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Roman S, Campos-Medina L, Leal-Mercado L. Personalized nutrition: the end of the one-diet-fits-all era. Front Nutr 2024; 11:1370595. [PMID: 38854164 PMCID: PMC11157041 DOI: 10.3389/fnut.2024.1370595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024] Open
Abstract
Personalized Nutrition emerged as a new trend for providing nutritional and food advice based on the individual's genetic composition, a field driven by the advancements in the multi-omic sciences throughout the last century. It intends not only to tailor the recommended daily allowances of nutrients and functional foods that a person may need but also to maintain the principles of sustainability and eco-friendliness. This principle implies the implementation of strategies within the healthcare system to advocate for the ending of the one-diet-fits-all paradigm by considering a personalized diet as an ally to prevent diet-related chronic diseases. In this Perspective, we highlight the potential benefits of such a paradigm within the region of Latin America, particularly Mexico, where the genetic admixture of the population, food biodiversity, and food culture provide unique opportunities to establish personalized nutrigenetic strategies. These strategies could play a crucial role in preventing chronic diseases and addressing the challenges confronted in the region.
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Affiliation(s)
- Sonia Roman
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Liliana Campos-Medina
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
- Doctoral Program in Molecular Biology in Medicine, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Leonardo Leal-Mercado
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
- Doctoral Program in Molecular Biology in Medicine, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
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Köksal Z, Meyer OL, Andersen JD, Gusmão L, Mogensen HS, Pereira V, Børsting C. Pitfalls and challenges with population assignments of individuals from admixed populations: Applying Genogeographer on Brazilian individuals. Forensic Sci Int Genet 2023; 67:102934. [PMID: 37713981 DOI: 10.1016/j.fsigen.2023.102934] [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: 01/09/2023] [Revised: 06/06/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
The assignment of individuals to a population can be of importance for the identification of mass disaster victims or criminal offenders in the field of forensic genetics. This assignment is based on biostatistical methods that process data of ancestry informative markers (AIMs), which are selected based on large allele frequency differences between the populations of interest. However, population assignments of individuals with an admixed genetic background are challenging. Admixed individuals are genetic mosaics of chromosomal segments from the parental populations, which may lead to ambiguous or no population assignment. This is problematic since admixture events are a substantial part of human history. In this study, we present challenges of interpreting the evidential weight of population assignments. We used Genogeographer for likelihood ratio (LR) calculations and Brazilians as examples of admixed individuals. Brazilians are a very heterogenous population representing a three-way admixture between Native Americans, Europeans, and Africans. Ancestry informative markers were typed in a total of 589 individuals from Brazil using the Precision ID Ancestry Panel. The Brazilians were assigned to six metapopulations (East Asia, Europe, Middle East, North Africa, South-Central Asia, Sub-Saharan Africa) defined in the Genogeographer software and LRs were calculated if the AIM profile was not an outlier in all metapopulations and simulated two-way (1:1) admixtures of the six metapopulations. Population assignments failed for 55% of the samples. These samples had significantly higher genetic contributions from East Asia, South-Central Asia and Sub-Saharan Africa, and significantly lower genetic contributions from Europe. Most of the individuals with population assignments were assigned to the metapopulations of Middle East (58%) or North Africa (36%), followed by Europe (4%), South-Central Asia (1%), and Sub-Saharan Africa (1%). For 8% of the samples, population assignments were only possible when assignments to simulated two-way (1:1) admixtures of the six metapopulations were considered. Most of these individuals were assigned to two-way admixtures of North Africa, South-Central Asia, or Sub-Saharan Africa. Relatively low median likelihood ratios (LRs<1000) were observed when comparing population likelihoods for Europe, Middle East, North Africa, South-Central Asia, or simulated 1:1 admixtures of these metapopulations. Comparisons including East Asian or Sub-Saharan African populations resulted in larger median LRs (LR>1010). The results suggested that the Precision ID Ancestry Panel provided too little information and that additional markers specifically selected for sub-continental differentiation may be required for accurate population assignment of admixed individuals. Furthermore, a Genogeographer database with additional populations including admixed populations would be advantageous for interpretation of admixed AIM profiles. It would likely increase the number of population assignments and illustrate alternatives to the most likely population, which would be valuable information for the case officer when writing the case report.
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Affiliation(s)
- Zehra Köksal
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Olivia Luxford Meyer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Helle Smidt Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Xiong Y, Kullberg S, Garman L, Pezant N, Ellinghaus D, Vasila V, Eklund A, Rybicki BA, Iannuzzi MC, Schreiber S, Müller-Quernheim J, Montgomery CG, Grunewald J, Padyukov L, Rivera NV. Sex differences in the genetics of sarcoidosis across European and African ancestry populations. Front Med (Lausanne) 2023; 10:1132799. [PMID: 37250650 PMCID: PMC10213734 DOI: 10.3389/fmed.2023.1132799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/10/2023] [Indexed: 05/31/2023] Open
Abstract
Background Sex differences in the susceptibility of sarcoidosis are unknown. The study aims to identify sex-dependent genetic variations in two clinical sarcoidosis phenotypes: Löfgren's syndrome (LS) and non-Löfgren's syndrome (non-LS). Methods A meta-analysis of genome-wide association studies was conducted on Europeans and African Americans, totaling 10,103 individuals from three population-based cohorts, Sweden (n = 3,843), Germany (n = 3,342), and the United States (n = 2,918), followed by an SNP lookup in the UK Biobank (UKB, n = 387,945). A genome-wide association study based on Immunochip data consisting of 141,000 single nucleotide polymorphisms (SNPs) was conducted in the sex groups. The association test was based on logistic regression using the additive model in LS and non-LS sex groups independently. Additionally, gene-based analysis, gene expression, expression quantitative trait loci (eQTL) mapping, and pathway analysis were performed to discover functionally relevant mechanisms related to sarcoidosis and biological sex. Results We identified sex-dependent genetic variations in LS and non-LS sex groups. Genetic findings in LS sex groups were explicitly located in the extended Major Histocompatibility Complex (xMHC). In non-LS, genetic differences in the sex groups were primarily located in the MHC class II subregion and ANXA11. Gene-based analysis and eQTL enrichment revealed distinct sex-specific gene expression patterns in various tissues and immune cell types. In LS sex groups, a pathway map related to antigen presentation machinery by IFN-gamma. In non-LS, pathway maps related to immune response lectin-induced complement pathway in males and related to maturation and migration of dendritic cells in skin sensitization in females were identified. Conclusion Our findings provide new evidence for a sex bias underlying sarcoidosis genetic architecture, particularly in clinical phenotypes LS and non-LS. Biological sex likely plays a role in disease mechanisms in sarcoidosis.
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Affiliation(s)
- Ying Xiong
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Susanna Kullberg
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Theme Inflammation and Ageing, Karolinska University Hospital, Stockholm, Sweden
| | - Lori Garman
- Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Nathan Pezant
- Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Vasiliki Vasila
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Anders Eklund
- Department of Respiratory Medicine and Allergy, Theme Inflammation and Ageing, Karolinska University Hospital, Stockholm, Sweden
| | - Benjamin A. Rybicki
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, United States
| | - Michael C. Iannuzzi
- Zucker School of Medicine, Staten Island University Hospital, Northwell/Hofstra University, Staten Island, NY, United States
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- Clinic for Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Joachim Müller-Quernheim
- Department of Pneumology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Courtney G. Montgomery
- Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Johan Grunewald
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Theme Inflammation and Ageing, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Padyukov
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Natalia V. Rivera
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Carlos RC, Obeng-Gyasi S, Cole SW, Zebrack BJ, Pisano ED, Troester MA, Timsina L, Wagner LI, Steingrimsson JA, Gareen I, Lee CI, Adams AS, Wilkins CH. Linking Structural Racism and Discrimination and Breast Cancer Outcomes: A Social Genomics Approach. J Clin Oncol 2022; 40:1407-1413. [PMID: 35108027 PMCID: PMC9851699 DOI: 10.1200/jco.21.02004] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/03/2021] [Accepted: 01/10/2022] [Indexed: 01/23/2023] Open
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Inamo J, Kochi Y, Takeuchi T. Is type 2 diabetes mellitus an inverse risk factor for the development of rheumatoid arthritis? J Hum Genet 2020; 66:219-223. [PMID: 32901113 DOI: 10.1038/s10038-020-00837-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/30/2020] [Accepted: 08/31/2020] [Indexed: 11/09/2022]
Abstract
Type 2 diabetes mellitus (T2DM) and rheumatoid arthritis (RA) are both chronic diseases. Although the link between metabolic abnormalities and dysregulated inflammation has received much attention, it is not known whether T2DM can be a risk for the development of RA. Also, observational studies have the disadvantage that the possibility of confounding factors, such as environmental factors, cannot be ruled out. Therefore, the current study performed the mendelian randomization (MR) analysis using recent large-scale genome-wide association studies datasets of T2DM and RA separately European and Asian ancestries. As a result, T2DM had an inverse causal effect on the risk of RA. This study proposed a novel hypothesis that a protective effect of T2DM for the risk of RA.
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Affiliation(s)
- Jun Inamo
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
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Abstract
Risk of disease is multifactorial and can be shaped by socio-economic, demographic, cultural, environmental and genetic factors. Our understanding of the genetic determinants of disease risk has greatly advanced with the advent of genome-wide association studies (GWAS), which detect associations between genetic variants and complex traits or diseases by comparing populations of cases and controls. However, much of this discovery has occurred through GWAS of individuals of European ancestry, with limited representation of other populations, including from Africa, The Americas, Asia and Oceania. Population demography, genetic drift and adaptation to environments over thousands of years have led globally to the diversification of populations. This global genomic diversity can provide new opportunities for discovery and translation into therapies, as well as a better understanding of population disease risk. Large-scale multi-ethnic and representative biobanks and population health resources provide unprecedented opportunities to understand the genetic determinants of disease on a global scale.
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Shraga R, Yarnall S, Elango S, Manoharan A, Rodriguez SA, Bristow SL, Kumar N, Niknazar M, Hoffman D, Ghadir S, Vassena R, Chen SH, Hershlag A, Grifo J, Puig O. Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening. BMC Genet 2017; 18:99. [PMID: 29179688 PMCID: PMC5704547 DOI: 10.1186/s12863-017-0570-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 11/16/2017] [Indexed: 11/10/2022] Open
Abstract
Background Current professional society guidelines recommend genetic carrier screening be offered on the basis of ethnicity, or when using expanded carrier screening panels, they recommend to compute residual risk based on ethnicity. We investigated the reliability of self-reported ethnicity in 9138 subjects referred to carrier screening. Self-reported ethnicity gathered from test requisition forms and during post-test genetic counseling, and genetic ancestry predicted by a statistical model, were compared for concordance. Results We identified several discrepancies between the two sources of self-reported ethnicity and genetic ancestry. Only 30.3% of individuals who indicated Mediterranean ancestry during consultation self-reported this on requisition forms. Additionally, the proportion of individuals who reported Southeast Asian but were estimated to have a different genetic ancestry was found to depend on the source of self-report. Finally, individuals who reported Latin American demonstrated a high degree of ancestral admixture. As a result, carrier rates and residual risks provided for patient decision-making are impacted if using self-reported ethnicity. Conclusion Our analysis highlights the unreliability of ethnicity classification based on patient self-reports. We recommend the routine use of pan-ethnic carrier screening panels in reproductive medicine. Furthermore, the use of an ancestry model would allow better estimation of carrier rates and residual risks. Electronic supplementary material The online version of this article (10.1186/s12863-017-0570-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roman Shraga
- Phosphorus, Inc, 25 West 26th St, New York, NY, 10010, USA
| | | | - Sonya Elango
- Sarah Lawrence College, Bronxville, New York, USA
| | | | | | - Sara L Bristow
- Phosphorus, Inc, 25 West 26th St, New York, NY, 10010, USA.,Northwell Fertility, North Shore University Hospital, Manhasset, NY, USA
| | | | | | - David Hoffman
- IVF Florida Reproductive Associates, Margate, FL, USA
| | - Shahin Ghadir
- Department of Obstetrics and Gynecology, The David Geffen School of Medicine at UCLA, California, Los Angeles, USA
| | | | - Serena H Chen
- Institute for Reproductive Medicine and Science, Saint Barnabas Medical Center, Livingston, NJ, USA
| | - Avner Hershlag
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Hofstra Northwell School of Medicine, Manhasset, NY, USA
| | - Jamie Grifo
- Division of Reproductive Endocrinology & Infertility, Department of Obstetrics and Gynecology, NYU Langone, New York, NY, USA
| | - Oscar Puig
- Phosphorus, Inc, 25 West 26th St, New York, NY, 10010, USA.
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Gupta J, Johansson E, Bernstein JA, Chakraborty R, Khurana Hershey GK, Rothenberg ME, Mersha TB. Resolving the etiology of atopic disorders by using genetic analysis of racial ancestry. J Allergy Clin Immunol 2016; 138:676-699. [PMID: 27297995 PMCID: PMC5014679 DOI: 10.1016/j.jaci.2016.02.045] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 02/09/2016] [Accepted: 02/25/2016] [Indexed: 12/23/2022]
Abstract
Atopic dermatitis (AD), food allergy, allergic rhinitis, and asthma are common atopic disorders of complex etiology. The frequently observed atopic march from early AD to asthma, allergic rhinitis, or both later in life and the extensive comorbidity of atopic disorders suggest common causal mechanisms in addition to distinct ones. Indeed, both disease-specific and shared genomic regions exist for atopic disorders. Their prevalence also varies among races; for example, AD and asthma have a higher prevalence in African Americans when compared with European Americans. Whether this disparity stems from true genetic or race-specific environmental risk factors or both is unknown. Thus far, the majority of the genetic studies on atopic diseases have used populations of European ancestry, limiting their generalizability. Large-cohort initiatives and new analytic methods, such as admixture mapping, are currently being used to address this knowledge gap. Here we discuss the unique and shared genetic risk factors for atopic disorders in the context of ancestry variations and the promise of high-throughput "-omics"-based systems biology approach in providing greater insight to deconstruct their genetic and nongenetic etiologies. Future research will also focus on deep phenotyping and genotyping of diverse racial ancestry, gene-environment, and gene-gene interactions.
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Affiliation(s)
- Jayanta Gupta
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Elisabet Johansson
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Jonathan A Bernstein
- Division of Immunology/Allergy Section, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Ranajit Chakraborty
- Center for Computational Genomics, Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Tex
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio.
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Spector SA, Brummel SS, Nievergelt CM, Maihofer AX, Singh KK, Purswani MU, Williams PL, Hazra R, Van Dyke R, Seage GR. Genetically determined ancestry is more informative than self-reported race in HIV-infected and -exposed children. Medicine (Baltimore) 2016; 95:e4733. [PMID: 27603370 PMCID: PMC5023893 DOI: 10.1097/md.0000000000004733] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Pediatric HIV/AIDS Cohort Study (PHACS), the largest ongoing longitudinal study of perinatal HIV-infected (PHIV) and HIV-exposed, uninfected (PHEU) children in the United States, comprises the Surveillance Monitoring of Antiretroviral Therapy [ART] Toxicities (SMARTT) Study in PHEU children and the Adolescent Master Protocol (AMP) that includes PHIV and PHEU children ≥7 years. Although race/ethnicity is often used to assess health outcomes, this approach remains controversial and may fail to accurately reflect the backgrounds of ancestry-diverse populations as represented in the PHACS participants.In this study, we compared genetically determined ancestry (GDA) and self-reported race/ethnicity (SRR) in the PHACS cohort. GDA was estimated using a highly discriminative panel of 41 single nucleotide polymorphisms and compared to SRR. Because SRR was similar between the PHIV and PHEU, and between the AMP and SMARTT cohorts, data for all unique 1958 participants were combined.According to SRR, 63% of study participants identified as Black/African-American, 27% White, and 34% Hispanic. Using the highest percentage of ancestry/ethnicity to identify GDA, 9.5% of subjects were placed in the incorrect superpopulation based on SRR. When ≥50% or ≥75% GDA of a given superpopulation was required, 12% and 25%, respectively, of subjects were placed in the incorrect superpopulation based on SRR, and the percent of subjects classified as multiracial increased. Of 126 participants with unidentified SRR, 71% were genetically identified as Eurasian.GDA provides a more robust assessment of race/ethnicity when compared to self-report, and study participants with unidentified SRR could be assigned GDA using genetic markers. In addition, identification of continental ancestry removes the taxonomic identification of race as a variable when identifying risk for clinical outcomes.
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Affiliation(s)
- Stephen A. Spector
- University of California, San Diego, La Jolla
- Rady Children's Hospital-San Diego, San Diego, CA
- Correspondence: Stephen A. Spector, University of California, San Diego, 9500 Gilman Drive, Stein Clinical Research Building, MC 0672, La Jolla, CA 92093-0672 (e-mail: )
| | - Sean S. Brummel
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA
| | | | | | | | - Murli U. Purswani
- Albert Einstein College of Medicine, Bronx Lebanon Hospital, Bronx, New York, NY
| | - Paige L. Williams
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA
- Departments of Biostatistics
- Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Rohan Hazra
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | | | - George R. Seage
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA
- Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
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10
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Gonzalez R, Gonzalez S, Villa E, Ramirez M, Zavala J, Armas R, Contreras J, Dassori A, Leach RJ, Flores D, Jerez A, Raventós H, Ontiveros A, Nicolini H, Escamilla M. Identification of circadian gene variants in bipolar disorder in Latino populations. J Affect Disord 2015; 186:367-75. [PMID: 26283580 DOI: 10.1016/j.jad.2015.07.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 06/23/2015] [Accepted: 07/08/2015] [Indexed: 01/02/2023]
Abstract
BACKGROUND Variations in circadian genes can impact biological rhythms. Given the rhythm disturbances that characterize bipolar disorder (BD), genes encoding components of molecular clocks are good candidate genes for the illness. METHODS A family based association analysis of circadian gene single nucleotide polymorphisms (SNPs) and BD was conducted in Latino pedigrees. 884 individuals from 207 pedigrees (473BP phenotype and 411 unaffected family members) were genotyped. Family based single marker association testing was performed. Ancestral haplotypes (SNPs found to be in strong LD defined using confidence intervals) were also tested for association with BD. RESULTS Multiple suggestive associations between circadian gene SNPs and BD were noted. These included CSNK1E (rs1534891, p=0.00689), ARNTL (rs3789327, p=0.021172), CSNK1D (rs4510078, p=0.022801), CLOCK (rs17777927, p=0.031664). Individually, none of the SNPs were significantly associated with BD after correction for multiple testing. However, a 4-locus CSNK1E haplotype encompassing the rs1534891 SNP (Z-score=2.685, permuted p=0.0076) and a 3-locus haplotype in ARNTL (Z-score=3.269, permuted p=0.0011) showed a significant association with BD. LIMITATIONS Larger samples are required to confirm these findings and assess the relationship between circadian gene SNPs and BD in Latinos. CONCLUSIONS The results suggest that ARNTL and CSKN1E variants may be associated with BD. Further studies are warranted to assess the relationships between these genes and BD in Latino populations.
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Affiliation(s)
- Robert Gonzalez
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA.
| | - Suzanne Gonzalez
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Erika Villa
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Mercedes Ramirez
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Juan Zavala
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Regina Armas
- Langley Porter Psychiatric Institute, University of California at San Francisco, San Francisco, CA, USA
| | - Javier Contreras
- Centro de Investigación en Biología Celular y Molecular y Escuela de Biologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Albana Dassori
- Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA; South Texas Veterans Health Care System, San Antonio, TX, USA
| | - Robin J Leach
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Deborah Flores
- Los Angeles Biomedical Research Center at Harbor, University of California Los Angeles Medical Center, Torrance, CA, USA
| | - Alvaro Jerez
- Centro Internacional de Trastornos Afectivos y de la Conducta Adictiva, Guatemala, Guatemala
| | - Henriette Raventós
- Centro de Investigación en Biología Celular y Molecular y Escuela de Biologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Alfonso Ontiveros
- Instituto de Información e Investigación en Salud Mental AC, Monterrey, Nuevo Leon, Mexico
| | - Humberto Nicolini
- Grupo de Estudios Médicos y Familiares Carracci, S.C., México, D.F., Mexico
| | - Michael Escamilla
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
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Gioli-Pereira L, Bernardez-Pereira S, Goulart Marcondes-Braga F, Rocha Spina JM, Muniz Miranda da Silva R, Evangelista Ferreira N, Bacal F, Fernandes F, Mansur AJ, Krieger JE, Costa Pereira A. Genetic and ElectroNic medIcal records to predict oUtcomeS in Heart Failure patients (GENIUS-HF) - design and rationale. BMC Cardiovasc Disord 2014; 14:32. [PMID: 24592820 PMCID: PMC3975857 DOI: 10.1186/1471-2261-14-32] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 02/25/2014] [Indexed: 12/21/2022] Open
Abstract
Background Studies adopting electronic medical records and genomic information are becoming widespread. Through this new modality in research, it is possible to study how genetic variants influence susceptibility towards chronic conditions and can improve patient care. Our aim is to develop a biobank with 2,000 heart failure patients treated in a tertiary cardiology hospital containing electronic medical records data and biologic samples for performing genome-wide association studies for validation and development of medical decision routines aimed at helping the clinical management of patients. Methods/Design Patients between 18 and 80 years old with heart failure diagnosis of different etiologies and left ventricular ejection fraction ≤ 50% in the past 2 years will be eligible for enrollment on the cohort. After consent, patients will be submitted to clinical baseline, echocardiography, cardiograph impedance and biochemical evaluation. Study data will be collected and managed using Research Electronic Data Capture tools. The follow up will take place every 6 months to assess cardiovascular outcomes (all-cause mortality, cardiovascular mortality, hospitalization for worsening heart failure and current medication use). Initial analytical strategy will focus on the establishment of the accuracy of electronic medical records extraction protocols for main predictor factors of morbidity and mortality in heart failure. Discussion Building a biobank with biologic samples and clinical data of 2,000 heart failure patients we will perform genome-wide association studies. By this way, we pretend to study how genetic variants influence susceptibility towards chronic conditions. Besides, it will be created a working group focused on the development and implementation of algorithms for validation and application of medical routines using the electronic medical records of the Heart Institute (InCor - HCFMUSP). Trial registration Current Controlled Trials NTC02043431.
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Affiliation(s)
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- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor) of University of São Paulo Medical School, Avenue Dr, Enéas de Carvalho Aguiar, 44 Cerqueira César, São Paulo, SP 05403-000, Brazil.
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