[Show abstract][Hide abstract] ABSTRACT: Large-scale sequencing information may provide a basis for genetic tests for predisposition to common disorders. In this study, participants in the Coriell Personalized Medicine Collaborative (N = 53) with a personal and/or family history of Major Depressive Disorder or Bipolar Disorder were interviewed based on the Health Belief Model around hypothetical intention to test one's children for probability of developing a mood disorder. Most participants (87 %) were interested in a hypothetical test for children that had high ("90 %") positive predictive value, while 51 % of participants remained interested in a modestly predictive test ("20 %"). Interest was driven by beliefs about effects of test results on parenting behaviors and on discrimination. Most participants favored testing before adolescence (64 %), and were reluctant to share results with asymptomatic children before adulthood. Participants anticipated both positive and negative effects of testing on parental treatment and on children's self-esteem. Further investigation will determine whether these findings will generalize to other complex disorders for which early intervention is possible but not clearly demonstrated to improve outcomes. More information is also needed about the effects of childhood genetic testing and sharing of results on parent-child relationships, and about the role of the child in the decision-making process.
Journal of Genetic Counseling 03/2014; · 1.45 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Use of genomic information in healthcare is increasing; however data on the needs of consumers of genomic information is limited. The Coriell Personalized Medicine Collaborative (CPMC) is a longitudinal study investigating the utility of personalized medicine. Participants receive results reflecting risk of common complex conditions and drug-gene pairs deemed actionable by an external review board. To explore the needs of individuals receiving genomic information we reviewed all genetic counseling sessions with CPMC participants. A retrospective qualitative review of notes from 157 genetic counseling inquiries was conducted. Notes were coded for salient themes. Five primary themes; "understanding risk", "basic genetics", "complex disease genetics", "what do I do now?" and "other" were identified. Further review revealed that participants had difficulty with basic genetic concepts, confused relative and absolute risks, and attributed too high a risk burden to individual single nucleotide polymorphisms (SNPs). Despite these hurdles, counseled participants recognized that behavior changes could potentially mitigate risk and there were few comments alluding to an overly deterministic or fatalistic interpretation of results. Participants appeared to recognize the multifactorial nature of the diseases for which results were provided; however education to understand the complexities of genomic risk information was often needed.
Journal of Genetic Counseling 02/2014; · 1.45 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We describe the development and implementation of a randomized controlled trial to investigate the impact of genomic counseling on a cohort of patients with heart failure (HF) or hypertension (HTN), managed at a large academic medical center, the Ohio State University Wexner Medical Center (OSUWMC). Our study is built upon the existing Coriell Personalized Medicine Collaborative (CPMC®). OSUWMC patient participants with chronic disease (CD) receive eight actionable complex disease and one pharmacogenomic test report through the CPMC® web portal. Participants are randomized to either the in-person post-test genomic counseling—active arm, versus web-based only return of results—control arm. Study-specific surveys measure: (1) change in risk perception; (2) knowledge retention; (3) perceived personal control; (4) health behavior change; and, for the active arm (5), overall satisfaction with genomic counseling. This ongoing partnership has spurred creation of both infrastructure and procedures necessary for the implementation of genomics and genomic counseling in clinical care and clinical research. This included creation of a comprehensive informed consent document and processes for prospective return of actionable results for multiple complex diseases and pharmacogenomics (PGx) through a web portal, and integration of genomic data files and clinical decision support into an EPIC-based electronic medical record. We present this partnership, the infrastructure, genomic counseling approach, and the challenges that arose in the design and conduct of this ongoing trial to inform subsequent collaborative efforts and best genomic counseling practices.
Journal of Personalized Medicine. 01/2014; 4(1):1-19.
[Show abstract][Hide abstract] ABSTRACT: Obesity rates in the United States have escalated in recent decades and present a major challenge in public health prevention efforts. Currently, testing to identify genetic risk for obesity is readily available through several direct-to-consumer companies. Despite the availability of this type of testing, there is a paucity of evidence as to whether providing people with personal genetic information on obesity risk will facilitate or impede desired behavioral responses.
We describe the key issues in the design and implementation of a randomized controlled trial examining the clinical utility of providing genetic risk information for obesity.
Participants are being recruited from the Coriell Personalized Medicine Collaborative, an ongoing, longitudinal research cohort study designed to determine the utility of personal genome information in health management and clinical decision making. The primary focus of the ancillary Obesity Risk Communication Study is to determine whether genetic risk information added value to traditional communication efforts for obesity, which are based on lifestyle risk factors. The trial employs a 2 × 2 factorial design in order to examine the effects of providing genetic risk information for obesity, alone or in combination with lifestyle risk information, on participants' psychological responses, behavioral intentions, health behaviors, and weight.
The factorial design generated four experimental arms based on communication of estimated risk to participants: (1) no risk feedback (control), (2) genetic risk only, (3) lifestyle risk only, and (4) both genetic and lifestyle risk (combined). Key issues in study design pertained to the selection of algorithms to estimate lifestyle risk and determination of information to be provided to participants assigned to each experimental arm to achieve a balance between clinical standards and methodological rigor. Following the launch of the trial in September 2011, implementation challenges pertaining to low enrollment and differential attrition became apparent and required immediate attention and modifications to the study protocol. Although monitoring of these efforts is ongoing, initial observations show a doubling of enrollment and reduced attrition.
The trial is evaluating the short-term impact of providing obesity risk information as participants are followed for only 3 months. This study is built upon the structure of an existing personalized medicine study wherein participants have been provided with genetic information for other diseases. This nesting in a larger study may attenuate the effects of obesity risk information and has implications for the generalizability of study findings.
This randomized trial examines value of obesity genetic information, both when provided independently and when combined with lifestyle risk assessment, to motivate individuals to engage in healthy lifestyle behaviors. Study findings will guide future intervention efforts to effectively communicate genetic risk information.
[Show abstract][Hide abstract] ABSTRACT: Implementation of pharmacogenomics (PGx) in clinical care can lead to improved drug efficacy and reduced adverse drug reactions. However, there has been a lag in adoption of PGx tests in clinical practice. This is due in part to a paucity of rigorous systems for translating published clinical and scientific data into standardized diagnostic tests with clear therapeutic recommendations. Here we describe the Pharmacogenomics Appraisal, Evidence Scoring and Interpretation System (PhAESIS), developed as part of the Coriell Personalized Medicine Collaborative research study, and its application to seven commonly prescribed drugs.
Genome Medicine 10/2013; 5(10):93. · 4.94 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Human Genetic Cell Repository sponsored by the National Institute of General Medical Sciences contains more than 11,000 cell lines and DNA samples collected from numerous individuals. All of these cell lines and DNA samples are categorized into several collections representing a variety of disease states, chromosomal abnormalities, heritable diseases, distinct human populations and apparently healthy individuals. Many of these cell lines have previously been studied with detailed conventional cytogenetic analyses including G-banded karyotyping and fluorescence in situ hybridization. This work was carried out by investigators at submitting institutions and scientists at Coriell Institute for Medical Research, where the NIGMS Repository is hosted. Recently, approximately 900 cell lines, mostly chosen from the Chromosomal Aberrations and Heritable Diseases collections, have been further characterized in detail at the Coriell Institute using the Affymetrix Genome-Wide Human SNP Array 6.0 to detect copy number variations and copy number neutral loss of heterozygosity. A database containing detailed cytogenetic and genomic information for these cell lines has been constructed and is freely available through several sources, such as the NIGMS Repository website and the UCSC Genome Browser. As additional cell lines are analyzed and subsequently added into it, the database will be maintained dynamically.
[Show abstract][Hide abstract] ABSTRACT: BACKGROUND: A recent, large genome-wide association study (GWAS) of European ancestry individuals has identified multiple genetic variants influencing serum lipids. Studies of the transferability of these associations to African Americans remain few, an important limitation given interethnic differences in serum lipids and the disproportionate burden of lipid-associated metabolic diseases among African Americans. METHODS: We attempted to evaluate the transferability of 95 lipid-associated loci recently identified in European ancestry individuals to 887 non-diabetic, unrelated African Americans from a population-based sample in the Washington, DC area. Additionally, we took advantage of the generally reduced linkage disequilibrium among African ancestry populations in comparison to European ancestry populations to fine-map replicated GWAS signals. RESULTS: We successfully replicated reported associations for 10 loci (CILP2/SF4, STARD3, LPL, CYP7A1, DOCK7/ANGPTL3, APOE, SORT1, IRS1, CETP, and UBASH3B). Through trans-ethnic fine-mapping, we were able to reduce associated regions around 75 % of the loci that replicated. CONCLUSIONS: Between this study and previous work in African Americans, 40 of the 95 loci reported in a large GWAS of European ancestry individuals also influence lipid levels in African Americans. While there is now evidence that the lipid-influencing role of a number of genetic variants is observed in both European and African ancestry populations, the still considerable lack of concordance highlights the importance of continued ancestry-specific studies to elucidate the genetic underpinnings of these traits.
BMC Medical Genetics 09/2012; 13(1):88. · 2.54 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Insulin resistance (IR) is a key determinant of type 2 diabetes (T2D) and other metabolic disorders. This genome-wide association study (GWAS) was designed to shed light on the genetic basis of fasting insulin (FI) and IR in 927 non-diabetic African Americans. 5 396 838 single-nucleotide polymorphisms (SNPs) were tested for associations with FI or IR with adjustments for age, sex, body mass index, hypertension status and first two principal components. Genotyped SNPs (n = 12) with P < 5 × 10(-6) in African Americans were carried forward for de novo genotyping in 570 non-diabetic West Africans. We replicated SNPs in or near SC4MOL and TCERG1L in West Africans. The meta-analysis of 1497 African Americans and West Africans yielded genome-wide significant associations for SNPs in the SC4MOL gene: rs17046216 (P = 1.7 × 10(-8) and 2.9 × 10(-8) for FI and IR, respectively); and near the TCERG1L gene with rs7077836 as the top scoring (P = 7.5 × 10(-9) and 4.9 × 10(-10) for FI and IR, respectively). In silico replication in the MAGIC study (n = 37 037) showed weak but significant association (adjusted P-value of 0.0097) for rs34602777 in the MYO5A gene. In addition, we replicated previous GWAS findings for IR and FI in Europeans for GCKR, and for variants in four T2D loci (FTO, IRS1, KLF14 and PPARG) which exert their action via IR. In summary, variants in/near SC4MOL, and TCERG1L were associated with FI and IR in this cohort of African Americans and were replicated in West Africans. SC4MOL is under-expressed in an animal model of T2D and plays a key role in lipid biosynthesis, with implications for the regulation of energy metabolism, obesity and dyslipidemia. TCERG1L is associated with plasma adiponectin, a key modulator of obesity, inflammation, IR and diabetes.
Human Molecular Genetics 07/2012; 21(20):4530-6. · 7.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: C-reactive protein (CRP) is an acute phase reactant protein produced primarily by the liver. Circulating CRP levels are influenced by genetic and non-genetic factors, including infection and obesity. Genome-wide association studies (GWAS) provide an unbiased approach towards identifying loci influencing CRP levels. None of the six GWAS for CRP levels has been conducted in an African ancestry population. The present study aims to: (i) identify genetic variants that influence serum CRP in African Americans (AA) using a genome-wide association approach and replicate these findings in West Africans (WA), (ii) assess transferability of major signals for CRP reported in European ancestry populations (EA) to AA and (iii) use the weak linkage disequilibrium (LD) structure characteristic of African ancestry populations to fine-map the previously reported CRP locus. The discovery cohort comprised 837 unrelated AA, with the replication of significant single-nucleotide polymorphisms (SNPs) assessed in 486 WA. The association analysis was conducted with 2 366 856 genotyped and imputed SNPs under an additive genetic model with adjustment for appropriate covariates. Genome-wide and replication significances were set at P < 5 × 10(-8) and P < 0.05, respectively. Ten SNPs in (CRP pseudogene-1) CRPP1 and CRP genes were associated with serum CRP (P = 2.4 × 10(-09) to 4.3 × 10(-11)). All but one of the top-scoring SNPs associated with CRP in AA were successfully replicated in WA. CRP signals previously identified in EA samples were transferable to AAs, and we were able to fine-map this signal, reducing the region of interest from the 25 kb of LD around the locus in the HapMap CEU sample to only 8 kb in our AA sample.
Human Molecular Genetics 04/2012; 21(13):3063-72. · 7.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Biobanks and archived data sets collecting samples and data have become crucial engines of genetic and genomic research. Unresolved, however, is what responsibilities biobanks should shoulder to manage incidental findings and individual research results of potential health, reproductive, or personal importance to individual contributors (using "biobank" here to refer both to collections of samples and collections of data). This article reports recommendations from a 2-year project funded by the National Institutes of Health. We analyze the responsibilities involved in managing the return of incidental findings and individual research results in a biobank research system (primary research or collection sites, the biobank itself, and secondary research sites). We suggest that biobanks shoulder significant responsibility for seeing that the biobank research system addresses the return question explicitly. When reidentification of individual contributors is possible, the biobank should work to enable the biobank research system to discharge four core responsibilities to (1) clarify the criteria for evaluating findings and the roster of returnable findings, (2) analyze a particular finding in relation to this, (3) reidentify the individual contributor, and (4) recontact the contributor to offer the finding. We suggest that findings that are analytically valid, reveal an established and substantial risk of a serious health condition, and are clinically actionable should generally be offered to consenting contributors. This article specifies 10 concrete recommendations, addressing new biobanks as well as those already in existence.
Genetics in medicine: official journal of the American College of Medical Genetics 03/2012; 14(4):361-84. · 3.92 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Genetic variant associations and advances in research technologies are generating an unprecedented volume of genomic data. Whole-genome sequencing will introduce even greater depth to current data sets and will propel medical research and development. Yet as one area of biomedical research evolves, another stagnates: informed consent. As presently employed, informed consent is not entirely attuned to the era of whole-genome sequencing. The greatest value of genomic data lays in its accessibility over time; the current model of informed consent restricts the use of data and does not readily accommodate prospective basic and clinical research, a priori research, or opportunities to act upon incidental findings. It also disengages the research participant from the discovery process, discouraging the provision of research results that may have clinical value to that individual. A revisited informed consent approach-the Informed Cohort Oversight Board (ICOB)-has been proven successful at consenting individuals to a model which facilitates the simultaneous construction of longitudinal data with the return of results to participants as scientific knowledge and technology allows. The opportunity to sequence once and consult often is cost-effective, encourages scientific innovation, and provides the opportunity to quickly translate genomics into better clinical care.
Genetics in medicine: official journal of the American College of Medical Genetics 03/2012; 14(4):432-6. · 3.92 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The incidence of chronic kidney disease varies by ethnic group in the USA, with African Americans displaying a two-fold higher rate than European Americans. One of the two defining variables underlying staging of chronic kidney disease is the glomerular filtration rate. Meta-analysis in individuals of European ancestry has identified 23 genetic loci associated with the estimated glomerular filtration rate (eGFR). We conducted a follow-up study of these 23 genetic loci using a population-based sample of 1,018 unrelated admixed African Americans. We included in our follow-up study two variants in APOL1 associated with end-stage kidney disease discovered by admixture mapping in admixed African Americans. To address confounding due to admixture, we estimated local ancestry at each marker and global ancestry. We performed regression analysis stratified by local ancestry and combined the resulting regression estimates across ancestry strata using an inverse variance-weighted fixed effects model. We found that 11 of the 24 loci were significantly associated with eGFR in our sample. The effect size estimates were not significantly different between the subgroups of individuals with two copies of African ancestry vs. two copies of European ancestry for any of the 11 loci. In contrast, allele frequencies were significantly different at 10 of the 11 loci. Collectively, the 11 loci, including four secondary signals revealed by conditional analyses, explained 14.2% of the phenotypic variance in eGFR, in contrast to the 1.4% explained by the 24 loci in individuals of European ancestry. Our findings provide insight into the genetic basis of variation in renal function among admixed African Americans.
PLoS ONE 01/2012; 7(9):e45112. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Interleukins (ILs) are key mediators of the immune response and inflammatory process. Plasma levels of IL-10, IL-1Ra, and IL-6 are associated with metabolic conditions, show large inter-individual variations, and are under strong genetic control. Therefore, elucidation of the genetic variants that influence levels of these ILs provides useful insights into mechanisms of immune response and pathogenesis of diseases. We conducted a genome-wide association study (GWAS) of IL-10, IL-1Ra, and IL-6 levels in 707 non-diabetic African Americans using 5,396,780 imputed and directly genotyped single nucleotide polymorphisms (SNPs) with adjustment for gender, age, and body mass index. IL-10 levels showed genome-wide significant associations (p < 5 × 10(-8)) with eight SNPs, the most significant of which was rs5743185 in the PMS1 gene (p = 2.30 × 10(-10)). We tested replication of SNPs that showed genome-wide significance in 425 non-diabetic individuals from West Africa, and successfully replicated rs17365948 in the YWHAZ gene (p = 0.02). IL-1Ra levels showed suggestive associations with two SNPs in the ASB3 gene (p = 2.55 × 10(-7)), ten SNPs in the IL-1 gene family (IL1F5, IL1F8, IL1F10, and IL1Ra, p = 1.04 × 10(-6) to 1.75 × 10(-6)), and 23 SNPs near the IL1A gene (p = 1.22 × 10(-6) to 1.63 × 10(-6)). We also successfully replicated rs4251961 (p = 0.009); this SNP was reported to be associated with IL-1Ra levels in a candidate gene study of Europeans. IL-6 levels showed genome-wide significant association with one SNP (RP11-314E23.1; chr6:133397598; p = 8.63 × 10(-9)). To our knowledge, this is the first GWAS on IL-10, IL-1Ra, and IL-6 levels. Follow-up of these findings may provide valuable insight into the pathobiology of IL actions and dysregulations in inflammation and human diseases.
[Show abstract][Hide abstract] ABSTRACT: Total serum bilirubin is associated with several clinical outcomes, including cardiovascular disease, diabetes and drug metabolism. We conducted a genome-wide association study in 619 healthy unrelated African Americans in an attempt to replicate reported findings in Europeans and Asians and to identify novel loci influencing total serum bilirubin levels. We analyzed a dense panel of over two million genotyped and imputed SNPs in additive genetic models adjusting for age, sex, and the first two significant principal components from the sample covariance matrix of genotypes. Thirty-nine SNPs spanning a 78 kb region within the UGT1A1 displayed P-values <5 × 10(-8). The lowest P-value was 1.7 × 10(-22) for SNP rs887829. None of SNPs in the UGT1A1 remained statistically significant in conditional association analyses that adjusted for rs887829. In addition, SNP rs10929302 located in phenobarbital response enhancer module was significantly associated with bilirubin level with a P-value of 1.37 × 10(-11); this enhancer module is believed to have a critical role in phenobarbital treatment of hyperbilirubinemia. Interestingly, the lead SNP, rs887829, is in strong linkage disequilibrium (LD) (r(2)≥0.74) with rs10929302. Taking advantage of the lower LD and shorter haplotypes in African-ancestry populations, we identified rs887829 as a more refined proxy for the causative variant influencing bilirubin levels. Also, we replicated the reported association between variants in SEMA3C and bilirubin levels. In summary, UGT1A1 is a major locus influencing bilirubin levels and the results of this study promise to contribute to understanding of the etiology and treatment of hyperbilirubinaemia in African-ancestry populations.
European journal of human genetics: EJHG 11/2011; 20(4):463-8. · 3.56 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To predict the potential public health impact of personal genomics, empirical research on public perceptions of these services is needed. In this study, 'early adopters' of personal genomics were surveyed to assess their motivations, perceptions and intentions.
Participants were recruited from everyone who registered to attend an enrollment event for the Coriell Personalized Medicine Collaborative, a United States-based (Camden, N.J.) research study of the utility of personalized medicine, between March 31, 2009 and April 1, 2010 (n = 369). Participants completed an Internet-based survey about their motivations, awareness of personalized medicine, perceptions of study risks and benefits, and intentions to share results with health care providers.
Respondents were motivated to participate for their own curiosity and to find out their disease risk to improve their health. Fewer than 10% expressed deterministic perspectives about genetic risk, but 32% had misperceptions about the research study or personal genomic testing. Most respondents perceived the study to have health-related benefits. Nearly all (92%) intended to share their results with physicians, primarily to request specific medical recommendations.
Early adopters of personal genomics are prospectively enthusiastic about using genomic profiling information to improve their health, in close consultation with their physicians. This suggests that early users (i.e. through direct-to-consumer companies or research) may follow up with the health care system. Further research should address whether intentions to seek care match actual behaviors.
Public Health Genomics 06/2011; 15(1):22-30. · 2.57 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Recent genome wide-association studies have identified hundreds of single nucleotide polymorphisms associated with common complex diseases. With the momentum of these discoveries comes a need to communicate this information to individuals.
The Coriell Personalized Medicine Collaborative is an observational research study designed to evaluate the utility of personalized genomic information in health care. Participants provide saliva samples for genotyping and complete extensive on-line medical history, family history, and lifestyle questionnaires. Only results for diseases deemed potentially actionable by an independent advisory board are reported.
We present our methodology for developing personalized reports containing risks for both genetic and nongenetic factors. Risk estimates are given as relative risk, derived or reported from representative peer-reviewed publications. Estimates of disease prevalence are also provided. Presenting risk as relative risk allows for consistent reporting across multiple diseases and across genetic and nongenetic factors. Using this approach eliminates the need for assumptions regarding population lifetime risk estimates. Publications used for risk reporting are selected based on the strength of the design and study quality.
Coriell Personalized Medicine Collaborative risk reports demonstrate an approach to communicating risk of complex disease via the web that encompasses risks due to genetic variants along with risks caused by family history and lifestyle factors.
Genetics in medicine: official journal of the American College of Medical Genetics 02/2011; 13(2):131-9. · 3.92 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Uric acid is the primary byproduct of purine metabolism. Hyperuricemia is associated with body mass index (BMI), sex, and multiple complex diseases including gout, hypertension (HTN), renal disease, and type 2 diabetes (T2D). Multiple genome-wide association studies (GWAS) in individuals of European ancestry (EA) have reported associations between serum uric acid levels (SUAL) and specific genomic loci. The purposes of this study were: 1) to replicate major signals reported in EA populations; and 2) to use the weak LD pattern in African ancestry population to better localize (fine-map) reported loci and 3) to explore the identification of novel findings cognizant of the moderate sample size.
African American (AA) participants (n = 1,017) from the Howard University Family Study were included in this study. Genotyping was performed using the Affymetrix® Genome-wide Human SNP Array 6.0. Imputation was performed using MACH and the HapMap reference panels for CEU and YRI. A total of 2,400,542 single nucleotide polymorphisms (SNPs) were assessed for association with serum uric acid under the additive genetic model with adjustment for age, sex, BMI, glomerular filtration rate, HTN, T2D, and the top two principal components identified in the assessment of admixture and population stratification.
Four variants in the gene SLC2A9 achieved genome-wide significance for association with SUAL (p-values ranging from 8.88 × 10(-9) to 1.38 × 10(-9)). Fine-mapping of the SLC2A9 signals identified a 263 kb interval of linkage disequilibrium in the HapMap CEU sample. This interval was reduced to 37 kb in our AA and the HapMap YRI samples.
The most strongly associated locus for SUAL in EA populations was also the most strongly associated locus in this AA sample. This finding provides evidence for the role of SLC2A9 in uric acid metabolism across human populations. Additionally, our findings demonstrate the utility of following-up EA populations GWAS signals in African-ancestry populations with weaker linkage disequilibrium.
BMC Medical Genomics 02/2011; 4:17. · 3.47 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Chronically elevated blood glucose (hyperglycaemia) is the primary indicator of type 2 diabetes, which has a prevalence that varies considerably by ethnicity in the USA, with African-Americans disproportionately affected. Genome-wide association studies (GWASs) have significantly enhanced our understanding of the genetic basis of diabetes and related traits, including fasting plasma glucose (FPG). However, the majority of GWASs have been conducted in populations of European ancestry. Thus, it is important to conduct replication analyses in populations with non-European ancestry to identify shared loci associated with FPG across populations.
We used data collected from non-diabetic unrelated African-American individuals (n = 927) who participated in the Howard University Family Study to attempt to replicate previously published GWASs of FPG. Of the 29 single nucleotide polymorphisms (SNPs) previously reported, we directly tested 20 in this study. In addition to the direct test, we queried a 500 kb window centred on all 29 reported SNPs for local replication of additional markers in linkage disequilibrium (LD).
Using direct SNP and LD-based comparisons, we replicated multiple SNPs previously associated with FPG and strongly associated with type 2 diabetes in populations with European ancestry. The replicated SNPs included those in or near TCF7L2, SLC30A8, G6PC2, MTNR1B, DGKB-TMEM195 and GCKR. We also replicated additional variants in LD with the reported SNPs in ZMAT4 and adjacent to IRS1.
We identified multiple GWAS variants for FPG in our cohort of African-Americans. Using an LD-based strategy we also identified SNPs not previously reported, demonstrating the utility of using diverse populations for replication analysis.