this SNP was also associated with a higher risk of an incident depression. This suggests that 11β-HSD1 is implicated in human HPA axis regulation and susceptibility to depression.
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Affiliation(s)
- M J H J Dekker
- Department of Internal Medicine, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
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Schuurhof A, Janssen R, de Groot H, Hodemaekers HM, de Klerk A, Kimpen JL, Bont L. Local interleukin-10 production during respiratory syncytial virus bronchiolitis is associated with post-bronchiolitis wheeze. Respir Res 2011; 12:121. [PMID: 21910858 PMCID: PMC3179726 DOI: 10.1186/1465-9921-12-121] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 09/12/2011] [Indexed: 01/11/2023] Open
Abstract
Background Respiratory syncytial virus (RSV) is the most common cause of bronchiolitis in infants. Following RSV bronchiolitis, 50% of children develop post-bronchiolitis wheeze (PBW). Animal studies have suggested that interleukin (IL)-10 plays a critical role in the pathogenesis of RSV bronchiolitis and subsequent airway hyperresponsiveness. Previously, we showed that ex vivo monocyte IL-10 production is a predictor of PBW. Additionally, heterozygosity of the single-nucleotide polymorphism (SNP) rs1800872 in the IL10 promoter region was associated with protection against RSV bronchiolitis. Methods This study aimed to determine the in vivo role of IL-10 in RSV pathogenesis and recurrent wheeze in a new cohort of 235 infants hospitalized for RSV bronchiolitis. IL-10 levels in nasopharyngeal aspirates (NPAs) were measured at the time of hospitalization and the IL10 SNP rs1800872 genotype was determined. Follow-up data were available for 185 children (79%). Results Local IL-10 levels during RSV infection turned out to be higher in infants that later developed physician diagnosed PBW as compared to infants without PBW in the first year after RSV infection (958 vs 692 pg/ml, p = 0.02). The IL10 promoter SNP rs1800872 was not associated with IL-10 concentration in NPAs. Conclusion The relationship between high local IL-10 levels during the initial RSV infection and physician diagnosed PBW provides further evidence of the importance of the IL-10 response during RSV bronchiolitis.
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Affiliation(s)
- Annemieke Schuurhof
- Laboratory for Health Protection Research, National Institute for Public Health and the Environment, Postbak 12 GBO, P.O.BOX 1, 3720 BA Bilthoven, The Netherlands
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Unluturk U, Harmanci A, Kocaefe C, Yildiz BO. The Genetic Basis of the Polycystic Ovary Syndrome: A Literature Review Including Discussion of PPAR-gamma. PPAR Res 2011; 2007:49109. [PMID: 17389770 PMCID: PMC1820621 DOI: 10.1155/2007/49109] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Revised: 11/24/2006] [Accepted: 12/03/2006] [Indexed: 02/06/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is the most common endocrine disorder of the women of reproductive age. Familial clustering of PCOS has been consistently reported suggesting that genetic factors play a role in the development of the syndrome although PCOS cases do not exhibit a clear pattern of Mendelian inheritance. It is now well established that PCOS represents a complex trait similar to type-2 diabetes and obesity, and that both inherited and environmental factors contribute to the PCOS pathogenesis. A large number of functional candidate genes have been tested for association or linkage with PCOS phenotypes with more negative than positive findings. Lack of universally accepted diagnostic criteria, difficulties in the assignment of male phenotype, obscurity in the mode of inheritance, and particularly small sample size of the study populations appear to be major limitations for the genetic studies of PCOS. In the near future, utilizing the genome-wide scan approach and the HapMap project will provide a stronger potential for the genetic analysis of the syndrome.
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Affiliation(s)
- Ugur Unluturk
- Department of Internal Medicine, Faculty of Medicine, Hacettepe University, Hacettepe, 06100 Ankara, Turkey
| | - Ayla Harmanci
- Department of Internal Medicine, Faculty of Medicine, Hacettepe University, Hacettepe, 06100 Ankara, Turkey
- Endocrinology and Metabolism Unit, Faculty of Medicine, Hacettepe University, Hacettepe, 06100 Ankara, Turkey
| | - Cetin Kocaefe
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Hacettepe, 06100 Ankara, Turkey
| | - Bulent O. Yildiz
- Department of Internal Medicine, Faculty of Medicine, Hacettepe University, Hacettepe, 06100 Ankara, Turkey
- Endocrinology and Metabolism Unit, Faculty of Medicine, Hacettepe University, Hacettepe, 06100 Ankara, Turkey
- *Bulent O. Yildiz:
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Davey Smith G. Use of genetic markers and gene-diet interactions for interrogating population-level causal influences of diet on health. GENES & NUTRITION 2011; 6:27-43. [PMID: 21437028 PMCID: PMC3040803 DOI: 10.1007/s12263-010-0181-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 08/07/2010] [Indexed: 01/20/2023]
Abstract
Differences in diet appear to contribute substantially to the burden of disease in populations, and therefore changes in diet could lead to major improvements in public health. This is predicated on the reliable identification of causal effects of nutrition on health, and unfortunately nutritional epidemiology has deficiencies in terms of identifying these. This is reflected in the many cases where observational studies have suggested that a nutritional factor is protective against disease, and randomized controlled trials have failed to verify this. The use of genetic variants as proxy measures of nutritional exposure-an application of the Mendelian randomization principle-can contribute to strengthening causal inference in this field. Genetic variants are not subject to bias due to reverse causation (disease processes influencing exposure, rather than vice versa) or recall bias, and if obvious precautions are applied are not influenced by confounding or attenuation by errors. This is illustrated in the case of epidemiological studies of alcohol intake and various health outcomes, through the use of genetic variants related to alcohol metabolism (in ALDH2 and ADH1B). Examples from other areas of nutritional epidemiology and of the informative nature of gene-environment interactions interpreted within the Mendelian randomization framework are presented, and the potential limitations of the approach addressed.
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Affiliation(s)
- George Davey Smith
- MRC Centre for Causal Analyses in Translational Epidemiology, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN UK
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Folwaczny M, Manolis V, Markus C, Glas J. Variants of the human PPARG locus and the susceptibility to chronic periodontitis. Innate Immun 2011; 17:541-7. [DOI: 10.1177/1753425910392089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Apart from its regulatory function in lipid and glucose metabolism, peroxisome proliferator-activated receptor (PPAR)γ has impact on the regulation of inflammation and bone metabolism. The aim of the study was to investigate the association of five polymorphisms (rs10865710, rs2067819, rs3892175, rs1801282, rs3856806) within the PPARG gene with chronic periodontitis. The study population comprised 402 periodontitis patients and 793 healthy individuals. Genotyping of the PPARG gene polymorphisms was performed by PCR and melting curve analysis. Comparison of frequency distribution of genotypes between individuals with periodontal disease and healthy controls for the polymorphism rs3856806 showed a P-value of 0.04 but failed to reach significance after correction for multiple testing ( P < 0.01). Two single nucleotide polymorphisms (SNPs) (rs10865710 and rs3892175) were found to be in strong linkage disequilibrium to rs2067819 (D’ > 0.90). A 3-site analysis (rs2067819-rs1801282-rs3856860) revealed five haplotypes with a frequency of ≥1% among cases and controls. Following adjustment for age, gender and smoking, none of the haplotypes was significantly different between periodontitis and healthy controls after Bonferroni correction. This study could not show a significant association between PPARG gene variants and chronic periodontitis.
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Affiliation(s)
- Matthias Folwaczny
- Poliklinik für Zahnerhaltung und Parodontologie, Ludwig-Maximilians-University, Munich, Germany
| | - Vasilios Manolis
- Poliklinik für Zahnerhaltung und Parodontologie, Ludwig-Maximilians-University, Munich, Germany
| | - Christian Markus
- Medizinische Klinik und Poliklinik II – Grosshadern, Ludwig-Maximilians-University, Munich, Germany
| | - Jürgen Glas
- Poliklinik für Zahnerhaltung und Parodontologie, Ludwig-Maximilians-University, Munich, Germany
- Institut für Humangenetik, RWTH Aachen, Aachen, Germany
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Posthumus M, September A, Schwellnus MP, Collins M. Identification of genetic risk factors underlying complex multifactorial phenotypes. Knee Surg Sports Traumatol Arthrosc 2010; 18:1810-1; author reply 812-3. [PMID: 20872134 DOI: 10.1007/s00167-010-1275-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 04/01/2010] [Indexed: 11/26/2022]
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Abstract
Genetic association studies explore the association between genetic polymorphisms and a certain trait, disease or predisposition to disease. It has long been acknowledged that many genetic association studies fail to replicate their initial positive findings. This raises concern about the methodological quality of these reports. Case-control genetic association studies often suffer from various methodological flaws in study design and data analysis, and are often reported poorly. Flawed methodology and poor reporting leads to distorted results and incorrect conclusions. Many journals have adopted guidelines for reporting genetic association studies. In this review, some major methodological determinants of genetic association studies will be discussed.
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Affiliation(s)
- Ana-Maria Simundic
- University Department of Chemistry, University Hospital "SESTRE MILOSRDNICE", Zagreb, Croatia.
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Williams MA, Carson R, Passmore P, Silvestri G, Craig D. Introduction to genetic epidemiology. ACTA ACUST UNITED AC 2010; 82:83-91. [PMID: 20947437 DOI: 10.1016/j.optm.2010.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2009] [Revised: 12/29/2009] [Accepted: 01/25/2010] [Indexed: 11/15/2022]
Abstract
Genetic epidemiology is of topical and increasingly practical relevance. The subject attempts to answer 2 questions: (1) is there a genetic component to a disease, and (2) what genes are involved? This article summarizes genetic epidemiologic methods, describing family- and population-based methods used to locate and identify genes and the advantages and disadvantages of each approach. Health care professionals are faced with more and more genetic information, both from interested patients and from the media, and understanding the principles underlying genetic studies allows such information to be placed in context.
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Affiliation(s)
- Michael A Williams
- Department of Geriatric Medicine, Queen's University of Belfast, Belfast, United Kingdom.
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Smith GD. Mendelian Randomization for Strengthening Causal Inference in Observational Studies: Application to Gene × Environment Interactions. PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2010; 5:527-45. [PMID: 26162196 DOI: 10.1177/1745691610383505] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Identification of environmentally modifiable factors causally influencing disease risk is fundamental to public-health improvement strategies. Unfortunately, observational epidemiological studies are limited in their ability to reliably identify such causal associations, reflected in the many cases in which conventional epidemiological studies have apparently identified associations that randomized controlled trials have failed to verify. The use of genetic variants as proxy measures of exposure -an application of the Mendelian randomization principle-can contribute to strengthening causal inference. Genetic variants are not subject to bias due to reverse causation (disease processes influencing exposure, rather than vice versa) or recall bias, and if simple precautions are applied, they are not influenced by confounding or attenuation by errors. The principles of Mendelian randomization are illustrated with specific reference to studies of the effects of alcohol intake on various health-related outcomes through the utilization of genetic variants related to alcohol metabolism (in ALDH2 and ADH1B). Ways of incorporating Gene × Environment interactions into the Mendelian randomization framework are developed, and the strengths and limitations of the approach discussed.
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Affiliation(s)
- George Davey Smith
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
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The impact of catechol-O-methyltransferase SNPs and haplotypes on treatment response phenotypes in major depressive disorder: a case-control association study. Int Clin Psychopharmacol 2010; 25:218-27. [PMID: 20531207 DOI: 10.1097/yic.0b013e328338b884] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Catechol-O-methyltransferase (COMT) has been suggested to be involved in the pathogenesis and pharmacological treatment of affective disorders. The nonsynonymous single nucleotide polymorphism (SNP) in exon 4 (Val108/158Met; rs4680) influences the COMT enzyme activity. Inconsistent results were found between Val158Met polymorphism (rs4680) and treatment response phenotypes in genetic association studies. However, the haplotype combinations of alleles at the Val108/158Met SNP with the other synonymous SNPs in the COMT gene region have shown association between enzyme activity/amount and COMT-dependent phenotypes. We carried out this study to define the functional impact of COMT genotypes/haplotypes on susceptibility and on treatment response phenotypes of major depressive disorder (MDD). Three hundred and ninety-six patients with MDD diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition [(DSM)-IV] and 295 healthy controls were recruited for this study and genotyped for the seven COMT SNPs (rs2075507, rs737865, rs6269, rs4633, rs4818, rs4680, and rs165599). This is the first study with all these SNPs to investigate for MDD and treatment response phenotypes. Our results show that none of the seven SNPs, including the rs4680, was significantly associated with MDD after permutation correction in single SNP analyses. Although several haplotype combinations showed significance, the combinations of G-T-G-G haplotype for rs6269, rs4633, rs4818 and rs4680 were only present in the MDD group (G-T 4.5%, corrected sim P=0.0001; G-T-G 3.87%, corrected sim P=0.001; G-T-G-G 3.3% corrected sim P=0.0025). In the treatment response phenotypes, the GG genotype of the rs2075507 SNP (located in the promoter region of MB-COMT) was less common in resistant patients in a single SNP analysis with low corrected sim P=0.052 and power=0.086. However, in the haplotype analysis, the haplotypes of exonic SNPs, rs4633, rs4818, and rs4680, were related to the treatment response phenotypes investigated, especially the phenotype of the response to antidepressant treatment. The C-C-A haplotype of these SNPs was overrepresented (almost four-and eight-fold) in the responders compared with the nonresponders and controls, respectively, after Bonferroni correction (corrected sim P=0.048, 0.0001, respectively). Both nonsynonymous and synonymous SNPs within haplotypes may be more relevant than the single SNP in conferring MDD susceptibility and treatment response phenotypes. Despite the limited power of our analysis, this finding suggests that the polymorphic COMT gene that influences catecholaminergic neurotransmission may play a role in the individual response to antidepressants.
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Rupec RA, Boneberger S, Ruzicka T. What is really in control of skin immunity: lymphocytes, dendritic cells, or keratinocytes? facts and controversies. Clin Dermatol 2010; 28:62-6. [PMID: 20082953 DOI: 10.1016/j.clindermatol.2009.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The pathophysiology of atopic dermatitis is still under discussion. Although it is widely accepted that environmental factors and a genetic predisposition are essential, the role of the innate and adaptive immune system and the functional cascade of the cells involved is still unclear. A concept that integrates all immune cells as equally essential has allure. In addition, barrier abnormalities due to mutations of the gene coding for filaggrin and down-regulation of antimicrobial peptides, such as LL-37 and beta-defensins 2 and 3, were very recently found to be relevant for the pathogenesis of atopic dermatitis.
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Affiliation(s)
- Rudolf A Rupec
- Department of Dermatology and Allergology, Ludwig-Maximilian-University, 80337 Munich, Germany.
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