1
|
Fernandez-Rhodes L, Young KL, Lilly AG, Raffield LM, Highland HM, Wojcik GL, Agler C, M Love SA, Okello S, Petty LE, Graff M, Below JE, Divaris K, North KE. Importance of Genetic Studies of Cardiometabolic Disease in Diverse Populations. Circ Res 2020; 126:1816-1840. [PMID: 32496918 PMCID: PMC7285892 DOI: 10.1161/circresaha.120.315893] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies have revolutionized our understanding of the genetic underpinnings of cardiometabolic disease. Yet, the inadequate representation of individuals of diverse ancestral backgrounds in these studies may undercut their ultimate potential for both public health and precision medicine. The goal of this review is to describe the imperativeness of studying the populations who are most affected by cardiometabolic disease, to the aim of better understanding the genetic underpinnings of the disease. We support this premise by describing the current variation in the global burden of cardiometabolic disease and emphasize the importance of building a globally and ancestrally representative genetics evidence base for the identification of population-specific variants, fine-mapping, and polygenic risk score estimation. We discuss the important ethical, legal, and social implications of increasing ancestral diversity in genetic studies of cardiometabolic disease and the challenges that arise from the (1) lack of diversity in current reference populations and available analytic samples and the (2) unequal generation of health-associated genomic data and their prediction accuracies. Despite these challenges, we conclude that additional, unprecedented opportunities lie ahead for public health genomics and the realization of precision medicine, provided that the gap in diversity can be systematically addressed. Achieving this goal will require concerted efforts by social, academic, professional and regulatory stakeholders and communities, and these efforts must be based on principles of equity and social justice.
Collapse
Affiliation(s)
- Lindsay Fernandez-Rhodes
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Adam G Lilly
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Cary Agler
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Shelly-Ann M Love
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Samson Okello
- Department of Internal Medicine, Mbarara University of Science and Technology, Uganda
- University of Virginia, Charlottesville, VA
- Harvard TH Chan School of Public Health, Boston, MA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Vanderbilt, TN
- Department of Genetic Medicine, Vanderbilt University, Vanderbilt, TN
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Vanderbilt, TN
- Department of Genetic Medicine, Vanderbilt University, Vanderbilt, TN
| | - Kimon Divaris
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Center for Genome Sciences, Chapel Hill, NC
| |
Collapse
|
2
|
Ballantine JL, Carlson JC, Ferreira Zandoná AG, Agler C, Zeldin LP, Rozier RG, Roberts MW, Basta PV, Luo J, Antonio‐Obese ME, McNeil DW, Weyant RJ, Crout RJ, Slayton RL, Levy SM, Shaffer JR, Marazita ML, North KE, Divaris K. Exploring the genomic basis of early childhood caries: a pilot study. Int J Paediatr Dent 2018; 28:217-225. [PMID: 29057527 PMCID: PMC5811369 DOI: 10.1111/ipd.12344] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
OBJECTIVE A genetic component in early childhood caries (ECC) is theorized, but no genome-wide investigations of ECC have been conducted. This pilot study is part of a long-term research program aimed to: (1) determine the proportion of ECC variance attributable to the human genome and (2) identify ECC-associated genetic loci. METHODS The study's community-based sample comprised 212 children (mean age=39 months; range = 30-52 months; males = 55%; Hispanic/Latino = 35%, African-American = 32%; American Academy of Pediatric Dentistry definition of ECC prevalence = 38%). Approximately 2.4 million single nucleotide polymorphisms (SNPs) were genotyped using DNA purified from saliva. A P < 5 × 10-8 criterion was used for genome-wide significance. SNPs with P < 5 × 10-5 were followed-up in three independent cohorts of 921 preschool-age children with similar ECC prevalence. RESULTS SNPs with minor allele frequency ≥5% explained 52% (standard error = 54%) of ECC variance (one-sided P = 0.03). Unsurprisingly, given the pilot's small sample size, no genome-wide significant associations were found. An intergenic locus on 4q32 (rs4690994) displayed the strongest association with ECC [P = 2.3 × 10-6 ; odds ratio (OR) = 3.5; 95% confidence interval (CI) = 2.1-5.9]. Thirteen loci with suggestive associations were followed-up - none showed evidence of association in the replication samples. CONCLUSION This study's findings support a heritable component of ECC and demonstrate the feasibility of conducting genomics studies among preschool-age children.
Collapse
Affiliation(s)
- Jami L. Ballantine
- Department of Pediatric DentistrySchool of DentistryUniversity of North Carolina‐Chapel HillChapel HillNCUSA
| | - Jenna C. Carlson
- Center for Craniofacial and Dental GeneticsSchool of Dental MedicineUniversity of PittsburghPittsburghPAUSA,Department of BiostatisticsGraduate School of Public HealthUniversity of PittsburghPittsburghPAUSA,Department of Human GeneticsGraduate School of Public HealthUniversity of PittsburghPittsburghPA USA
| | - Andrea G. Ferreira Zandoná
- Department of Operative DentistrySchool of DentistryUniversity of North Carolina‐Chapel HillChapel HillNCUSA
| | - Cary Agler
- Oral and Craniofacial Health SciencesSchool of DentistryUniversity of North Carolina‐Chapel HillChapel HillNCUSA
| | - Leslie P. Zeldin
- Oral and Craniofacial Health SciencesSchool of DentistryUniversity of North Carolina‐Chapel HillChapel HillNCUSA
| | - Richard Gary Rozier
- Department of Health Policy and ManagementGillings School of Global Public HealthUniversity of North Carolina‐Chapel HillChapel HillNCUSA
| | - Michael W. Roberts
- Department of Pediatric DentistrySchool of DentistryUniversity of North Carolina‐Chapel HillChapel HillNCUSA
| | - Patricia V. Basta
- Department of EpidemiologyGillings School of Global Public HealthUniversity of North Carolina‐Chapel HillChapel HillNCUSA,Biospecimen Processing Facility coreUniversity of North CarolinaChapel HillNCUSA
| | - Jason Luo
- Lineberger Comprehensive Cancer CenterSchool of MedicineUniversity of North CarolinaChapel HillNCUSA,Mammalian Genotyping coreUniversity of North CarolinaChapel HillNCUSA
| | - Mikafui E. Antonio‐Obese
- Oral and Craniofacial Health SciencesSchool of DentistryUniversity of North Carolina‐Chapel HillChapel HillNCUSA
| | - Daniel W. McNeil
- Departments of Dental Practice & Rural Health and PsychologyWest Virginia UniversityMorgantownWVUSA
| | - Robert J. Weyant
- Department of Dental Public Health and Information ManagementSchool of Dental MedicineUniversity of PittsburghPittsburghPAUSA
| | - Richard J. Crout
- Department of PeriodonticsSchool of DentistryWest Virginia UniversityMorgantownWVUSA
| | - Rebecca L. Slayton
- Department of Pediatric DentistrySchool of DentistryUniversity of WashingtonSeattleWAUSA
| | - Steven M. Levy
- Department of Preventive and Community DentistryUniversity of Iowa College of DentistryIowa CityIAUSA,Department of EpidemiologyUniversity of Iowa College of Public HealthIowa CityIAUSA
| | - John R. Shaffer
- Center for Craniofacial and Dental GeneticsSchool of Dental MedicineUniversity of PittsburghPittsburghPAUSA,Department of Human GeneticsGraduate School of Public HealthUniversity of PittsburghPittsburghPA USA,Department of Oral BiologySchool of Dental MedicineUniversity of PittsburghPittsburghPAUSA
| | - Mary L. Marazita
- Center for Craniofacial and Dental GeneticsSchool of Dental MedicineUniversity of PittsburghPittsburghPAUSA,Department of Human GeneticsGraduate School of Public HealthUniversity of PittsburghPittsburghPA USA,Department of Oral BiologySchool of Dental MedicineUniversity of PittsburghPittsburghPAUSA,Department of PsychiatrySchool of MedicineUniversity of PittsburghPittsburghPAUSA,Clinical and Translational Science InstituteSchool of MedicineUniversity of PittsburghPittsburghPAUSA
| | - Kari E. North
- Department of EpidemiologyGillings School of Global Public HealthUniversity of North Carolina‐Chapel HillChapel HillNCUSA
| | - Kimon Divaris
- Department of Pediatric DentistrySchool of DentistryUniversity of North Carolina‐Chapel HillChapel HillNCUSA,Department of EpidemiologyGillings School of Global Public HealthUniversity of North Carolina‐Chapel HillChapel HillNCUSA
| |
Collapse
|
3
|
Urkasemsin G, Nielsen DM, Singleton A, Arepalli S, Hernandez D, Agler C, Olby NJ. Genetics of Hereditary Ataxia in Scottish Terriers. J Vet Intern Med 2017; 31:1132-1139. [PMID: 28556454 PMCID: PMC5508367 DOI: 10.1111/jvim.14738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/05/2017] [Accepted: 04/19/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Scottish Terriers have a high incidence of juvenile onset hereditary ataxia primarily affecting the Purkinje neuron of the cerebellar cortex and causing slowly progressive cerebellar dysfunction. OBJECTIVE To identify chromosomal regions associated with hereditary ataxia in Scottish Terriers. ANIMALS One hundred and fifty-three Scottish Terriers were recruited through the Scottish Terrier Club of America. MATERIALS AND METHODS Prospective study. Dogs were classified as affected if they had slowly progressive cerebellar signs. When possible, magnetic resonance imaging and histopathological evaluation of the brain were completed as diagnostic aids. To identify genomic regions connected with the disease, genome-wide mapping was performed using both linkage- and association-based approaches. Pedigree evaluation and homozygosity mapping were also performed to examine mode of inheritance and to investigate the region of interest, respectively. RESULTS Linkage and genome-wide association studies in a cohort of Scottish Terriers both identified a region on CFA X strongly associated with the disease trait. Homozygosity mapping revealed a 4 Mb region of interest. Pedigree evaluation failed to identify the possible mode of inheritance due to the lack of complete litter information. CONCLUSION AND CLINICAL IMPORTANCE This finding suggests that further genetic investigation of the potential region of interest on CFA X should be considered in order to identify the causal mutation as well as develop a genetic test to eliminate the disease from this breed.
Collapse
Affiliation(s)
- G Urkasemsin
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC
| | - D M Nielsen
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC
| | - A Singleton
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD
| | - S Arepalli
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD
| | - D Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD
| | - C Agler
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC
| | - N J Olby
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC
| |
Collapse
|
4
|
Sanders AE, Sofer T, Wong Q, Kerr KF, Agler C, Shaffer JR, Beck JD, Offenbacher S, Salazar CR, North KE, Marazita ML, Laurie CC, Singer RH, Cai J, Finlayson TL, Divaris K. Chronic Periodontitis Genome-wide Association Study in the Hispanic Community Health Study / Study of Latinos. J Dent Res 2016; 96:64-72. [PMID: 27601451 DOI: 10.1177/0022034516664509] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Chronic periodontitis (CP) has a genetic component, particularly its severe forms. Evidence from genome-wide association studies (GWASs) has highlighted several potential novel loci. Here, the authors report the first GWAS of CP among a large community-based sample of Hispanics/Latinos. The authors interrogated a quantitative trait of CP (mean interproximal clinical attachment level determined by full-mouth periodontal examinations) among 10,935 adult participants (mean age: 45 y, range: 18 to 76 y) from the Hispanic Community Health Study / Study of Latinos. Genotyping was done with a custom Illumina Omni2.5M array, and imputation to approximately 20 million single-nucleotide polymorphisms was based on the 1000 Genomes Project phase 1 reference panel. Analyses were based on linear mixed models adjusting for sex, age, study design features, ancestry, and kinship and employed a conventional P < 5 × 10-8 statistical significance threshold. The authors identified a genome-wide significant association signal in the 1q42.2 locus ( TSNAX-DISC1 noncoding RNA, lead single-nucleotide polymorphism: rs149133391, minor allele [C] frequency = 0.01, P = 7.9 × 10-9) and 4 more loci with suggestive evidence of association ( P < 5 × 10-6): 1q22 (rs13373934), 5p15.33 (rs186066047), 6p22.3 (rs10456847), and 11p15.1 (rs75715012). We tested these loci for replication in independent samples of European-American ( n = 4,402) and African-American ( n = 908) participants of the Atherosclerosis Risk in Communities study. There was no replication among the European Americans; however, the TSNAX-DISC1 locus replicated in the African-American sample (rs149133391, minor allele frequency = 0.02, P = 9.1 × 10-3), while the 1q22 locus was directionally concordant and nominally significant (rs13373934, P = 4.0 × 10-2). This discovery GWAS of interproximal clinical attachment level-a measure of lifetime periodontal tissue destruction-was conducted in a large, community-based sample of Hispanic/Latinos. It identified a genome-wide significant locus that was independently replicated in an African-American population. Identifying this genetic marker offers direction for interrogation in subsequent genomic and experimental studies of CP.
Collapse
Affiliation(s)
- A E Sanders
- 1 Department of Dental Ecology, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - T Sofer
- 2 Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Q Wong
- 2 Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - K F Kerr
- 2 Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - C Agler
- 3 Oral and Craniofacial Health Sciences, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J R Shaffer
- 4 Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - J D Beck
- 1 Department of Dental Ecology, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - S Offenbacher
- 5 Department of Periodontology and Center for Oral and Systemic Diseases, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - C R Salazar
- 6 Department of Epidemiology and Department of Population Health, Albert Einstein College of Medicine and Montefiore Medical Center, New York City, NY, USA
| | - K E North
- 7 Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M L Marazita
- 4 Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.,8 Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,9 Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,10 Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,11 Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - C C Laurie
- 2 Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - R H Singer
- 12 Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - J Cai
- 13 Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - T L Finlayson
- 14 Graduate School of Public Health, San Diego State University, San Diego, CA, USA
| | - K Divaris
- 7 Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,15 Department of Pediatric Dentistry, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
5
|
Zhang S, Divaris K, Moss K, Yu N, Barros S, Marchesan J, Morelli T, Agler C, Kim SJ, Wu D, North KE, Beck J, Offenbacher S. The Novel ASIC2 Locus is Associated with Severe Gingival Inflammation. JDR Clin Trans Res 2016; 1:163-170. [PMID: 28459102 DOI: 10.1177/2380084416645290] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
An increasing body of evidence suggests a significant genetic regulation of inflammatory response mechanisms; however, little is known regarding the genetic determinants of severe gingival inflammation (GI). We conducted a genome-wide association study of severe GI among 4077 European American adults, participants in the Dental Atherosclerosis Risk In Communities cohort. The severe GI trait was defined dichotomously using the 90th percentile of gingival index ≥2 extent score. Genotyping was performed with the Affymetrix 6.0 array platform and an imputed set of 2.5 million markers, based on HapMap Phase II CEU build 36, was interrogated. Genetic models were based on logistic regression and controlled for ancestry (10 principal components), sex, age, and examination center. One locus on chromosome 17 met genome-wide statistical significance criteria-lead single nucleotide polymorphism (SNP): rs11652874 [minor allele frequency=0.06, intronic to ASIC2 (acid sensing ionic channel-2, formerly named ACCN1); odds ratio=2.1, 95% confidence interval=1.6-2.7, p=3.9×10-8]. This association persisted among subjects with severe periodontitis and was robust to adjustment for microbial plaque index. Moreover, the minor [G] allele was associated with higher levels of severe GI in stratified analyses among subsets of participants with high load of either "red" or "orange" complex pathogens, although this association was not statistically significant. While these results will require replication in independent samples and confirmation by mechanistic studies, this locus appears as a promising candidate for severe gingival inflammation. Our findings suggest that genetic variation in ASIC2 is significantly associated with severe gingival inflammation and the association is plaque-independent.
Collapse
Affiliation(s)
- Shaoping Zhang
- Department of Periodontology, School of Dentistry, University of North Carolina at Chapel Hill.,Center for Oral and Systemic Disease, School of Dentistry, University of North Carolina at Chapel Hill
| | - Kimon Divaris
- Department of Pediatric Dentistry, School of Dentistry, University of North Carolina at Chapel Hill.,Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill
| | - Kevin Moss
- Center for Oral and Systemic Disease, School of Dentistry, University of North Carolina at Chapel Hill
| | - Ning Yu
- Center for Oral and Systemic Disease, School of Dentistry, University of North Carolina at Chapel Hill
| | - Silvana Barros
- Department of Periodontology, School of Dentistry, University of North Carolina at Chapel Hill.,Center for Oral and Systemic Disease, School of Dentistry, University of North Carolina at Chapel Hill
| | - Julie Marchesan
- Department of Periodontology, School of Dentistry, University of North Carolina at Chapel Hill.,Center for Oral and Systemic Disease, School of Dentistry, University of North Carolina at Chapel Hill
| | - Thiago Morelli
- Department of Periodontology, School of Dentistry, University of North Carolina at Chapel Hill
| | - Cary Agler
- Center for Oral & Craniofacial Health Sciences, School of Dentistry, University of North Carolina at Chapel Hill
| | - Steven J Kim
- Center for Oral and Systemic Disease, School of Dentistry, University of North Carolina at Chapel Hill
| | - Di Wu
- Department of Periodontology, School of Dentistry, University of North Carolina at Chapel Hill
| | - Kari E North
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill Gillings School of Global Public Health
| | - James Beck
- Center for Oral and Systemic Disease, School of Dentistry, University of North Carolina at Chapel Hill.,Department of Dental Ecology, School of Dentistry, University of North Carolina at Chapel Hill
| | - Steven Offenbacher
- Department of Periodontology, School of Dentistry, University of North Carolina at Chapel Hill.,Center for Oral and Systemic Disease, School of Dentistry, University of North Carolina at Chapel Hill
| |
Collapse
|