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Brugger SW, Davis MF. Influence of Admixture on Phenotypes. Curr Protoc 2023; 3:e953. [PMID: 38146906 DOI: 10.1002/cpz1.953] [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] [Indexed: 12/27/2023]
Abstract
Individuals of European descent have historically been the focus of genetic studies and possess relatively homogenous genomes. As a result, analytical methods have been developed and optimized with such genomes in mind. African-descent and Latino individuals generally possess genomes of greater architectural complexity due to mosaic genomic ancestry, which can extensively and intricately impact phenotypic expression. As such, genetic analyses of admixed individuals require that genetic admixture be quantified to accurately model the impact of genetic variation on phenotypic expression. In this overview, we explore how fundamental genetic concepts such as linkage disequilibrium and differential allele frequency interact with genetic admixture to uniquely influence phenotypes in admixed individuals. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Steven W Brugger
- Department of Molecular Biology and Microbiology, Brigham Young University, Provo, Utah
| | - Mary F Davis
- Department of Molecular Biology and Microbiology, Brigham Young University, Provo, Utah
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Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases. Int J Mol Sci 2021; 22:ijms22136962. [PMID: 34203440 PMCID: PMC8269095 DOI: 10.3390/ijms22136962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Admixed populations arise when two or more ancestral populations interbreed. As a result of this admixture, the genome of admixed populations is defined by tracts of variable size inherited from these parental groups and has particular genetic features that provide valuable information about their demographic history. Diverse methods can be used to derive the ancestry apportionment of admixed individuals, and such inferences can be leveraged for the discovery of genetic loci associated with diseases and traits, therefore having important biomedical implications. In this review article, we summarize the most common methods of global and local genetic ancestry estimation and discuss the use of admixture mapping studies in human diseases.
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Lee EY, Mak ACY, Hu D, Sajuthi S, White MJ, Keys KL, Eckalbar W, Bonser L, Huntsman S, Urbanek C, Eng C, Jain D, Abecasis G, Kang HM, Germer S, Zody MC, Nickerson DA, Erle D, Ziv E, Rodriguez-Santana J, Seibold MA, Burchard EG. Whole-Genome Sequencing Identifies Novel Functional Loci Associated with Lung Function in Puerto Rican Youth. Am J Respir Crit Care Med 2020; 202:962-972. [PMID: 32459537 PMCID: PMC7528787 DOI: 10.1164/rccm.202002-0351oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/27/2020] [Indexed: 12/22/2022] Open
Abstract
Rationale: Puerto Ricans have the highest childhood asthma prevalence in the United States (23.6%); however, the etiology is uncertain.Objectives: In this study, we sought to uncover the genetic architecture of lung function in Puerto Rican youth with and without asthma who were recruited from the island (n = 836).Methods: We used admixture-mapping and whole-genome sequencing data to discover genomic regions associated with lung function. Functional roles of the prioritized candidate SNPs were examined with chromatin immunoprecipitation sequencing, RNA sequencing, and expression quantitative trait loci data.Measurements and Main Results: We discovered a genomic region at 1q32 that was significantly associated with a 0.12-L decrease in the lung volume of exhaled air (95% confidence interval, -0.17 to -0.07; P = 6.62 × 10-8) with each allele of African ancestry. Within this region, two SNPs were expression quantitative trait loci of TMEM9 in nasal airway epithelial cells and MROH3P in esophagus mucosa. The minor alleles of these SNPs were associated with significantly decreased lung function and decreased TMEM9 gene expression. Another admixture-mapping peak was observed on chromosome 5q35.1, indicating that each Native American ancestry allele was associated with a 0.15-L increase in lung function (95% confidence interval, 0.08-0.21; P = 5.03 × 10-6). The region-based association tests identified four suggestive windows that harbored candidate rare variants associated with lung function.Conclusions: We identified common and rare genetic variants that may play a critical role in lung function among Puerto Rican youth. We independently validated an inflammatory pathway that could potentially be used to develop more targeted treatments and interventions for patients with asthma.
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Affiliation(s)
- Eunice Y. Lee
- Department of Bioengineering and Therapeutic Sciences and
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Angel C. Y. Mak
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Satria Sajuthi
- Department of Pediatrics, Center for Genes, Environment, and Health, and
| | - Marquitta J. White
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Kevin L. Keys
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Luke Bonser
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Cydney Urbanek
- Department of Pediatrics, Center for Genes, Environment, and Health, and
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Gonçalo Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
- Regeneron Pharmaceuticals, Tarrytown, New York
| | - Hyun M. Kang
- Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | | | | | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Northwest Genomics Center, Seattle, Washington
- Brotman Baty Institute, Seattle, Washington
| | - David Erle
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Elad Ziv
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Max A. Seibold
- Department of Pediatrics, Center for Genes, Environment, and Health, and
- Department of Pediatrics, National Jewish Health, Denver, Colorado
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado–Anschutz Medical Campus, Aurora, Colorado
| | - Esteban G. Burchard
- Department of Bioengineering and Therapeutic Sciences and
- Department of Medicine, University of California, San Francisco, San Francisco, California
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Uncovering Outcome Disparities of β 2 Adrenergic Agonists in Blacks: A Systematic Review. J Natl Med Assoc 2020; 113:8-29. [PMID: 32732018 DOI: 10.1016/j.jnma.2020.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/01/2020] [Accepted: 07/04/2020] [Indexed: 01/25/2023]
Abstract
PURPOSE Outcome differences driven by variation in Blacks' biologic response to treatment may contribute to persistent racial disparities in asthma morbidity and mortality. This review assessed systematic variation in β2 agonist treatment outcomes among Blacks compared to other groups. METHODS We conducted a systematic review of studies reporting differential response to β2 agonists among Blacks, including studies identifying pharmacogenetic variants. RESULTS Of 3158 papers, 20 compared safety or efficacy of β2 agonists among Blacks as compared with other subgroups. Six papers evaluating efficacy of short-acting β2 agonists (SABA) found similar or improved results among Blacks compared with other groups, while one small study found reduced response to SABA therapy among Blacks. Reports of safety and efficacy of long-acting β2 agonists (LABA) indicated similar results among Blacks in four papers, while four reports found reduced safety among Blacks, as compared with other groups. Four papers assessed genomic variation and relative treatment response in Blacks, with two finding significant effects of the p.Arg16Gly variant in ADRB2 on β2 agonist response and one finding significant gene-gene IL6/IL6R interaction effects on albuterol response. CONCLUSIONS Evidence suggests the potential for differences in β2 agonist outcomes among Blacks compared with other groups. This literature, however, remains small and significantly underpowered for substantive conclusions. There are notable opportunities for adequately-powered investigations exploring safety and efficacy of β2 agonists among Blacks, including pharmacogenomic modifiers of response.
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Haga SB. Pharmacogenomic Testing In Pediatrics: Navigating The Ethical, Social, And Legal Challenges. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2019; 12:273-285. [PMID: 31686893 PMCID: PMC6800463 DOI: 10.2147/pgpm.s179172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/12/2019] [Indexed: 12/17/2022]
Abstract
For the past several years, the implementation of pharmacogenetic (PGx) testing has become widespread in several centers and clinical practice settings. PGx testing may be ordered at the point-of-care when treatment is needed or in advance of treatment for future use. The potential benefits of PGx testing are not limited to adult patients, as children are increasingly using medications more often and at earlier ages. This review provides some background on the use of PGx testing in children as well as mothers (prenatally and post-natally) and discusses the challenges, benefits, and the ethical, legal, and social implications of providing PGx testing to children.
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Affiliation(s)
- Susanne B Haga
- Department of Medicine, Division of General Internal Medicine, Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA
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Association of Native American ancestry and common variants in ACE, ADIPOR2, MTNR1B, GCK, TCF7L2 and FTO genes with glycemic traits in Colombian population. Gene 2018; 677:198-210. [DOI: 10.1016/j.gene.2018.07.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 07/10/2018] [Accepted: 07/26/2018] [Indexed: 12/17/2022]
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Talwar A, Garcia JGN, Tsai H, Moreno M, Lahm T, Zamanian RT, Machado R, Kawut SM, Selej M, Mathai S, D'Anna LH, Sahni S, Rodriquez EJ, Channick R, Fagan K, Gray M, Armstrong J, Rodriguez Lopez J, de Jesus Perez V. Health Disparities in Patients with Pulmonary Arterial Hypertension: A Blueprint for Action. An Official American Thoracic Society Statement. Am J Respir Crit Care Med 2017; 196:e32-e47. [PMID: 29028375 DOI: 10.1164/rccm.201709-1821st] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Health disparities have a major impact in the quality of life and clinical care received by minorities in the United States. Pulmonary arterial hypertension (PAH) is a rare cardiopulmonary disorder that affects children and adults and that, if untreated, results in premature death. The impact of health disparities in the diagnosis, treatment, and clinical outcome of patients with PAH has not been systematically investigated. OBJECTIVES The specific goals of this research statement were to conduct a critical review of the literature concerning health disparities in PAH, identify major research gaps and prioritize direction for future research. METHODS Literature searches from multiple reference databases were performed using medical subject headings and text words for pulmonary hypertension and health disparities. Members of the committee discussed the evidence and provided recommendations for future research. RESULTS Few studies were found discussing the impact of health disparities in PAH. Using recent research statements focused on health disparities, the group identified six major study topics that would help address the contribution of health disparities to PAH. Representative studies in each topic were discussed and specific recommendations were made by the group concerning the most urgent questions to address in future research studies. CONCLUSIONS At present, there are few studies that address health disparities in PAH. Given the potential adverse impact of health disparities, we recommend that research efforts be undertaken to address the topics discussed in the document. Awareness of health disparities will likely improve advocacy efforts, public health policy and the quality of care of vulnerable populations with PAH.
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Karol SE, Larsen E, Cheng C, Cao X, Yang W, Ramsey LB, Fernandez CA, McCorkle JR, Paugh SW, Autry RJ, Lopez-Lopez E, Diouf B, Jeha S, Pui CH, Raetz EA, Winick NJ, Carroll WL, Hunger SP, Loh ML, Devidas M, Evans WE, Yang JJ, Relling MV. Genetics of ancestry-specific risk for relapse in acute lymphoblastic leukemia. Leukemia 2017; 31:1325-1332. [PMID: 28096535 PMCID: PMC5462853 DOI: 10.1038/leu.2017.24] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/16/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023]
Abstract
The causes of individual relapses in children with acute lymphoblastic leukemia (ALL) remain incompletely understood. We evaluated the contribution of germline genetic factors to relapse in 2225 children treated on Children's Oncology Group trial AALL0232. We identified 302 germline single-nucleotide polymorphisms (SNPs) associated with relapse after adjusting for treatment and ancestry and 715 additional SNPs associated with relapse in an ancestry-specific manner. We tested for replication of these relapse-associated SNPs in external data sets of antileukemic drug pharmacokinetics and pharmacodynamics and an independent clinical cohort. 224 SNPs were associated with rapid drug clearance or drug resistance, and 32 were replicated in the independent cohort. The adverse risk associated with black and Hispanic ancestries was attenuated by addition of the 4 SNPs most strongly associated with relapse in these populations (for blacks: model without SNPs hazard ratio (HR)=2.32, P=2.27 × 10-4, model with SNPs HR=1.07, P=0.79; for Hispanics: model without SNPs HR=1.7, P=8.23 × 10-5, model with SNPs HR=1.31, P=0.065). Relapse SNPs associated with asparaginase resistance or allergy were overrepresented among SNPs associated with relapse in the more asparaginase intensive treatment arm (20/54 in Capizzi-methorexate arm vs 8/54 in high-dose methotrexate arm, P=0.015). Inherited genetic variation contributes to race-specific and treatment-specific relapse risk.
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Affiliation(s)
- S E Karol
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - E Larsen
- Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - C Cheng
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - X Cao
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - W Yang
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - L B Ramsey
- Department of Pharmacy Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - C A Fernandez
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - J R McCorkle
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - S W Paugh
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - R J Autry
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - E Lopez-Lopez
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - B Diouf
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - S Jeha
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - C-H Pui
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - E A Raetz
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - N J Winick
- Department of Pediatrics, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | - W L Carroll
- Perlmutter Cancer Center, Department of Pediatrics and Pathology, New York University Langone Medical Center, New York, NY, USA
| | - S P Hunger
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - M L Loh
- Department of Pediatrics, University of California School of Medicine, San Francisco, CA, USA
| | - M Devidas
- Department of Biostatistics, Colleges of Medicine, Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - W E Evans
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J J Yang
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - M V Relling
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
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Association of Gene Polymorphisms in Interleukin 6 in Infantile Bronchial Asthma. Arch Bronconeumol 2017; 53:381-386. [PMID: 28185773 DOI: 10.1016/j.arbres.2016.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/22/2016] [Accepted: 09/22/2016] [Indexed: 12/22/2022]
Abstract
INTRODUCTION The genetic background of bronchial asthma is complex, and it is likely that multiple genes contribute to its development both directly and through gene-gene interactions. Cytokines contribute to different aspects of asthma, as they determine the type, severity and outcomes of asthma pathogenesis. Allergic asthmatics undergoing an asthmatic attack exhibit significantly higher levels of pro-inflammatory cytokines, such as interleukins and chemokines. In recent years, cytokines and their receptors have been shown to be highly polymorphic, and this prompted us to investigate interleukin 6 promoter polymorphisms at position -174G/C (rs1800795) and at -572G/C (rs1800796) in relation to asthma in children. METHODS Interleukin 6 promoter polymorphisms were analyzed in bronchial asthma patients and healthy children using polymerase chain reaction-restriction fragment length polymorphism analysis. RESULTS We observed a significant association between polymorphism at -174G/C and bronchial asthma (OR=3.4, 95% CI: 2.045-5.638, P<.001). Higher associations between polymorphism at IL-6 -174G/C and bronchial asthma were observed in atopic patients (OR=4.1, 95% CI: 2.308-7.280, P<8.10-7). CONCLUSIONS Interleukin 6 polymorphism is associated with bronchial asthma, particularly its atopic phenotype. Expression and secretion of interleukins in asthmatic patients may be affected by genetic polymorphisms, and could have a disease-modifying effect in the asthmatic airway and modify the therapeutic response.
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Abstract
This review focuses on obesity, asthma and mental health functioning as salient health issues affecting Hispanic youth. Burden of these conditions and consequences for adult health are also discussed. Hispanic youth are affected by obesity at an early age; the prevalence of obesity among Hispanic children 6-11 years old is twice as high as the prevalence for non-Hispanic White children of the same age, but among 2-5 years old is 4 times higher. Asthma disproportionally affects certain Hispanic groups, notably children of Puerto Rican ancestry, and the comorbidity of asthma and obesity is an emerging health issue. Another area of concern is the scant data on mental health functioning among Hispanic youth. Research on Hispanic youth mental health have reported high rates of depressive symptomatology and high rates of alcohol use among Hispanic adolescents but despite these findings, they have inadequate access to mental health services. This review highlights the need for better data to gain a better understanding of the health status of Hispanic youth and help develop preventive programs that addresses the need of this population. Improving access to health services, in particular mental health services, is also a crucial aspect.
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Affiliation(s)
- Carmen R Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine
| | - Deepa Rastogi
- Department of Pediatrics, Albert Einstein College of Medicine
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Genetic ancestry as an effect modifier of naltrexone in smoking cessation among African Americans: an analysis of a randomized controlled trial. Pharmacogenet Genomics 2016; 25:305-12. [PMID: 25918964 DOI: 10.1097/fpc.0000000000000138] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To determine whether there were differential quit rates between African Americans (AA) and European Americans with the experimental treatment naltrexone, and examine the role of genetic ancestry on these outcomes among AAs. METHODS Data from a previous randomized trial of 315 smokers to naltrexone versus placebo were reanalyzed using West African (WA) genetic ancestry to define subpopulations. Logistic regression models were used to estimate treatment effects on early and end of treatment quit rates, by race and WA ancestry. RESULTS Among European Americans (n=136), naltrexone significantly increased quit rates at 4 weeks (62 vs. 43%, P=0.03) with directional, but not statistically significant effects at 12 weeks (30 vs. 18%, P=0.12). In contrast, among the AAs (n=95), quit rates did not differ between naltrexone and placebo groups at either interval (4 weeks: 43 vs. 32%, P=0.27; 12 weeks: 22 vs. 18%, P=0.60). A median split was conducted in AAs for WA ancestry. Among AAs with low WA ancestry, quit rates were significantly higher with naltrexone compared with placebo (60 vs. 27%, P=0.03). There was no advantage in quit rates with naltrexone for the high WA ancestry group. CONCLUSION Naltrexone efficacy for smoking cessation varies across AA individuals with different levels of WA ancestry. These results suggest that genetic background may partially explain racial differences in drug response.
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Giovannini-Chami L, Albertini M, Scheinmann P, de Blic J. New insights into the treatment of severe asthma in children. Paediatr Respir Rev 2015; 16:167-73. [PMID: 25182669 DOI: 10.1016/j.prrv.2014.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/21/2014] [Accepted: 07/27/2014] [Indexed: 02/02/2023]
Abstract
Severe asthma accounts for 0.5% of the general paediatric population and 4.5% of children with asthma, representing the major burden of asthma-health-care-associated costs. After ensuring a diagnosis of asthma and excluding difficult-to-treat patients with co-morbidities and non-adherence profiles, there remains children with real therapy-resistant asthma for whom the recommendations are to treat beyond guidelines. We describe new insights into the treatment of severe asthma in children, regarding both "classic drugs" (corticosteroids, bronchodilators) and innovative biological therapies targeting airway inflammation and impaired innate immunity. All of these new avenues remain to be studied and validated in children and will require fine clinical and biological phenotyping.
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Affiliation(s)
- Lisa Giovannini-Chami
- Paediatric Pulmonology and Allergology Department, Hôpitaux pédiatriques de Nice CHU-Lenval, Nice, F-06200, France; Université de Nice Sophia Antipolis, Nice, F-06000, France.
| | - Marc Albertini
- Paediatric Pulmonology and Allergology Department, Hôpitaux pédiatriques de Nice CHU-Lenval, Nice, F-06200, France; Université de Nice Sophia Antipolis, Nice, F-06000, France
| | - Pierre Scheinmann
- Paediatric Pulmonology and Allergology Department, AP-HP, Hôpital Necker Enfants Malades, Paris, F-75015, France; Université Paris Descartes-Paris 5, Paris, F-75005, France
| | - Jacques de Blic
- Paediatric Pulmonology and Allergology Department, AP-HP, Hôpital Necker Enfants Malades, Paris, F-75015, France; Université Paris Descartes-Paris 5, Paris, F-75005, France
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Genetic association of key Th1/Th2 pathway candidate genes, IRF2, IL6, IFNGR2, STAT4 and IL4RA, with atopic asthma in the Indian population. J Hum Genet 2015; 60:443-8. [PMID: 25994869 DOI: 10.1038/jhg.2015.45] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 04/06/2015] [Accepted: 04/10/2015] [Indexed: 02/01/2023]
Abstract
Asthma is a complex, multifactorial disease resulting due to dysregulated immune responses. Genetic factors contribute significantly to asthma pathogenesis, and identification of these factors is one of the major goals in understanding the disease. Th1/Th2 helper differentiation has a critical role in modulating the phenotypes associated with atopic asthma. This study was aimed at identifying genetic modifiers of asthma in selected genes involved in T helper differentiation. A total of 354 single-nucleotide polymorphisms (SNPs) in 33 candidate genes were genotyped in a case-control cohort (cases=147, controls=199) and families (n=247) using Illumina's Golden Gate Assay. Five SNPs, rs3733475A/C (IRF2), rs2069832A/G (IL6), rs2012075G/A (IFNGR2) and rs1400656G/A (STAT4) and rs1805011C/A (IL4RA) were found to be associated with asthma in family based as well as in case-control analyses (P=0.002, P=0.001, P=0.004, P=0.003 and P=0.001, respectively). Interestingly, the minor alleles at these loci showed a protective effect. A five loci haplotype, TAACG, in IRF2 gene, was significantly associated with asthma in families (P=1.1 × 10(-6)) and in case-control cohort (P=0.01). In conclusion, our studies led to identification of some key candidate genes, namely IRF2, IL6, IFNGR2, STAT4 and IL4RA that modulate genetic susceptibility to asthma in the Indian population. Also, this is the first report of independent association of IL6 gene polymorphism with atopic asthma.
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Mandal S, Abebe F, Chaudhary J. -174G/C polymorphism in the interleukin-6 promoter is differently associated with prostate cancer incidence depending on race. GENETICS AND MOLECULAR RESEARCH 2014; 13:139-51. [PMID: 24446297 DOI: 10.4238/2014.january.10.5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Interleukin-6 (IL-6), a pro-inflammatory cytokine, is involved in prostate cancer progression, including androgen independence. Serum IL-6 levels also correlate with prostate tumor burden, prostate-specific antigen levels and metastasis. Since circulating cytokine levels vary considerably inter-individually, such variation could be linked to genetic factors, including genetic polymorphism. The -174G>C/rs1800795 polymorphism in the IL-6 promoter is functionally relevant in terms of transcriptional regulation and disease association. We investigated a possible association of the -174G/C polymorphism with prostate cancer. Since significant racial disparities exist in prostate cancer incidence, we also investigated this association between the -174G/C polymorphism and prostate cancer in Caucasians and African-Americans, separately. Direct sequencing of the PCR amplicon from genomic DNA was used for genotyping rs1800795 in all subjects [age-matched controls (N = 140) and prostate cancer patients (N = 164)]. Sample size and power was calculated using the PGA software. We found the GG genotype to be associated with increased risk of prostate cancer in Caucasian subjects, whereas the CC genotype was associated with increased risk in the African-American sample set. Such a dimorphic genotypic association with cancer and race is unique and suggests a complex gene-gene and gene-environment interaction.
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Affiliation(s)
- S Mandal
- Center for Cancer Research and Therapeutics Development, Clark Atlanta University, Atlanta, GA, USA
| | - F Abebe
- Department of Mathematics, Clark Atlanta University, Atlanta, GA, USA
| | - J Chaudhary
- Center for Cancer Research and Therapeutics Development, Clark Atlanta University, Atlanta, GA, USA
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Ross LF, Ross LF, Saal HM, David KL, Anderson RR. Technical report: Ethical and policy issues in genetic testing and screening of children. Genet Med 2013; 15:234-45. [PMID: 23429433 DOI: 10.1038/gim.2012.176] [Citation(s) in RCA: 307] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The genetic testing and genetic screening of children are commonplace. Decisions about whether to offer genetic testing and screening should be driven by the best interest of the child. The growing literature on the psychosocial and clinical effects of such testing and screening can help inform best practices. This technical report provides ethical justification and empirical data in support of the proposed policy recommendations regarding such practices in a myriad of settings.
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Leong AB, Ramsey CD, Celedón JC. The challenge of asthma in minority populations. Clin Rev Allergy Immunol 2013; 43:156-83. [PMID: 21538075 DOI: 10.1007/s12016-011-8263-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The burden and disparity of asthma in race/ethnic minorities present a significant challenge. In this review, we will evaluate data on asthma epidemiology in minorities, examine potential reasons for asthma disparities, and discuss strategies of intervention and culturally sensitive care.
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Affiliation(s)
- Albin B Leong
- Pediatric Pulmonology and Allergy, Roseville Kaiser Medical Center, 1600 Eureka Road, Roseville, CA 95661, USA.
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Isaza C, Sepúlveda-Arias JC, Agudelo BI, Arciniegas W, Henao J, Porras GL, Beltrán L. β(2) -adrenoreceptor polymorphisms in asthmatic and non-asthmatic schoolchildren from Colombia and their relationship to treatment response. Pediatr Pulmonol 2012; 47:848-55. [PMID: 22328447 DOI: 10.1002/ppul.22521] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 11/19/2011] [Indexed: 11/10/2022]
Abstract
Asthma is a chronic and recurrent disease. Its high prevalence around the world is the result of a complex interaction between genetic and environmental factors. The genetic aspects of susceptibility, severity, and response to treatment in asthma are of great scientific interest. The purpose of the study was to establish the relationship between the Gln27Glu and Arg16Gly alleles of the β(2) -adrenergic receptor (ADRB2) gene with respect to the susceptibility to and severity of asthma, as well as the response to treatment in mestizo schoolchildren. 109 schoolchildren with asthma diagnosis and 137 asymptomatic controls were genotyped for the Arg16Gly and Gln27Glu alleles of the ADRB2 gene by minisequencing. Allele, genotype, and haplotype frequencies of the ADRB2 gene between asthmatic and non-asthmatic as well as demographic, clinical, and spirometric variables among asthmatic patients according to their genotype were compared. ADRB2 gene expression was determined by real-time quantitative PCR. No statistical differences were found in allele, genotype, and haplotype frequencies of the ADRB2 gene between cases and controls. We did not find differences between asthmatic patients classified according to their ADRB2 genotypes and haplotypes when evaluating demographic, clinical, and spirometric variables. The ADRB2 genotype and haplotype are not associated with spirometric responses or ADRB2 gene expression after administration of a β-(2) agonist plus a glucocorticoid. These results suggest that in the group of mestizo schoolchildren studied, the Arg16Gly and Gln27Glu polymorphisms are not markers of susceptibility or severity of asthma and do not affect ADRB2 gene expression during the rescue therapy.
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Affiliation(s)
- Carlos Isaza
- Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira, Colombia
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Lane HY, Tsai GE, Lin E. Assessing Gene-Gene Interactions in Pharmacogenomics. Mol Diagn Ther 2012; 16:15-27. [DOI: 10.1007/bf03256426] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Abstract
Pharmacogenetic analyses of treatments for alcohol dependence attempt to predict treatment response and side-effect risk for specific medications. We review the literature on pharmacogenetics relevant to alcohol dependence treatment, and describe state-of-the-art methods of pharmacogenetic research in this area. Two main pharmacogenetic study designs predominate: challenge studies and treatment-trial analyses. Medications studied include US FDA-approved naltrexone and acamprosate, both indicated for treating alcohol dependence, as well as several investigational (and off-label) treatments such as sertraline, olanzapine and ondansetron. The best-studied functional genetic variant relevant to alcoholism treatment is rs1799971, a single-nucleotide polymorphism in exon 1 of the OPRM1 gene that encodes the μ-opioid receptor. Evidence from clinical trials suggests that the presence of the variant G allele of rs1799971 may predict better treatment response to opioid receptor antagonists such as naltrexone. Evidence from clinical trials also suggests that several medications interact pharmacogenetically with variation in genes that encode proteins involved in dopaminergic and serotonergic neurotransmission. Variation in the DRD4 gene, which encodes the dopamine D(4) receptor, may predict better response to naltrexone and olanzapine. A polymorphism in the serotonin transporter gene SLC6A4 promoter region appears related to differential treatment response to sertraline depending on the subject's age of onset of alcoholism. Genetic variation in SLC6A4 may also be associated with better treatment response to ondansetron. Initial pharmacogenetic efforts in alcohol research have identified functional variants with potential clinical utility, but more research is needed to further elucidate the mechanism of these pharmacogenetic interactions and their moderators in order to translate them into clinical practice.
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Affiliation(s)
- Albert J. Arias
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA,VA Connecticut Healthcare System, West Haven, CT, USA
| | - R. Andrew Sewell
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA,VA Connecticut Healthcare System, West Haven, CT, USA
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Elwali NE, Mariani Costantini R, Di Gioacchino M. Environment and immune-mediated diseases in Sub-Saharan Africa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2012; 423:190-192. [PMID: 20961598 DOI: 10.1016/j.scitotenv.2010.08.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 08/26/2010] [Indexed: 05/30/2023]
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21
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Avena S, Via M, Ziv E, Pérez-Stable EJ, Gignoux CR, Dejean C, Huntsman S, Torres-Mejía G, Dutil J, Matta JL, Beckman K, Burchard EG, Parolin ML, Goicoechea A, Acreche N, Boquet M, Ríos Part MDC, Fernández V, Rey J, Stern MC, Carnese RF, Fejerman L. Heterogeneity in genetic admixture across different regions of Argentina. PLoS One 2012; 7:e34695. [PMID: 22506044 PMCID: PMC3323559 DOI: 10.1371/journal.pone.0034695] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 03/05/2012] [Indexed: 01/15/2023] Open
Abstract
The population of Argentina is the result of the intermixing between several groups, including Indigenous American, European and African populations. Despite the commonly held idea that the population of Argentina is of mostly European origin, multiple studies have shown that this process of admixture had an impact in the entire Argentine population. In the present study we characterized the distribution of Indigenous American, European and African ancestry among individuals from different regions of Argentina and evaluated the level of discrepancy between self-reported grandparental origin and genetic ancestry estimates. A set of 99 autosomal ancestry informative markers (AIMs) was genotyped in a sample of 441 Argentine individuals to estimate genetic ancestry. We used non-parametric tests to evaluate statistical significance. The average ancestry for the Argentine sample overall was 65% European (95%CI: 63-68%), 31% Indigenous American (28-33%) and 4% African (3-4%). We observed statistically significant differences in European ancestry across Argentine regions [Buenos Aires province (BA) 76%, 95%CI: 73-79%; Northeast (NEA) 54%, 95%CI: 49-58%; Northwest (NWA) 33%, 95%CI: 21-41%; South 54%, 95%CI: 49-59%; p<0.0001] as well as between the capital and immediate suburbs of Buenos Aires city compared to more distant suburbs [80% (95%CI: 75-86%) versus 68% (95%CI: 58-77%), p = 0.01]. European ancestry among individuals that declared all grandparents born in Europe was 91% (95%CI: 88-94%) compared to 54% (95%CI: 51-57%) among those with no European grandparents (p<0.001). Our results demonstrate the range of variation in genetic ancestry among Argentine individuals from different regions in the country, highlighting the importance of taking this variation into account in genetic association and admixture mapping studies in this population.
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Affiliation(s)
- Sergio Avena
- Departamento de Antropología, University of Buenos Aires, Buenos Aires, Argentina
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnósticos, Universidad Maimónides, Buenos Aires, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires, Argentina
| | - Marc Via
- Division of Pulmonary and Critical Care, University of California San Francisco, San Francisco, California, United States of America
- Unit of Anthropology, Department of Animal Biology, Universitat de Barcelona, Barcelona, Spain
| | - Elad Ziv
- Division of General Internal Medicine, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Eliseo J. Pérez-Stable
- Division of General Internal Medicine, University of California San Francisco, San Francisco, California, United States of America
- Medical Effectiveness Research Center for Diverse Populations, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Christopher R. Gignoux
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Cristina Dejean
- Departamento de Antropología, University of Buenos Aires, Buenos Aires, Argentina
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnósticos, Universidad Maimónides, Buenos Aires, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires, Argentina
| | - Scott Huntsman
- Division of General Internal Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Gabriela Torres-Mejía
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Julie Dutil
- Department of Biochemistry, Ponce School of Medicine and Health Sciences, Ponce, Puerto Rico
| | - Jaime L. Matta
- Department of Physiology and Pharmacology, Ponce School of Medicine and Health Sciences, Ponce, Puerto Rico
| | - Kenneth Beckman
- Deptartment of Genetics, Cell Biology and Developmental Biology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Esteban González Burchard
- Division of Pulmonary and Critical Care, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - María Laura Parolin
- Departamento de Antropología, University of Buenos Aires, Buenos Aires, Argentina
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnósticos, Universidad Maimónides, Buenos Aires, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires, Argentina
| | - Alicia Goicoechea
- Departamento de Antropología, University of Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas, Buenos Aires, Argentina
| | - Noemí Acreche
- Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Mariel Boquet
- Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia, Esquel, Chubut, Argentina
| | | | - Vanesa Fernández
- Servicio de Hemoterapia Hospital Penna de Bahía Blanca, Bahía Blanca, Buenos Aires, Argentina
| | - Jorge Rey
- Servicio de Hemoterapia Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariana C. Stern
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Raúl F. Carnese
- Departamento de Antropología, University of Buenos Aires, Buenos Aires, Argentina
| | - Laura Fejerman
- Division of General Internal Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Abstract
Identifying that health inequalities exist is not enough; nor does the knowledge that a patient has a high-risk genotype or comes from a higher risk socioeconomic background does not, by itself, help the patient. To thoroughly examine the origins of health disparities, a broad view of environmental and molecular influences must be included. As these factors are identified, it is important to focus on interventions that can change outcomes for patients. Tools for education, community involvement, literacy, and environmental safety need to be developed, tested and disseminated. The basic science of health disparities must move forward in a coordinated fashion by structuring research that is an integrated effort between basic sciences, clinical medicine and include all traditionally underserved communities. Only through these collaborations can we hope to eliminate health inequalities in the future.
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Affiliation(s)
- Kimberly Danieli Watts
- Children's Memorial Hospital, Northwestern University Feinberg School of Medicine, 2300 Children's Plaza Box # 43, Chicago, IL 60614, USA.
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Perinatal gene-gene and gene-environment interactions on IgE production and asthma development. Clin Dev Immunol 2012; 2012:270869. [PMID: 22481967 PMCID: PMC3299317 DOI: 10.1155/2012/270869] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 11/01/2011] [Accepted: 11/17/2011] [Indexed: 12/23/2022]
Abstract
Atopic asthma is a complex disease associated with IgE-mediated immune reactions. Numerous genome-wide studies identified more than 100 genes in 22 chromosomes associated with atopic asthma, and different genetic backgrounds in different environments could modulate susceptibility to atopic asthma. Current knowledge emphasizes the effect of tobacco smoke on the development of childhood asthma. This suggests that asthma, although heritable, is significantly affected by gene-gene and gene-environment interactions. Evidence has recently shown that molecular mechanism of a complex disease may be limited to not only DNA sequence differences, but also gene-environmental interactions for epigenetic difference. This paper reviews and summarizes how gene-gene and gene-environment interactions affect IgE production and the development of atopic asthma in prenatal and childhood stages. Based on the mechanisms responsible for perinatal gene-environment interactions on IgE production and development of asthma, we formulate several potential strategies to prevent the development of asthma in the perinatal stage.
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Affiliation(s)
- Kathleen C Barnes
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21224, USA.
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Gould W, Peterson EL, Karungi G, Zoratti A, Gaggin J, Toma G, Yan S, Levin AM, Yang JJ, Wells K, Wang M, Burke RR, Beckman K, Popadic D, Land SJ, Kumar R, Seibold MA, Lanfear DE, Burchard EG, Williams LK. Factors predicting inhaled corticosteroid responsiveness in African American patients with asthma. J Allergy Clin Immunol 2011; 126:1131-8. [PMID: 20864153 DOI: 10.1016/j.jaci.2010.08.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 07/30/2010] [Accepted: 08/02/2010] [Indexed: 01/13/2023]
Abstract
BACKGROUND African American patients disproportionately experience uncontrolled asthma. Treatment with an inhaled corticosteroid (ICS) is considered first-line therapy for persistent asthma. OBJECTIVE We sought to determine the degree to which African American patients respond to ICS medication and whether the level of response is influenced by other factors, including genetic ancestry. METHODS Patients aged 12 to 56 years who received care from a large health system in southeast Michigan and who resided in Detroit were recruited to participate if they had a diagnosis of asthma. Patients were treated with 6 weeks of inhaled beclomethasone dipropionate, and pulmonary function was remeasured after treatment. Ancestry was determined by genotyping ancestry-informative markers. The main outcome measure was ICS responsiveness defined as the change in prebronchodilator FEV(1) over the 6-week course of treatment. RESULTS Among 147 participating African American patients with asthma, average improvement in FEV(1) after 6 weeks of ICS treatment was 11.6%. The mean proportion of African ancestry in this group was 78.4%. The degree of baseline bronchodilator reversibility was the only factor consistently associated with ICS responsiveness, as measured by both an improvement in FEV(1) and patient-reported asthma control (P = .001 and P = .021, respectively). The proportion of African ancestry was not significantly associated with ICS responsiveness. CONCLUSIONS Although baseline pulmonary function parameters appear to be associated with the likelihood to respond to ICS treatment, the proportion of genetic African ancestry does not. This study suggests that genetic ancestry might not contribute to differences in ICS controller response among African American patients with asthma.
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Affiliation(s)
- Wendy Gould
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI 48202, USA
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26
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Barnes KC. Ancestry, ancestry-informative markers, asthma, and the quest for personalized medicine. J Allergy Clin Immunol 2011; 126:1139-40. [PMID: 21134571 DOI: 10.1016/j.jaci.2010.10.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 10/25/2010] [Indexed: 10/18/2022]
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Moore PE. Influence of gene-gene interactions on response to albuterol therapy. Pharmacogenomics 2011; 12:1-3. [PMID: 21174616 DOI: 10.2217/pgs.10.192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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Tcheurekdjian H, Via M, De Giacomo A, Corvol H, Eng C, Thyne S, Chapela R, Rodriguez-Cintron W, Rodriguez-Santana JR, Avila PC, Burchard EG. ALOX5AP and LTA4H polymorphisms modify augmentation of bronchodilator responsiveness by leukotriene modifiers in Latinos. J Allergy Clin Immunol 2010; 126:853-8. [PMID: 20810156 PMCID: PMC2950217 DOI: 10.1016/j.jaci.2010.06.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 05/25/2010] [Accepted: 06/28/2010] [Indexed: 11/25/2022]
Abstract
BACKGROUND Understanding the effects of interactions between multiple genes and asthma medications may aid in the understanding of the heterogeneous response to asthma therapies. OBJECTIVE To identify modulating effects of arachidonate 5-lipoxygenase-activating protein (ALOX5AP) and leukotriene A(4) hydrolase (LTA4H) gene polymorphisms on the drug-drug interaction between leukotriene modifiers and albuterol in Mexicans and Puerto Ricans. METHODS In a cross-sectional study of 293 Mexicans and 356 Puerto Ricans with asthma, ALOX5AP and LTA4H genes were sequenced, and interactions between gene polymorphisms and bronchodilator responsiveness to albuterol were compared between leukotriene modifier users and nonusers. RESULTS In heterozygotes and homozygotes for the minor allele at LTA4H single nucleotide polymorphism (SNP) rs2540491 and heterozygotes for the major allele at LTA4H SNP rs2540487, leukotriene modifier use was associated with a clinically significant increase in percent change in FEV(1) after albuterol administration of 7.10% (P = .002), 10.06% (P = .001), and 10.03% (P < .001), respectively. Presence of the major allele at ALOX5AP SNP rs10507391 or the minor allele at ALOX5AP SNP rs9551963 augmented this response. When stratified by ethnicity, these findings held true for Puerto Ricans but not Mexicans. CONCLUSION LTA4H and ALOX5AP gene polymorphisms modify the augmentation of bronchodilator responsiveness by leukotriene modifiers in Puerto Ricans but not Mexicans with asthma.
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Affiliation(s)
- Haig Tcheurekdjian
- Allergy/Immunology Associates, Inc, and Case Western Reserve University, Cleveland, Ohio, USA.
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Kim JH, Cheong HS, Park BL, Bae JS, Jung S, Yoon SH, Park JS, Jang AS, Park SW, Uh ST, Kim YH, Hwang HK, Park CS, Shin HD. A new association between polymorphisms of the SLC6A7 gene in the chromosome 5q31-32 region and asthma. J Hum Genet 2010; 55:358-65. [PMID: 20431603 DOI: 10.1038/jhg.2010.34] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human chromosomal 5q31-33 region has been implicated as a susceptibility locus for several immune-mediated diseases including asthma in several populations. Recently, the extraneuronal GABAergic system has been implicated as a new link to airway obstruction in asthma. In addition, the SLC6A7 gene, which is positioned at 5q31-32 and encodes the transporter for an excitatory neurotransmitter of L-proline, has never been studied for its association with asthma. In this study, resequencing of all exon, promoter region (2 kb), and exon-intron boundary regions in the SLC6A7 gene found a total of 33 single nucleotide polymorphisms (SNPs) in 24 Korean asthmatic patients. After the initial SNP survey, a total of 17 common SNPs with minor allele frequency (MAF) over 10% were genotyped in 498 asthmatic patients and 303 normal controls. Logistic analyses revealed significant associations between genetic variants of the SLC6A7 gene and asthma (P-value up to 6.0 x 10(-4); P(corr) value up to 0.009). In further regression analyses, minor alleles of intronic +11431T>C, +12213C>T and +12927A>G in linkage disequilibrium block 2 and +20113T>C in 3'UTR significantly increased the bronchodilator response in asthmatics (P-value of recessive model up to 0.008; which are not significant after multiple correction). Therefore, our findings suggest that SLC6A7 could be a susceptible gene for asthma.
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Affiliation(s)
- Jeong-Hyun Kim
- Department of Life Science, Sogang University, Seoul, Republic of Korea
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Kroetz DL, Ahituv N, Burchard EG, Guo S, Sali A, Giacomini KM. Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy. Pharmacogenomics 2010; 10:1569-76. [PMID: 19842929 DOI: 10.2217/pgs.09.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Pharmacogenomics Center of the University of California, San Francisco (CA, USA) fosters research and educational activities focused on the genomic basis for variation in drug response. Investigators in the Center conduct multidisciplinary and multicenter research on a diverse array of clinically used drugs with the goal of understanding the genetic factors that contribute to variation in therapeutic and adverse drug response. The Center houses the large NIH-supported Pharmacogenomics of Membrane Transporters Project, which is a leader in understanding genetic variation in membrane transporters that are important in clinical drug response. Center investigators study racially and ethnically diverse populations, are pioneers in the education of PharmD, MD and PhD students in pharmacogenomics, and have led the establishment of unique graduate and postdoctoral training programs focused on pharmacogenomics. A key emphasis of the Center is on biological mechanisms with a goal of facilitating the development of safer and more effective medications.
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Affiliation(s)
- Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, CA, USA
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Lemanske RF, Mauger DT, Sorkness CA, Jackson DJ, Boehmer SJ, Martinez FD, Strunk RC, Szefler SJ, Zeiger RS, Bacharier LB, Covar RA, Guilbert TW, Larsen G, Morgan WJ, Moss MH, Spahn JD, Taussig LM. Step-up therapy for children with uncontrolled asthma receiving inhaled corticosteroids. N Engl J Med 2010; 362:975-85. [PMID: 20197425 PMCID: PMC2989902 DOI: 10.1056/nejmoa1001278] [Citation(s) in RCA: 296] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND For children who have uncontrolled asthma despite the use of low-dose inhaled corticosteroids (ICS), evidence to guide step-up therapy is lacking. METHODS We randomly assigned 182 children (6 to 17 years of age), who had uncontrolled asthma while receiving 100 microg of fluticasone twice daily, to receive each of three blinded step-up therapies in random order for 16 weeks: 250 microg of fluticasone twice daily (ICS step-up), 100 microg of fluticasone plus 50 microg of a long-acting beta-agonist twice daily (LABA step-up), or 100 microg of fluticasone twice daily plus 5 or 10 mg of a leukotriene-receptor antagonist daily (LTRA step-up). We used a triple-crossover design and a composite of three outcomes (exacerbations, asthma-control days, and the forced expiratory volume in 1 second) to determine whether the frequency of a differential response to the step-up regimens was more than 25%. RESULTS A differential response occurred in 161 of 165 patients who were evaluated (P<0.001). The response to LABA step-up therapy was most likely to be the best response, as compared with responses to LTRA step-up (relative probability, 1.6; 95% confidence interval [CI], 1.1 to 2.3; P=0.004) and ICS step-up (relative probability, 1.7; 95% CI, 1.2 to 2.4; P=0.002). Higher scores on the Asthma Control Test before randomization (indicating better control at baseline) predicted a better response to LABA step-up (P=0.009). White race predicted a better response to LABA step-up, whereas black patients were least likely to have a best response to LTRA step-up (P=0.005). CONCLUSIONS Nearly all the children had a differential response to each step-up therapy. LABA step-up was significantly more likely to provide the best response than either ICS or LTRA step-up. However, many children had a best response to ICS or LTRA step-up therapy, highlighting the need to regularly monitor and appropriately adjust each child's asthma therapy. (ClinicalTrials.gov number, NCT00395304.)
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Affiliation(s)
- Robert F Lemanske
- University of Wisconsin School of Medicine and Public Health, Madison, USA.
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Sissung TM, English BC, Venzon D, Figg WD, Deeken JF. Clinical pharmacology and pharmacogenetics in a genomics era: the DMET platform. Pharmacogenomics 2010; 11:89-103. [PMID: 20017675 DOI: 10.2217/pgs.09.154] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
While no genome-wide pharmacogenetics study has yet been published, the field of pharmacogenetics is moving towards exploratory, large-scale analyses of the interaction between genetic variation and drug treatment. The Drug Metabolizing Enzymes and Transporters (DMET) platform offers a standardized set of 1936 variants in 225 genes related to drug absorption, distribution, metabolism and elimination that is useful to scan the genome for previously unknown associations between variation in absorption, distribution, metabolism and elimination genes and pharmacokinetic and pharmacodynamic outcomes of drug treatment. The purpose of this review is to put the DMET platform into context within the current study designs that have been used in pharmacogenetics, and to explore the role that DMET has played - and will play - in future pharmacogenetics studies.
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Via M, Ziv E, Burchard EG. Recent advances of genetic ancestry testing in biomedical research and direct to consumer testing. Clin Genet 2010; 76:225-35. [PMID: 19793051 DOI: 10.1111/j.1399-0004.2009.01263.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In the post-Human Genome Project era, the debate on the concept of race/ethnicity and its implications for biomedical research are dependent on two critical issues: whether and how to classify individuals and whether biological factors play a role in health disparities. The advent of reliable estimates of genetic (or biogeographic) ancestry has provided this debate with a quantitative and more objective tool. The estimation of genetic ancestry allows investigators to control for population stratification in association studies and helps to detect biological causation behind population-specific differences in disease and drug response. New techniques such as admixture mapping can specifically detect population-specific risk alleles for a disease in admixed populations. However, researchers have to be mindful of the correlation between genetic ancestry and socioeconomic and environmental factors that could underlie these differences. More importantly, researchers must avoid the stigmatization of individuals based on perceived or real genetic risks. The latter point will become increasingly sensitive as several 'for profit companies' are offering ancestry and genetic testing directly to consumers and the consequences of the spread of the services of these companies are still unforeseeable.
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Affiliation(s)
- M Via
- Institute for Human Genetics, University of California, San Francisco, CA 94143-2911, USA.
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Duconge J, Ruaño G. The Emerging Role of Admixture in the Pharmacogenetics of Puerto Rican Hispanics. ACTA ACUST UNITED AC 2010; 1. [PMID: 23227441 DOI: 10.4172/2153-0645.1000101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Admixture is of great relevance to the clinical application of pharmacogenetics and personalized medicine. Preliminary findings in Puerto Ricans further substantiate the argument for admixture as a critical covariate in a customized DNA-guided warfarin dosing algorithm. To this purpose, a genome-wide approach that incorporates admixture as an independent predictor of dose variability in DNA-guided algorithms has been postulated. Admixture is expected to be able to reveal some relevant associations in the genetic epidemiology of Hispanics and will be indispensable to assure that pharmacogenomic research can be pursued in such mixed populations. Consequently, the clinical utility of knowing an individual's genotype before initiating drug treatment in Puerto Ricans, and Hispanics in general, will finally be untangled by developing a "Genetic Prescription Model" that takes admixture into consideration. This approach will help lead physicians and patients to their desired treatment goal, resulting in more effective healthcare in admixed people.
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Affiliation(s)
- Jorge Duconge
- University of Puerto Rico School of Pharmacy, Medical Sciences Campus, Pharmaceutical Sciences Department, San Juan PR 00936
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