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Cao TV, Sutherland HG, Benton MC, Haupt LM, Lea RA, Griffiths LR. Exploring the Functional Basis of Epigenetic Aging in Relation to Body Fat Phenotypes in the Norfolk Island Cohort. Curr Issues Mol Biol 2023; 45:7862-7877. [PMID: 37886940 PMCID: PMC10605526 DOI: 10.3390/cimb45100497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
DNA methylation is an epigenetic factor that is modifiable and can change over a lifespan. While many studies have identified methylation sites (CpGs) related to aging, the relationship of these to gene function and age-related disease phenotypes remains unclear. This research explores this question by testing for the conjoint association of age-related CpGs with gene expression and the relation of these to body fat phenotypes. The study included blood-based gene transcripts and intragenic CpG methylation data from Illumina 450 K arrays in 74 healthy adults from the Norfolk Island population. First, a series of regression analyses were performed to detect associations between gene transcript level and intragenic CpGs and their conjoint relationship with age. Second, we explored how these age-related expression CpGs (eCpGs) correlated with obesity-related phenotypes, including body fat percentage, body mass index, and waist-to-hip ratio. We identified 35 age-related eCpGs associated with age. Of these, ten eCpGs were associated with at least one body fat phenotype. Collagen Type XI Alpha 2 Chain (COL11A2), Complement C1s (C1s), and four and a half LIM domains 2 (FHL2) genes were among the most significant genes with multiple eCpGs associated with both age and multiple body fat phenotypes. The COL11A2 gene contributes to the correct assembly of the extracellular matrix in maintaining the healthy structural arrangement of various components, with the C1s gene part of complement systems functioning in inflammation. Moreover, FHL2 expression was upregulated under hypermethylation in both blood and adipose tissue with aging. These results suggest new targets for future studies and require further validation to confirm the specific function of these genes on body fat regulation.
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Affiliation(s)
- Thao Van Cao
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
| | - Heidi G. Sutherland
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
| | - Miles C. Benton
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
| | - Larisa M. Haupt
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
- ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia
- Max Planck Queensland Centre for the Materials Sciences of Extracellular Matrices, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia
| | - Rodney A. Lea
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
| | - Lyn R. Griffiths
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
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O’Brien S, Lea RA, Jadhao S, Lee S, Sukhadia S, Arunachalam V, Roulis E, Flower RL, Griffiths L, Nagaraj SH. Genetic Characterization of Blood Group Antigens for Polynesian Heritage Norfolk Island Residents. Genes (Basel) 2023; 14:1740. [PMID: 37761880 PMCID: PMC10530796 DOI: 10.3390/genes14091740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Improvements in blood group genotyping methods have allowed large scale population-based blood group genetics studies, facilitating the discovery of rare blood group antigens. Norfolk Island, an external and isolated territory of Australia, is one example of an underrepresented segment of the broader Australian population. Our study utilized whole genome sequencing data to characterize 43 blood group systems in 108 Norfolk Island residents. Blood group genotypes and phenotypes across the 43 systems were predicted using RBCeq. Predicted frequencies were compared to data available from the 1000G project. Additional copy number variation analysis was performed, investigating deletions outside of RHCE, RHD, and MNS systems. Examination of the ABO blood group system predicted a higher distribution of group A1 (45.37%) compared to group O (35.19%) in residents of the Norfolk Island group, similar to the distribution within European populations (42.94% and 38.97%, respectively). Examination of the Kidd blood group system demonstrated an increased prevalence of variants encoding the weakened Kidd phenotype at a combined prevalence of 12.04%, which is higher than that of the European population (5.96%) but lower than other populations in 1000G. Copy number variation analysis showed deletions within the Chido/Rodgers and ABO blood group systems. This study is the first step towards understanding blood group genotype and antigen distribution on Norfolk Island.
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Affiliation(s)
- Stacie O’Brien
- Centre for Genomics and Personalized Health, Queensland University of Technology, Brisbane, QLD 4059, Australia; (S.O.); (R.A.L.); (S.J.); (S.L.); (S.S.); (V.A.); (L.G.)
| | - Rodney A. Lea
- Centre for Genomics and Personalized Health, Queensland University of Technology, Brisbane, QLD 4059, Australia; (S.O.); (R.A.L.); (S.J.); (S.L.); (S.S.); (V.A.); (L.G.)
| | - Sudhir Jadhao
- Centre for Genomics and Personalized Health, Queensland University of Technology, Brisbane, QLD 4059, Australia; (S.O.); (R.A.L.); (S.J.); (S.L.); (S.S.); (V.A.); (L.G.)
- Clinical Services and Research, Australian Red Cross Lifeblood, Brisbane, QLD 4059, Australia; (E.R.); (R.L.F.)
| | - Simon Lee
- Centre for Genomics and Personalized Health, Queensland University of Technology, Brisbane, QLD 4059, Australia; (S.O.); (R.A.L.); (S.J.); (S.L.); (S.S.); (V.A.); (L.G.)
| | - Shrey Sukhadia
- Centre for Genomics and Personalized Health, Queensland University of Technology, Brisbane, QLD 4059, Australia; (S.O.); (R.A.L.); (S.J.); (S.L.); (S.S.); (V.A.); (L.G.)
| | - Vignesh Arunachalam
- Centre for Genomics and Personalized Health, Queensland University of Technology, Brisbane, QLD 4059, Australia; (S.O.); (R.A.L.); (S.J.); (S.L.); (S.S.); (V.A.); (L.G.)
| | - Eileen Roulis
- Clinical Services and Research, Australian Red Cross Lifeblood, Brisbane, QLD 4059, Australia; (E.R.); (R.L.F.)
| | - Robert L. Flower
- Clinical Services and Research, Australian Red Cross Lifeblood, Brisbane, QLD 4059, Australia; (E.R.); (R.L.F.)
| | - Lyn Griffiths
- Centre for Genomics and Personalized Health, Queensland University of Technology, Brisbane, QLD 4059, Australia; (S.O.); (R.A.L.); (S.J.); (S.L.); (S.S.); (V.A.); (L.G.)
| | - Shivashankar H. Nagaraj
- Centre for Genomics and Personalized Health, Queensland University of Technology, Brisbane, QLD 4059, Australia; (S.O.); (R.A.L.); (S.J.); (S.L.); (S.S.); (V.A.); (L.G.)
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Pedigree derived mutation rate across the entire mitochondrial genome of the Norfolk Island population. Sci Rep 2022; 12:6827. [PMID: 35473946 PMCID: PMC9042960 DOI: 10.1038/s41598-022-10530-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/17/2022] [Indexed: 11/09/2022] Open
Abstract
Estimates of mutation rates for various regions of the human mitochondrial genome (mtGenome) vary widely, depending on whether they are inferred using a phylogenetic approach or obtained directly from pedigrees. Traditionally, only the control region, or small portions of the coding region have been targeted for analysis due to the cost and effort required to produce whole mtGenome Sanger profiles. Here, we report one of the first pedigree derived mutation rates for the entire human mtGenome. The entire mtGenome from 225 individuals originating from Norfolk Island was analysed to estimate the pedigree derived mutation rate and compared against published mutation rates. These individuals were from 45 maternal lineages spanning 345 generational events. Mutation rates for various portions of the mtGenome were calculated. Nine mutations (including two transitions and seven cases of heteroplasmy) were observed, resulting in a rate of 0.058 mutations/site/million years (95% CI 0.031-0.108). These mutation rates are approximately 16 times higher than estimates derived from phylogenetic analysis with heteroplasmy detected in 13 samples (n = 225, 5.8% individuals). Providing one of the first pedigree derived estimates for the entire mtGenome, this study provides a better understanding of human mtGenome evolution and has relevance to many research fields, including medicine, anthropology and forensics.
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Tran NK, Lea RA, Holland S, Nguyen Q, Raghubar AM, Sutherland HG, Benton MC, Haupt LM, Blackburn NB, Curran JE, Blangero J, Mallett AJ, Griffiths LR. Multi-phenotype genome-wide association studies of the Norfolk Island isolate implicate pleiotropic loci involved in chronic kidney disease. Sci Rep 2021; 11:19425. [PMID: 34593906 PMCID: PMC8484585 DOI: 10.1038/s41598-021-98935-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/14/2021] [Indexed: 11/14/2022] Open
Abstract
Chronic kidney disease (CKD) is a persistent impairment of kidney function. Genome-wide association studies (GWAS) have revealed multiple genetic loci associated with CKD susceptibility but the complete genetic basis is not yet clear. Since CKD shares risk factors with cardiovascular diseases and diabetes, there may be pleiotropic loci at play but may go undetected when using single phenotype GWAS. Here, we used multi-phenotype GWAS in the Norfolk Island isolate (n = 380) to identify new loci associated with CKD. We performed a principal components analysis on different combinations of 29 quantitative traits to extract principal components (PCs) representative of multiple correlated phenotypes. GWAS of a PC derived from glomerular filtration rate, serum creatinine, and serum urea identified a suggestive peak (pmin = 1.67 × 10-7) that mapped to KCNIP4. Inclusion of other secondary CKD measurements with these three kidney function traits identified the KCNIP4 locus with GWAS significance (pmin = 1.59 × 10-9). Finally, we identified a group of two SNPs with increased minor allele frequencies as potential functional variants. With the use of genetic isolate and the PCA-based multi-phenotype GWAS approach, we have revealed a potential pleotropic effect locus for CKD. Further studies are required to assess functional relevance of this locus.
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Affiliation(s)
- Ngan K Tran
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD, 4059, Australia
| | - Rodney A Lea
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD, 4059, Australia
| | - Samuel Holland
- Institute for Molecular Bioscience & Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience & Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Arti M Raghubar
- Institute for Molecular Bioscience & Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Heidi G Sutherland
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD, 4059, Australia
| | - Miles C Benton
- Institute of Environmental Science and Research, Kenepuru, New Zealand
| | - Larisa M Haupt
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD, 4059, Australia
| | - Nicholas B Blackburn
- School of Medicine, South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, USA
- Department of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Joanne E Curran
- School of Medicine, South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, USA
- Department of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - John Blangero
- School of Medicine, South Texas Diabetes and Obesity Institute, The University of Texas Rio Grande Valley, Brownsville, TX, USA
- Department of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Andrew J Mallett
- Institute for Molecular Bioscience & Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia
- College of Medicine & Dentistry, James Cook University, Townsville, QLD, Australia
| | - Lyn R Griffiths
- School of Biomedical Sciences, Centre for Genomics and Personalised Health, Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD, 4059, Australia.
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Kim MS, Patel KP, Teng AK, Berens AJ, Lachance J. Genetic disease risks can be misestimated across global populations. Genome Biol 2018; 19:179. [PMID: 30424772 PMCID: PMC6234640 DOI: 10.1186/s13059-018-1561-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/09/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Accurate assessment of health disparities requires unbiased knowledge of genetic risks in different populations. Unfortunately, most genome-wide association studies use genotyping arrays and European samples. Here, we integrate whole genome sequence data from global populations, results from thousands of genome-wide association studies (GWAS), and extensive computer simulations to identify how genetic disease risks can be misestimated. RESULTS In contrast to null expectations, we find that risk allele frequencies at known disease loci are significantly different for African populations compared to other continents. Strikingly, ancestral risk alleles are found at 9.51% higher frequency in Africa, and derived risk alleles are found at 5.40% lower frequency in Africa. By simulating GWAS with different study populations, we find that non-African cohorts yield disease associations that have biased allele frequencies and that African cohorts yield disease associations that are relatively free of bias. We also find empirical evidence that genotyping arrays and SNP ascertainment bias contribute to continental differences in risk allele frequencies. Because of these causes, polygenic risk scores can be grossly misestimated for individuals of African descent. Importantly, continental differences in risk allele frequencies are only moderately reduced if GWAS use whole genome sequences and hundreds of thousands of cases and controls. Finally, comparisons between uncorrected and corrected genetic risk scores reveal the benefits of considering whether risk alleles are ancestral or derived. CONCLUSIONS Our results imply that caution must be taken when extrapolating GWAS results from one population to predict disease risks in another population.
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Affiliation(s)
- Michelle S Kim
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Kane P Patel
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Andrew K Teng
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Ali J Berens
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA.
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Matovinovic E, Kho PF, Lea RA, Benton MC, Eccles DA, Haupt LM, Hewitt AW, Sherwin JC, Mackey DA, Griffiths LR. Genome-wide linkage and association analysis of primary open-angle glaucoma endophenotypes in the Norfolk Island isolate. Mol Vis 2017; 23:660-665. [PMID: 28966548 PMCID: PMC5620381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/26/2017] [Indexed: 12/04/2022] Open
Abstract
PURPOSE Primary open-angle glaucoma (POAG) refers to a group of heterogeneous diseases involving optic nerve damage. Two well-established risk factors for POAG are elevated intraocular pressure (IOP) and a thinner central corneal thickness (CCT). These endophenotypes exhibit a high degree of heritability across populations. Large-scale genome-wide association studies (GWASs) of outbred populations have robustly implicated several susceptibility gene variants for both IOP and CCT. Despite this progress, a substantial amount of genetic variance remains unexplained. Population-specific variants that might be rare in outbred populations may also influence POAG endophenotypes. The Norfolk Island population is a founder-effect genetic isolate that has been well characterized for POAG endophenotypes. This population is therefore a suitable candidate for mapping new variants that influence these complex traits. METHODS Three hundred and thirty participants from the Norfolk Island Eye Study (NIES) core pedigree provided DNA. Ocular measurements of CCT and IOP were also taken for analysis. Heritability analyses and genome-wide linkage analyses of short tandem repeats (STRs) were conducted using SOLAR. Pedigree-based GWASs of single-nucleotide polymorphisms (SNPs) were performed using the GenABEL software. RESULTS CCT was the most heritable endophenotype in this cohort (h2 = 0.77, p = 6×10-6), while IOP showed a heritability of 0.39 (p = 0.008). A genome-wide linkage analysis of these POAG phenotypes identified a maximum logarithm of the odds (LOD) score of 1.9 for CCT on chromosome 20 (p = 0.0016) and 1.3 for IOP on chromosome 15 (p = 0.0072). The GWAS results revealed a study-wise significant association for IOP at rs790357, which is located within DLG2 on chr11q14.1 (p = 1.02×10-7). DLG2 is involved in neuronal signaling and development, and while it has not previously been associated with IOP, it has been associated with myopia. An analysis of 12 known SNPs for IOP showed that rs12419342 in RAPSN on chromosome 11 was nominally associated in Norfolk Island (NI; p = 0.0021). For CCT, an analysis of 26 known SNPs showed rs9938149 in BANP-ZNF469 on chromosome 16 was nominally associated in NI (p = 0.002). CONCLUSIONS These study results indicate that CCT and IOP exhibit a substantial degree of heritability in the NI pedigree, indicating a genetic component. A genome-wide linkage analysis of POAG endophenotypes did not reveal any major effect loci, but the GWASs did implicate several known loci, as well as a potential new locus in DLG2, suggesting a role for neuronal signaling in development in IOP and perhaps POAG. These results also highlight the need to target rarer variants via whole genome sequencing in this genetic isolate.
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Affiliation(s)
- Elizabeth Matovinovic
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Pik Fang Kho
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Rodney A. Lea
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Miles C. Benton
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - David A. Eccles
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Larisa M. Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Alex W. Hewitt
- Centre for Eye Research Australia & Royal Victorian Eye and Ear Hospital, University of Melbourne, East Melbourne, Victoria, Australia,Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, Australia
| | - Justin C. Sherwin
- Centre for Eye Research Australia & Royal Victorian Eye and Ear Hospital, University of Melbourne, East Melbourne, Victoria, Australia
| | - David A. Mackey
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, Australia,Lions Eye Institute, Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Australia
| | - Lyn R. Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
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Stuart S, Benton MC, Eccles DA, Sutherland HG, Haupt LM, Lea RA, Griffiths LR. Gene-centric analysis implicates nuclear encoded mitochondrial protein gene variants in migraine susceptibility. Mol Genet Genomic Med 2017; 5:157-163. [PMID: 28361102 PMCID: PMC5370233 DOI: 10.1002/mgg3.270] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 01/13/2023] Open
Abstract
Background Migraine is a common neurological disorder which affects a large proportion of the population. The Norfolk Island population is a genetically isolated population and is an ideal discovery cohort for genetic variants involved in complex disease susceptibility given the reduced genetic and environmental heterogeneity. Given that the majority of proteins responsible for mitochondrial function are nuclear encoded, this study aimed to investigate the role of Nuclear Encoded Mitochondrial Protein (NEMP) genes in relation to migraine susceptibility. Methods A gene‐centric association analysis of NEMP genes was undertaken in the most related individuals (n = 315) within the genetically isolated Norfolk Island population. The discovery phase included genes with three or more SNP associations (P < 0.005), which were investigated further in a replication phase using an unrelated migraine case–control cohort (544 patients and 584 controls). Results The discovery phase of the study implicated SNPs in 5 NEMP genes to be associated with migraine susceptibility (P < 0.005). Replication analysis validated some of these implicated genes with SNPs in three NEMP genes shown to be associated with migraine in the replication cohort. These were CSNK1G3 (P = 0.00037), ELOVL6 (P = 0.00035) and SARDH (P = 0.00081), which are involved in phosphorylation, fatty acid metabolism, and oxidative demethylation, respectively. Conclusion Here we provide evidence that variation in NEMP genes is associated with migraine susceptibility. This study provides evidence for a link between mitochondrial function and migraine susceptibility.
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Affiliation(s)
- Shani Stuart
- Genomics Research Centre Institute for Biomedical Health and Innovation School of Biomedical Sciences Queensland University of Technology Brisbane Queensland 4059 Australia
| | - Miles C Benton
- Genomics Research Centre Institute for Biomedical Health and Innovation School of Biomedical Sciences Queensland University of Technology Brisbane Queensland 4059 Australia
| | - David A Eccles
- Genomics Research Centre Institute for Biomedical Health and Innovation School of Biomedical Sciences Queensland University of Technology Brisbane Queensland 4059 Australia
| | - Heidi G Sutherland
- Genomics Research Centre Institute for Biomedical Health and Innovation School of Biomedical Sciences Queensland University of Technology Brisbane Queensland 4059 Australia
| | - Larisa M Haupt
- Genomics Research Centre Institute for Biomedical Health and Innovation School of Biomedical Sciences Queensland University of Technology Brisbane Queensland 4059 Australia
| | - Rodney A Lea
- Genomics Research Centre Institute for Biomedical Health and Innovation School of Biomedical Sciences Queensland University of Technology Brisbane Queensland 4059 Australia
| | - Lyn R Griffiths
- Genomics Research Centre Institute for Biomedical Health and Innovation School of Biomedical Sciences Queensland University of Technology Brisbane Queensland 4059 Australia
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Benton MC, Lea RA, Macartney-Coxson D, Bellis C, Carless MA, Curran JE, Hanna M, Eccles D, Chambers GK, Blangero J, Griffiths LR. Serum bilirubin concentration is modified by UGT1A1 haplotypes and influences risk of type-2 diabetes in the Norfolk Island genetic isolate. BMC Genet 2015; 16:136. [PMID: 26628212 PMCID: PMC4667444 DOI: 10.1186/s12863-015-0291-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/02/2015] [Indexed: 02/06/2023] Open
Abstract
Background Located in the Pacific Ocean between Australia and New Zealand, the unique population isolate of Norfolk Island has been shown to exhibit increased prevalence of metabolic disorders (type-2 diabetes, cardiovascular disease) compared to mainland Australia. We investigated this well-established genetic isolate, utilising its unique genomic structure to increase the ability to detect related genetic markers. A pedigree-based genome-wide association study of 16 routinely collected blood-based clinical traits in 382 Norfolk Island individuals was performed. Results A striking association peak was located at chromosome 2q37.1 for both total bilirubin and direct bilirubin, with 29 SNPs reaching statistical significance (P < 1.84 × 10−7). Strong linkage disequilibrium was observed across a 200 kb region spanning the UDP-glucuronosyltransferase family, including UGT1A1, an enzyme known to metabolise bilirubin. Given the epidemiological literature suggesting negative association between CVD-risk and serum bilirubin we further explored potential associations using stepwise multivariate regression, revealing significant association between direct bilirubin concentration and type-2 diabetes risk. In the Norfolk Island cohort increased direct bilirubin was associated with a 28 % reduction in type-2 diabetes risk (OR: 0.72, 95 % CI: 0.57-0.91, P = 0.005). When adjusted for genotypic effects the overall model was validated, with the adjusted model predicting a 30 % reduction in type-2 diabetes risk with increasing direct bilirubin concentrations (OR: 0.70, 95 % CI: 0.53-0.89, P = 0.0001). Conclusions In summary, a pedigree-based GWAS of blood-based clinical traits in the Norfolk Island population has identified variants within the UDPGT family directly associated with serum bilirubin levels, which is in turn implicated with reduced risk of developing type-2 diabetes within this population. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0291-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M C Benton
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia.
| | - R A Lea
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia.
| | - D Macartney-Coxson
- Kenepuru Science Centre, Institute of Environmental Science and Research, Wellington, 5240, New Zealand.
| | - C Bellis
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia. .,Texas Biomedical Research Institute, San Antonio, TX, 78227-5301, USA.
| | - M A Carless
- Texas Biomedical Research Institute, San Antonio, TX, 78227-5301, USA.
| | - J E Curran
- Texas Biomedical Research Institute, San Antonio, TX, 78227-5301, USA.
| | - M Hanna
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia.
| | - D Eccles
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia.
| | - G K Chambers
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand.
| | - J Blangero
- South Texas Diabetes and Obesity Institute, University of Texas, Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA.
| | - L R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia.
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Benton MC, Lea RA, Macartney-Coxson D, Hanna M, Eccles DA, Carless MA, Chambers GK, Bellis C, Goring HH, Curran JE, Harper JL, Gibson G, Blangero J, Griffiths LR. A Phenomic Scan of the Norfolk Island Genetic Isolate Identifies a Major Pleiotropic Effect Locus Associated with Metabolic and Renal Disorder Markers. PLoS Genet 2015; 11:e1005593. [PMID: 26474483 PMCID: PMC4608754 DOI: 10.1371/journal.pgen.1005593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 09/18/2015] [Indexed: 11/23/2022] Open
Abstract
Multiphenotype genome-wide association studies (GWAS) may reveal pleiotropic genes, which would remain undetected using single phenotype analyses. Analysis of large pedigrees offers the added advantage of more accurately assessing trait heritability, which can help prioritise genetically influenced phenotypes for GWAS analysis. In this study we performed a principal component analysis (PCA), heritability (h2) estimation and pedigree-based GWAS of 37 cardiovascular disease -related phenotypes in 330 related individuals forming a large pedigree from the Norfolk Island genetic isolate. PCA revealed 13 components explaining >75% of the total variance. Nine components yielded statistically significant h2 values ranging from 0.22 to 0.54 (P<0.05). The most heritable component was loaded with 7 phenotypic measures reflecting metabolic and renal dysfunction. A GWAS of this composite phenotype revealed statistically significant associations for 3 adjacent SNPs on chromosome 1p22.2 (P<1x10-8). These SNPs form a 42kb haplotype block and explain 11% of the genetic variance for this renal function phenotype. Replication analysis of the tagging SNP (rs1396315) in an independent US cohort supports the association (P = 0.000011). Blood transcript analysis showed 35 genes were associated with rs1396315 (P<0.05). Gene set enrichment analysis of these genes revealed the most enriched pathway was purine metabolism (P = 0.0015). Overall, our findings provide convincing evidence for a major pleiotropic effect locus on chromosome 1p22.2 influencing risk of renal dysfunction via purine metabolism pathways in the Norfolk Island population. Further studies are now warranted to interrogate the functional relevance of this locus in terms of renal pathology and cardiovascular disease risk. While many large genetic association studies have identified genes playing a role in complex disorders, there is still concern over the amount of missing genetic heritability. With this in mind, we have used a data reduction approach alongside pedigree-based association to obtain highly heritable components which explain 'hidden' variance of multiphenotypes within a large pedigree from the Norfolk Island genetic isolate. The most heritable of these components involved 7 traits reflecting metabolic and renal functionality, association of which locates to an intergenic region on chromosome 1p22.2. By integrating gene expression information, we identified enrichment of a purine metabolism pathway, further strengthening the metabolic nature of the observed association. Adding additional support to our approach, we show association of the tagging SNP (rs1396315) in an independent US population. The findings presented here are of particular interest as they implicate pleiotropic effect loci and newly associated biological pathways underlying cardiovascular disease risk.
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Affiliation(s)
- Miles C. Benton
- Genomics Research Centre, Institute of Biomedical Health and Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Rodney A. Lea
- Genomics Research Centre, Institute of Biomedical Health and Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Donia Macartney-Coxson
- Biomarkers Group, Kenepuru Science Centre, Institute of Environmental Science and Research, Wellington, New Zealand
| | - Michelle Hanna
- Genomics Research Centre, Institute of Biomedical Health and Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - David A. Eccles
- Genomics Research Centre, Institute of Biomedical Health and Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Melanie A. Carless
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Geoffrey K. Chambers
- School of Biological Science, Victoria University of Wellington, Wellington, New Zealand
| | - Claire Bellis
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Harald H. Goring
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Joanne E. Curran
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | | | - Gregory Gibson
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - John Blangero
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Lyn R. Griffiths
- Genomics Research Centre, Institute of Biomedical Health and Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- * E-mail:
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10
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Benton MC, Stuart S, Bellis C, Macartney-Coxson D, Eccles D, Curran JE, Chambers G, Blangero J, Lea RA, Grffiths LR. 'Mutiny on the Bounty': the genetic history of Norfolk Island reveals extreme gender-biased admixture. INVESTIGATIVE GENETICS 2015; 6:11. [PMID: 26339467 PMCID: PMC4558825 DOI: 10.1186/s13323-015-0028-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/28/2015] [Indexed: 11/17/2022]
Abstract
Background The Pacific Oceania region was one of the last regions of the world to be settled via human migration. Here we outline a settlement of this region that has given rise to a uniquely admixed population. The current Norfolk Island population has arisen from a small number of founders with mixed Caucasian and Polynesian ancestry, descendants of a famous historical event. The ‘Mutiny on the Bounty’ has been told in history books, songs and the big screen, but recently this story can be portrayed through comprehensive molecular genetics. Written history details betrayal and murder leading to the founding of Pitcairn Island by European mutineers and the Polynesian women who left Tahiti with them. Investigation of detailed genealogical records supports historical accounts. Findings Using genetics, we show distinct maternal Polynesian mitochondrial lineages in the present day population, as well as a European centric Y-chromosome phylogeny. These results comprehensively characterise the unique gender-biased admixture of this genetic isolate and further support the historical records relating to Norfolk Island. Conclusions Our results significantly refine previous population genetic studies investigating Polynesian versus Caucasian diversity in the Norfolk Island population and add information that is beneficial to future disease and gene mapping studies. Electronic supplementary material The online version of this article (doi:10.1186/s13323-015-0028-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miles C Benton
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Q Block, 66 Musk Avenue, Kelvin Grove Campus, Brisbane, QLD 4001 Australia
| | - Shani Stuart
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Q Block, 66 Musk Avenue, Kelvin Grove Campus, Brisbane, QLD 4001 Australia
| | - Claire Bellis
- Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Donia Macartney-Coxson
- Kenepuru Science Centre, Institute of Environmental Science and Research, Wellington, 5240 New Zealand
| | - David Eccles
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Q Block, 66 Musk Avenue, Kelvin Grove Campus, Brisbane, QLD 4001 Australia
| | - Joanne E Curran
- Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Geoff Chambers
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140 New Zealand
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520 USA
| | - Rod A Lea
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Q Block, 66 Musk Avenue, Kelvin Grove Campus, Brisbane, QLD 4001 Australia
| | - Lyn R Grffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Q Block, 66 Musk Avenue, Kelvin Grove Campus, Brisbane, QLD 4001 Australia
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11
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An estimate of the average number of recessive lethal mutations carried by humans. Genetics 2015; 199:1243-54. [PMID: 25697177 PMCID: PMC4391560 DOI: 10.1534/genetics.114.173351] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/11/2015] [Indexed: 12/27/2022] Open
Abstract
The effects of inbreeding on human health depend critically on the number and severity of recessive, deleterious mutations carried by individuals. In humans, existing estimates of these quantities are based on comparisons between consanguineous and nonconsanguineous couples, an approach that confounds socioeconomic and genetic effects of inbreeding. To overcome this limitation, we focused on a founder population that practices a communal lifestyle, for which there is almost complete Mendelian disease ascertainment and a known pedigree. Focusing on recessive lethal diseases and simulating allele transmissions, we estimated that each haploid set of human autosomes carries on average 0.29 (95% credible interval [0.10, 0.84]) recessive alleles that lead to complete sterility or death by reproductive age when homozygous. Comparison to existing estimates in humans suggests that a substantial fraction of the total burden imposed by recessive deleterious variants is due to single mutations that lead to sterility or death between birth and reproductive age. In turn, comparison to estimates from other eukaryotes points to a surprising constancy of the average number of recessive lethal mutations across organisms with markedly different genome sizes.
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12
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Bonner JD, Fisher R, Klein J, Lu Q, Wilch E, Friderici KH, Elfenbein JL, Schutte DL, Schutte BC. Pedigree structure and kinship measurements of a mid-Michigan community: a new North American population isolate identified. Hum Biol 2014; 86:59-68. [PMID: 25401987 DOI: 10.3378/027.086.0103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2014] [Indexed: 11/05/2022]
Abstract
Previous studies identified a cluster of individuals with an autosomal recessive form of deafness that reside in a small region of mid-Michigan. We hypothesized that affected members from this community descend from a defined founder population. Using public records and personal interviews, we constructed a genealogical database that includes the affected individuals and their extended families as descendants of 461 settlers who emigrated from the Eifel region of Germany between 1836 and 1875. The genealogical database represents a 13-generation pedigree that includes 27,747 descendants of these settlers. Among these descendants, 13,784 are presumed living. Many of the extant descendants reside in a 90-square-mile area, and 52% were born to parents who share at least one common ancestor. Among those born to related parents, the median kinship coefficient is 3.7 × 10(-3). While the pedigree contains 2,510 founders, 344 of the 461 settlers accounted for 67% of the genome in the extant population. These data suggest that we identified a new population isolate in North America and that, as demonstrated for congenital hearing loss, this rural mid-Michigan community is a new resource to discover heritable factors that contribute to common health-related conditions.
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Affiliation(s)
- Joseph D Bonner
- Department of Comparative Medicine and Integrative Biology, East Lansing, Michigan, USA
| | - Rachel Fisher
- Department of Pediatrics and Human Development, East Lansing, Michigan, USA
| | | | - Qing Lu
- Department of Epidemiology and Biostatistics, East Lansing, Michigan, USA
| | - Ellen Wilch
- Department of Microbiology and Molecular Genetics, East Lansing, Michigan, USA
| | - Karen H Friderici
- Department of Comparative Medicine and Integrative Biology, East Lansing, Michigan, USA; Department of Pediatrics and Human Development, East Lansing, Michigan, USA; Department of Microbiology and Molecular Genetics, East Lansing, Michigan, USA
| | - Jill L Elfenbein
- Department of Communicative Sciences and Disorders, Michigan State University, East Lansing, Michigan, USA, now deceased
| | - Debra L Schutte
- College of Nursing, Wayne State University, Detroit, Michigan, USA
| | - Brian C Schutte
- Department of Comparative Medicine and Integrative Biology, East Lansing, Michigan, USA; Department of Pediatrics and Human Development, East Lansing, Michigan, USA; Department of Microbiology and Molecular Genetics, East Lansing, Michigan, USA
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13
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Panoutsopoulou K, Hatzikotoulas K, Xifara DK, Colonna V, Farmaki AE, Ritchie GRS, Southam L, Gilly A, Tachmazidou I, Fatumo S, Matchan A, Rayner NW, Ntalla I, Mezzavilla M, Chen Y, Kiagiadaki C, Zengini E, Mamakou V, Athanasiadis A, Giannakopoulou M, Kariakli VE, Nsubuga RN, Karabarinde A, Sandhu M, McVean G, Tyler-Smith C, Tsafantakis E, Karaleftheri M, Xue Y, Dedoussis G, Zeggini E. Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants. Nat Commun 2014; 5:5345. [PMID: 25373335 PMCID: PMC4242463 DOI: 10.1038/ncomms6345] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 09/22/2014] [Indexed: 11/09/2022] Open
Abstract
Isolated populations are emerging as a powerful study design in the search for low-frequency and rare variant associations with complex phenotypes. Here we genotype 2,296 samples from two isolated Greek populations, the Pomak villages (HELIC-Pomak) in the North of Greece and the Mylopotamos villages (HELIC-MANOLIS) in Crete. We compare their genomic characteristics to the general Greek population and establish them as genetic isolates. In the MANOLIS cohort, we observe an enrichment of missense variants among the variants that have drifted up in frequency by more than fivefold. In the Pomak cohort, we find novel associations at variants on chr11p15.4 showing large allele frequency increases (from 0.2% in the general Greek population to 4.6% in the isolate) with haematological traits, for example, with mean corpuscular volume (rs7116019, P=2.3 × 10(-26)). We replicate this association in a second set of Pomak samples (combined P=2.0 × 10(-36)). We demonstrate significant power gains in detecting medical trait associations.
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Affiliation(s)
| | | | - Dionysia Kiara Xifara
- 1] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK [2] Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', National Research Council (CNR), Naples 80131, Italy
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece
| | - Graham R S Ritchie
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Lorraine Southam
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Arthur Gilly
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - Ioanna Tachmazidou
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - Segun Fatumo
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] H3Africa Bioinformatics Network (H3ABioNet) Node, National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja 900107, Nigeria [3] International Health Research Group, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8NR, UK
| | - Angela Matchan
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - Nigel W Rayner
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK [3] Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Ioanna Ntalla
- 1] Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece [2] Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Massimo Mezzavilla
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] Division of Medical Genetics, Department of Reproductive Sciences and Development, IRCCS-Burlo Garofolo, University of Trieste, Trieste 34137, Italy
| | - Yuan Chen
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | | | - Eleni Zengini
- 1] Dromokaiteio Psychiatric Hospital of Athens, Chaidari, Athens 12461, Greece [2] Department of Human Metabolism, University of Sheffield, Sheffield S10 2TN, UK
| | - Vasiliki Mamakou
- 1] Dromokaiteio Psychiatric Hospital of Athens, Chaidari, Athens 12461, Greece [2] School of Medicine, National and Kapodistrian University of Athens, Goudi, Athens 11527, Greece
| | | | - Margarita Giannakopoulou
- School of Health Sciences, Faculty of Nursing, National and Kapodistrian University of Athens, Goudi, Athens 11527, Greece
| | | | - Rebecca N Nsubuga
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit on AIDS, PO Box 49, Entebbe, Uganda
| | - Alex Karabarinde
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit on AIDS, PO Box 49, Entebbe, Uganda
| | - Manjinder Sandhu
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] International Health Research Group, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8NR, UK
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Chris Tyler-Smith
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | | | | | - Yali Xue
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
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14
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Benton MC, Lea RA, Macartney-Coxson D, Carless MA, Göring HH, Bellis C, Hanna M, Eccles D, Chambers GK, Curran JE, Harper JL, Blangero J, Griffiths LR. Mapping eQTLs in the Norfolk Island genetic isolate identifies candidate genes for CVD risk traits. Am J Hum Genet 2013; 93:1087-99. [PMID: 24314549 DOI: 10.1016/j.ajhg.2013.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/29/2013] [Accepted: 11/07/2013] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular disease (CVD) affects millions of people worldwide and is influenced by numerous factors, including lifestyle and genetics. Expression quantitative trait loci (eQTLs) influence gene expression and are good candidates for CVD risk. Founder-effect pedigrees can provide additional power to map genes associated with disease risk. Therefore, we identified eQTLs in the genetic isolate of Norfolk Island (NI) and tested for associations between these and CVD risk factors. We measured genome-wide transcript levels of blood lymphocytes in 330 individuals and used pedigree-based heritability analysis to identify heritable transcripts. eQTLs were identified by genome-wide association testing of these transcripts. Testing for association between CVD risk factors (i.e., blood lipids, blood pressure, and body fat indices) and eQTLs revealed 1,712 heritable transcripts (p < 0.05) with heritability values ranging from 0.18 to 0.84. From these, we identified 200 cis-acting and 70 trans-acting eQTLs (p < 1.84 × 10(-7)) An eQTL-centric analysis of CVD risk traits revealed multiple associations, including 12 previously associated with CVD-related traits. Trait versus eQTL regression modeling identified four CVD risk candidates (NAAA, PAPSS1, NME1, and PRDX1), all of which have known biological roles in disease. In addition, we implicated several genes previously associated with CVD risk traits, including MTHFR and FN3KRP. We have successfully identified a panel of eQTLs in the NI pedigree and used this to implicate several genes in CVD risk. Future studies are required for further assessing the functional importance of these eQTLs and whether the findings here also relate to outbred populations.
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Affiliation(s)
- Miles C Benton
- Genomics Research Centre, Griffith Health Institute, Griffith University, Southport, QLD 4222, Australia
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15
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Abstract
Stature is a classical and highly heritable complex trait, with 80%–90% of variation explained by genetic factors. In recent years, genome-wide association studies (GWAS) have successfully identified many common additive variants influencing human height; however, little attention has been given to the potential role of recessive genetic effects. Here, we investigated genome-wide recessive effects by an analysis of inbreeding depression on adult height in over 35,000 people from 21 different population samples. We found a highly significant inverse association between height and genome-wide homozygosity, equivalent to a height reduction of up to 3 cm in the offspring of first cousins compared with the offspring of unrelated individuals, an effect which remained after controlling for the effects of socio-economic status, an important confounder (χ2 = 83.89, df = 1; p = 5.2×10−20). There was, however, a high degree of heterogeneity among populations: whereas the direction of the effect was consistent across most population samples, the effect size differed significantly among populations. It is likely that this reflects true biological heterogeneity: whether or not an effect can be observed will depend on both the variance in homozygosity in the population and the chance inheritance of individual recessive genotypes. These results predict that multiple, rare, recessive variants influence human height. Although this exploratory work focuses on height alone, the methodology developed is generally applicable to heritable quantitative traits (QT), paving the way for an investigation into inbreeding effects, and therefore genetic architecture, on a range of QT of biomedical importance. Studies investigating the extent to which genetics influences human characteristics such as height have concentrated mainly on common variants of genes, where having one or two copies of a given variant influences the trait or risk of disease. This study explores whether a different type of genetic variant might also be important. We investigate the role of recessive genetic variants, where two identical copies of a variant are required to have an effect. By measuring genome-wide homozygosity—the phenomenon of inheriting two identical copies at a given point of the genome—in 35,000 individuals from 21 European populations, and by comparing this to individual height, we found that the more homozygous the genome, the shorter the individual. The offspring of first cousins (who have increased homozygosity) were predicted to be up to 3 cm shorter on average than the offspring of unrelated parents. Height is influenced by the combined effect of many recessive variants dispersed across the genome. This may also be true for other human characteristics and diseases, opening up a new way to understand how genetic variation influences our health.
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16
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A genome-wide analysis of 'Bounty' descendants implicates several novel variants in migraine susceptibility. Neurogenetics 2012; 13:261-6. [PMID: 22678113 DOI: 10.1007/s10048-012-0325-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/16/2012] [Indexed: 10/28/2022]
Abstract
Migraine is a common neurological disease with a complex genetic aetiology. The disease affects ~12% of the Caucasian population and females are three times more likely than males to be diagnosed. In an effort to identify loci involved in migraine susceptibility, we performed a pedigree-based genome-wide association study of the isolated population of Norfolk Island, which has a high prevalence of migraine. This unique population originates from a small number of British and Polynesian founders who are descendents of the Bounty mutiny and forms a very large multigenerational pedigree (Bellis et al.; Human Genetics, 124(5):543-5542, 2008). These population genetic features may facilitate disease gene mapping strategies (Peltonen et al.; Nat Rev Genet, 1(3):182-90, 2000. In this study, we identified a high heritability of migraine in the Norfolk Island population (h (2) = 0.53, P = 0.016). We performed a pedigree-based GWAS and utilised a statistical and pathological prioritisation approach to implicate a number of variants in migraine. An SNP located in the zinc finger protein 555 (ZNF555) gene (rs4807347) showed evidence of statistical association in our Norfolk Island pedigree (P = 9.6 × 10(-6)) as well as replication in a large independent and unrelated cohort with >500 migraineurs. In addition, we utilised a biological prioritisation to implicate four SNPs, in within the ADARB2 gene, two SNPs within the GRM7 gene and a single SNP in close proximity to a HTR7 gene. Association of SNPs within these neurotransmitter-related genes suggests a disrupted serotoninergic system that is perhaps specific to the Norfolk Island pedigree, but that might provide clues to understanding migraine more generally.
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Maher BH, Lea RA, Benton M, Cox HC, Bellis C, Carless M, Dyer TD, Curran J, Charlesworth JC, Buring JE, Kurth T, Chasman DI, Ridker PM, Schürks M, Blangero J, Griffiths LR. An X chromosome association scan of the Norfolk Island genetic isolate provides evidence for a novel migraine susceptibility locus at Xq12. PLoS One 2012; 7:e37903. [PMID: 22666411 PMCID: PMC3362572 DOI: 10.1371/journal.pone.0037903] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 04/27/2012] [Indexed: 12/03/2022] Open
Abstract
Migraine is a common and debilitating neurovascular disorder with a complex envirogenomic aetiology. Numerous studies have demonstrated a preponderance of women affected with migraine and previous pedigree linkage studies in our laboratory have identified susceptibility loci on chromosome Xq24-Xq28. In this study we have used the genetic isolate of Norfolk Island to further analyse the X chromosome for migraine susceptibility loci.An association approach was employed to analyse 14,124 SNPs spanning the entire X chromosome. Genotype data from 288 individuals comprising a large core-pedigree, of which 76 were affected with migraine, were analysed. Although no SNP reached chromosome-wide significance (empirical α = 1 × 10(-5)) ranking by P-value revealed two primary clusters of SNPs in the top 25. A 10 SNP cluster represents a novel migraine susceptibility locus at Xq12 whilst a 11 SNP cluster represents a previously identified migraine susceptibility locus at Xq27. The strongest association at Xq12 was seen for rs599958 (OR = 1.75, P = 8.92 × 10(-4)), whilst at Xq27 the strongest association was for rs6525667 (OR = 1.53, P = 1.65 × 10(-4)). Further analysis of SNPs at these loci was performed in 5,122 migraineurs from the Women's Genome Health Study and provided additional evidence for association at the novel Xq12 locus (P<0.05).Overall, this study provides evidence for a novel migraine susceptibility locus on Xq12. The strongest effect SNP (rs102834, joint P = 1.63 × 10(-5)) is located within the 5'UTR of the HEPH gene, which is involved in iron homeostasis in the brain and may represent a novel pathway for involvement in migraine pathogenesis.
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Affiliation(s)
- Bridget H. Maher
- Genomics Research Centre, Griffith Health Institute, Griffith University, Queensland, Australia
| | - Rod A. Lea
- Genomics Research Centre, Griffith Health Institute, Griffith University, Queensland, Australia
| | - Miles Benton
- Genomics Research Centre, Griffith Health Institute, Griffith University, Queensland, Australia
| | - Hannah C. Cox
- Genomics Research Centre, Griffith Health Institute, Griffith University, Queensland, Australia
| | - Claire Bellis
- Genomics Research Centre, Griffith Health Institute, Griffith University, Queensland, Australia
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Melanie Carless
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Thomas D. Dyer
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Joanne Curran
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Jac C. Charlesworth
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- Menzies Research Institute Tasmania, Hobart, Tasmania, Australia
| | - Julie E. Buring
- Division of Preventive Medicine, Department of Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Tobias Kurth
- Division of Preventive Medicine, Department of Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Neurology, University Hospital Essen, Essen, Germany
- INSERM Unit 708 - Neuroepidemiology, Paris, France
| | - Daniel I. Chasman
- Division of Preventive Medicine, Department of Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Donald W. Reynolds Center for Cardiovascular Disease Prevention, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Paul M. Ridker
- Division of Preventive Medicine, Department of Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Donald W. Reynolds Center for Cardiovascular Disease Prevention, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Markus Schürks
- Division of Preventive Medicine, Department of Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Neurology, University Hospital Essen, Essen, Germany
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Lyn R. Griffiths
- Genomics Research Centre, Griffith Health Institute, Griffith University, Queensland, Australia
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Cox HC, Lea RA, Bellis C, Nyholt DR, Dyer TD, Haupt LM, Charlesworth J, Matovinovic E, Blangero J, Griffiths LR. Heritability and genome-wide linkage analysis of migraine in the genetic isolate of Norfolk Island. Gene 2011; 494:119-23. [PMID: 22197687 DOI: 10.1016/j.gene.2011.11.056] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 11/02/2011] [Accepted: 11/22/2011] [Indexed: 10/14/2022]
Abstract
Migraine is a common neurovascular disorder with a complex envirogenomic aetiology. In an effort to identify migraine susceptibility genes, we conducted a study of the isolated population of Norfolk Island, Australia. A large portion of the permanent inhabitants of Norfolk Island are descended from 18th Century English sailors involved in the infamous mutiny on the Bounty and their Polynesian consorts. In total, 600 subjects were recruited including a large pedigree of 377 individuals with lineage to the founders. All individuals were phenotyped for migraine using International Classification of Headache Disorders-II criterion. All subjects were genotyped for a genome-wide panel of microsatellite markers. Genotype and phenotype data for the pedigree were analysed using heritability and linkage methods implemented in the programme SOLAR. Follow-up association analysis was performed using the CLUMP programme. A total of 154 migraine cases (25%) were identified indicating the Norfolk Island population is high-risk for migraine. Heritability estimation of the 377-member pedigree indicated a significant genetic component for migraine (h(2)=0.53, P=0.016). Linkage analysis showed peaks on chromosome 13q33.1 (P=0.003) and chromosome 9q22.32 (P=0.008). Association analysis of the key microsatellites in the remaining 223 unrelated Norfolk Island individuals showed evidence of association, which strengthen support for the linkage findings (P≤0.05). In conclusion, a genome-wide linkage analysis and follow-up association analysis of migraine in the genetic isolate of Norfolk Island provided evidence for migraine susceptibility loci on chromosomes 9q22.22 and 13q33.1.
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Affiliation(s)
- Hannah C Cox
- Genomics Research Centre, Griffith Health Institute, Gold Coast Campus, Griffith University, Queensland, Australia
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Cox HC, Lea RA, Bellis C, Carless M, Dyer T, Blangero J, Griffiths LR. Variants in the human potassium channel gene (KCNN3) are associated with migraine in a high risk genetic isolate. J Headache Pain 2011; 12:603-8. [PMID: 22030984 PMCID: PMC3208049 DOI: 10.1007/s10194-011-0392-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 11/14/2010] [Indexed: 11/30/2022] Open
Abstract
The calcium-activated potassium ion channel gene (KCNN3) is located in the vicinity of the familial hemiplegic migraine type 2 locus on chromosome 1q21.3. This gene is expressed in the central nervous system and plays a role in neural excitability. Previous association studies have provided some, although not conclusive, evidence for involvement of this gene in migraine susceptibility. To elucidate KCNN3 involvement in migraine, we performed gene-wide SNP genotyping in a high-risk genetic isolate from Norfolk Island, a population descended from a small number of eighteenth century Isle of Man ‘Bounty Mutineer’ and Tahitian founders. Phenotype information was available for 377 individuals who are related through the single, well-defined Norfolk pedigree (96 were affected: 64 MA, 32 MO). A total of 85 SNPs spanning the KCNN3 gene were genotyped in a sub-sample of 285 related individuals (76 affected), all core members of the extensive Norfolk Island ‘Bounty Mutineer’ genealogy. All genotyping was performed using the Illumina BeadArray platform. The analysis was performed using the statistical program SOLAR v4.0.6 assuming an additive model of allelic effect adjusted for the effects of age and sex. Haplotype analysis was undertaken using the program HAPLOVIEW v4.0. A total of four intronic SNPs in the KCNN3 gene displayed significant association (P < 0.05) with migraine. Two SNPs, rs73532286 and rs6426929, separated by approximately 0.1 kb, displayed complete LD (r2 = 1.00, D′ = 1.00, D′ 95% CI = 0.96–1.00). In all cases, the minor allele led to a decrease in migraine risk (beta coefficient = 0.286–0.315), suggesting that common gene variants confer an increased risk of migraine in the Norfolk pedigree. This effect may be explained by founder effect in this genetic isolate. This study provides evidence for association of variants in the KCNN3 ion channel gene with migraine susceptibility in the Norfolk genetic isolate with the rarer allelic variants conferring a possible protective role. This the first comprehensive analysis of this potential candidate gene in migraine and also the first study that has utilised the unique Norfolk Island large pedigree isolate to implicate a specific migraine gene. Studies of additional variants in KCNN3 in the Norfolk pedigree are now required (e.g. polyglutamine variants) and further analyses in other population data sets are required to clarify the association of the KCNN3 gene and migraine risk in the general outbred population.
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Affiliation(s)
- Hannah C Cox
- Genomics Research Centre, Griffith Health Institute, Gold Coast Campus, Griffith University, Southport, QLD, 4222, Australia
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Sherwin JC, Kearns LS, Hewitt AW, Ma Y, Kelly J, Griffiths LR, Mackey DA. Prevalence of chronic ocular diseases in a genetic isolate: the Norfolk Island Eye Study (NIES). Ophthalmic Epidemiol 2011; 18:61-71. [PMID: 21401413 DOI: 10.3109/09286586.2010.545933] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
PURPOSE Over 40% of the permanent population of Norfolk Island possesses a unique genetic admixture dating to Pitcairn Island in the late 18(th) century, with descendents having varying degrees of combined Polynesian and European ancestry. We conducted a population-based study to determine the prevalence and causes of blindness and low vision on Norfolk Island. METHODS All permanent residents of Norfolk Island aged ≥ 15 years were invited to participate. Participants completed a structured questionnaire/interview and underwent a comprehensive ophthalmic examination including slit-lamp biomicroscopy. RESULTS We recruited 781 people aged ≥ 15, equal to 62% of the permanent population, 44% of whom could trace their ancestry to Pitcairn Island. No one was bilaterally blind. Prevalence of unilateral blindness (visual acuity [VA] < 6/60) in those aged ≥ 40 was 1.5%. Blindness was more common in females (P=0.049) and less common in people with Pitcairn Island ancestry (P<0.001). The most common causes of unilateral blindness were age-related macular degeneration (AMD), amblyopia, and glaucoma. Five people had low vision (Best-Corrected VA < 6/18 in better eye), with 4 (80%) due to AMD. People with Pitcairn Island ancestry had a lower prevalence of AMD (P<0.001) but a similar prevalence of glaucoma to those without Pitcairn Island ancestry. CONCLUSIONS The prevalence of blindness and visual impairment in this isolated Australian territory is low, especially amongst those with Pitcairn Island ancestry. AMD was the most common cause of unilateral blindness and low vision. The distribution of chronic ocular diseases on Norfolk Island is similar to mainland Australian estimates.
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Affiliation(s)
- Justin C Sherwin
- Centre for Eye Research Australia, University of Melbourne, Department of Ophthalmology, Royal Victorian Eye and Ear Hospital, Victoria, Australia
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Mackey DA, Sherwin JC, Kearns LS, Ma Y, Kelly J, Chu BS, Macmillan R, Barbour JM, Wilkinson CH, Matovinovic E, Cox HC, Bellis C, Lea RA, Quinlan S, Griffiths LR, Hewitt AW. The Norfolk Island Eye Study (NIES): rationale, methodology and distribution of ocular biometry (biometry of the bounty). Twin Res Hum Genet 2011; 14:42-52. [PMID: 21314255 DOI: 10.1375/twin.14.1.42] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
AIM To describe the recruitment, ophthalmic examination methods and distribution of ocular biometry of participants in the Norfolk Island Eye Study, who were individuals descended from the English Bounty mutineers and their Polynesian wives. METHODS All 1,275 permanent residents of Norfolk Island aged over 15 years were invited to participate, including 602 individuals involved in a 2001 cardiovascular disease study. Participants completed a detailed questionnaire and underwent a comprehensive eye assessment including stereo disc and retinal photography, ocular coherence topography and conjunctival autofluorescence assessment. Additionally, blood or saliva was taken for DNA testing. RESULTS 781 participants aged over 15 years were seen (54% female), comprising 61% of the permanent Island population. 343 people (43.9%) could trace their family history to the Pitcairn Islanders (Norfolk Island Pitcairn Pedigree). Mean anterior chamber depth was 3.32mm, mean axial length (AL) was 23.5mm, and mean central corneal thickness was 546 microns. There were no statistically significant differences in these characteristics between persons with and without Pitcairn Island ancestry. Mean intra-ocular pressure was lower in people with Pitcairn Island ancestry: 15.89mmHg compared to those without Pitcairn Island ancestry 16.49mmHg (P = .007). The mean keratometry value was lower in people with Pitcairn Island ancestry (43.22 vs. 43.52, P = .007). The corneas were flatter in people of Pitcairn ancestry but there was no corresponding difference in AL or refraction. CONCLUSION Our study population is highly representative of the permanent population of Norfolk Island. Ocular biometry was similar to that of other white populations. Heritability estimates, linkage analysis and genome-wide studies will further elucidate the genetic determinants of chronic ocular diseases in this genetic isolate.
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Affiliation(s)
- David A Mackey
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Australia.
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Abstract
The Norfolk Island population in the South Pacific is primarily the product of recent admixture between a small number of British male and Polynesian female founders. We identified and genotyped 128 Ancestry Informative Markers (AIMs) spread across the autosomes, X/Y chromosomes and mitochondrial DNA genome, to explore and quantify the current levels of genetic admixture in the Norfolk Islanders. On the basis of autosomal AIMs, the population shows mean European and Polynesian ancestry proportions of 88 and 12%, respectively. However, there is a substantial variation between individuals ranging from total European ancestry to near total Polynesian origin. There is a strong correlation between individual genetic estimates of Polynesian ancestry and those derived from the extensive pedigree and genealogical records of Islanders. Also in line with historical accounts, there is a substantial asymmetry in the maternal and paternal origins of the Islanders with almost all Y-chromosomes of European origin whereas at least 25% of mtDNAs appear to have a Polynesian origin. Accurate knowledge of ancestry will be important in future attempts to use the Island population in admixture mapping approaches to find the genes that underlie differences in the risk to some diseases between Europeans and Polynesians.
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