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Assary E, Coleman J, Hemani G, van Der Veijer M, Howe L, Palviainen T, Grasby K, Ahlskog R, Nygaard M, Cheesman R, Lim K, Reynolds C, Ordoñana J, Colodro-Conde L, Gordon S, Madrid-Valero J, Thalamuthu A, Hottenga JJ, Mengel-From J, Armstrong NJ, Sachdev P, Lee T, Brodaty H, Trollor J, Wright M, Ames D, Catts V, Latvala A, Vuoksimaa E, Mallard T, Harden K, Tucker-Drob E, Oskarsson S, Hammond C, Christensen K, Taylor M, Lundström S, Larsson H, Karlsson R, Pedersen N, Mather K, Medland S, Boomsma D, Martin N, Plomin R, Bartels M, Lichtenstein P, Kaprio J, Eley T, Davies N, Munroe P, Keers R. Genetics of environmental sensitivity to psychiatric and neurodevelopmental phenotypes: evidence from GWAS of monozygotic twins. RESEARCH SQUARE 2024:rs.3.rs-4333635. [PMID: 38746362 PMCID: PMC11092831 DOI: 10.21203/rs.3.rs-4333635/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Individual sensitivity to environmental exposures may be genetically influenced. This genotype-by-environment interplay implies differences in phenotypic variance across genotypes. However, environmental sensitivity genetic variants have proven challenging to detect. GWAS of monozygotic twin differences is a family-based variance analysis method, which is more robust to systemic biases that impact population-based methods. We combined data from up to 21,792 monozygotic twins (10,896 pairs) from 11 studies to conduct the largest GWAS meta-analysis of monozygotic phenotypic differences in children and adolescents/adults for seven psychiatric and neurodevelopmental phenotypes: attention deficit hyperactivity disorder (ADHD) symptoms, autistic traits, anxiety and depression symptoms, psychotic-like experiences, neuroticism, and wellbeing. The SNP-heritability of variance in these phenotypes were estimated (h2: 0% to 18%), but were imprecise. We identified a total of 13 genome-wide significant associations (SNP, gene, and gene-set), including genes related to stress-reactivity for depression, growth factor-related genes for autistic traits and catecholamine uptake-related genes for psychotic-like experiences. Monozygotic twins are an important new source of evidence about the genetics of environmental sensitivity.
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Affiliation(s)
| | - Jonathan Coleman
- Institute of Psychiatry, Psychology, and Neuroscience, King's College London
| | | | | | | | - Teemu Palviainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Karen Mather
- Centre for Healthy Brain Ageing, Psychiatry, University of New South Wales (UNSW)
| | | | - D Boomsma
- Vrije Universiteit Amsterdam, The Netherlands
| | | | - Robert Plomin
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London
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Yeung MW, Wang S, van de Vegte YJ, Borisov O, van Setten J, Snieder H, Verweij N, Said MA, van der Harst P. Twenty-Five Novel Loci for Carotid Intima-Media Thickness: A Genome-Wide Association Study in >45 000 Individuals and Meta-Analysis of >100 000 Individuals. Arterioscler Thromb Vasc Biol 2022; 42:484-501. [PMID: 34852643 PMCID: PMC8939707 DOI: 10.1161/atvbaha.121.317007] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/22/2021] [Indexed: 01/06/2023]
Abstract
OBJECTIVE Carotid artery intima-media thickness (cIMT) is a widely accepted marker of subclinical atherosclerosis. Twenty susceptibility loci for cIMT were previously identified and the identification of additional susceptibility loci furthers our knowledge on the genetic architecture underlying atherosclerosis. APPROACH AND RESULTS We performed 3 genome-wide association studies in 45 185 participants from the UK Biobank study who underwent cIMT measurements and had data on minimum, mean, and maximum thickness. We replicated 15 known loci and identified 20 novel loci associated with cIMT at P<5×10-8. Seven novel loci (ZNF385D, ADAMTS9, EDNRA, HAND2, MYOCD, ITCH/EDEM2/MMP24, and MRTFA) were identified in all 3 phenotypes. An additional new locus (LOXL1) was identified in the meta-analysis of the 3 phenotypes. Sex interaction analysis revealed sex differences in 7 loci including a novel locus (SYNE3) in males. Meta-analysis of UK Biobank data with a previous meta-analysis led to identification of three novel loci (APOB, FIP1L1, and LOXL4). Transcriptome-wide association analyses implicated additional genes ARHGAP42, NDRG4, and KANK2. Gene set analysis showed an enrichment in extracellular organization and the PDGF (platelet-derived growth factor) signaling pathway. We found positive genetic correlations of cIMT with coronary artery disease rg=0.21 (P=1.4×10-7), peripheral artery disease rg=0.45 (P=5.3×10-5), and systolic blood pressure rg=0.30 (P=4.0×10-18). A negative genetic correlation between average of maximum cIMT and high-density lipoprotein was found rg=-0.12 (P=7.0×10-4). CONCLUSIONS Genome-wide association meta-analyses in >100 000 individuals identified 25 novel loci associated with cIMT providing insights into genes and tissue-specific regulatory mechanisms of proatherosclerotic processes. We found evidence for shared biological mechanisms with cardiovascular diseases.
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Affiliation(s)
- Ming Wai Yeung
- Department of Cardiology (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Siqi Wang
- Department of Cardiology (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.), University of Groningen, University Medical Center Groningen, the Netherlands
- Department of Epidemiology (S.W., H.S.), University of Groningen, University Medical Center Groningen, the Netherlands
- Division of Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, the Netherlands (M.W.Y., J.v.S., P.v.d.H.)
| | - Yordi J. van de Vegte
- Department of Cardiology (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Germany (O.B.)
| | - Jessica van Setten
- Department of Epidemiology (S.W., H.S.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Harold Snieder
- Department of Epidemiology (S.W., H.S.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Niek Verweij
- Department of Cardiology (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - M. Abdullah Said
- Department of Cardiology (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Pim van der Harst
- Department of Cardiology (M.W.Y., S.W., Y.J.v.d.V., N.V., M.A.S., P.v.d.H.), University of Groningen, University Medical Center Groningen, the Netherlands
- Division of Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, the Netherlands (M.W.Y., J.v.S., P.v.d.H.)
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Wuni R, Kuhnle GGC, Wynn-Jones AA, Vimaleswaran KS. A Nutrigenetic Update on CETP Gene–Diet Interactions on Lipid-Related Outcomes. Curr Atheroscler Rep 2022; 24:119-132. [PMID: 35098451 PMCID: PMC8924099 DOI: 10.1007/s11883-022-00987-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2021] [Indexed: 02/08/2023]
Abstract
Purpose of Review An abnormal lipid profile is considered a main risk factor for cardiovascular diseases and evidence suggests that single nucleotide polymorphisms (SNPs) in the cholesteryl ester transfer protein (CETP) gene contribute to variations in lipid levels in response to dietary intake. The objective of this review was to identify and discuss nutrigenetic studies assessing the interactions between CETP SNPs and dietary factors on blood lipids. Recent Findings Relevant articles were obtained through a literature search of PubMed and Google Scholar through to July 2021. An article was included if it examined an interaction between CETP SNPs and dietary factors on blood lipids. From 49 eligible nutrigenetic studies, 27 studies reported significant interactions between 8 CETP SNPs and 17 dietary factors on blood lipids in 18 ethnicities. The discrepancies in the study findings could be attributed to genetic heterogeneity, and differences in sample size, study design, lifestyle and measurement of dietary intake. The most extensively studied ethnicities were those of Caucasian populations and majority of the studies reported an interaction with dietary fat intake. The rs708272 (TaqIB) was the most widely studied CETP SNP, where ‘B1’ allele was associated with higher CETP activity, resulting in lower high-density lipoprotein cholesterol and higher serum triglycerides under the influence of high dietary fat intake. Summary Overall, the findings suggest that CETP SNPs might alter blood lipid profiles by modifying responses to diet, but further large studies in multiple ethnic groups are warranted to identify individuals at risk of adverse lipid response to diet. Supplementary Information The online version contains supplementary material available at 10.1007/s11883-022-00987-y.
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Genetics of Biochemical Phenotypes. Twin Res Hum Genet 2020; 23:77-79. [PMID: 32482194 DOI: 10.1017/thg.2020.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Biomarkers diagnose, predict or assess the risk of disease, and studies of the effects of genetic variation on biomarker phenotypes in the general population complement studies on patients diagnosed with disease. This paper traces the evolution of studies on biomarker genetics over the past 40 years through examples drawn from the work of Professor Martin and his colleagues.
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Cohorts. Twin Res Hum Genet 2020; 23:114-115. [PMID: 32450941 DOI: 10.1017/thg.2020.33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cohort studies are essential for conducting large studies of multiple exposures and outcomes in humans. Recently, the ability to combine data from multiple cohorts in, for example, meta-analyses, and the willingness in the genetics community to collaborate to enable replication studies has led to many new insights into the genetic and environmental determinants of human health and behaviors. The contribution of Professor Nicholas Martin to the development of cohort studies, particularly of twin and twin-family studies, over a period of several decades is reviewed. He has contributed to the development and use of both Australian and international resources. The contributions of Australian twin studies to genomewide association projects are multiple, and across multiple domains, from biomarkers, lifestyle and behavior to disorders and disease.
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Abstract
The Swedish Twin Registry functions as research infrastructure containing information on 216,258 twins born between 1886 and 2015, of whom 86,199 pairs have zygosity determined by DNA, an intrapair similarity algorithm, or being of opposite sex. In essence, practically all twins alive and currently 9 years or older have been invited for participation and donation of DNA on which genomewide single nucleotide polymorphisms array genotyping has been performed. Content, management and alternatives for future improvements are discussed.
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Abstract
The Danish Twin Registry (DTR) was established in the 1950s, when twins born from 1870 to 1910 were ascertained, and has since been extended to include twins from birth cohorts until 2009. The DTR currently comprises of more than 175,000 twins from the 140 birth cohorts. This makes the DTR the oldest nationwide twin register and among the largest in the world. The combination of data from several surveys, including biological samples and repeated measurements on the same individuals, and data from Danish national registers provides a unique resource for a wide range of twin studies. This article provides an updated overview of the data in the DTR: First, we provide a summary of the establishment of the register, the different ascertainment methods and the twins included; then follows an overview of major surveys conducted in the DTR since 1994 and a description of the DTR biobank, including a description of the molecular data created so far; finally, a short description is given of the linkage to Danish national registers at Statistics Denmark and some recent examples of studies using the various data resources in the DTR are highlighted.
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Pikó P, Fiatal S, Kósa Z, Sándor J, Ádány R. Generalizability and applicability of results obtained from populations of European descent regarding the effect direction and size of HDL-C level-associated genetic variants to the Hungarian general and Roma populations. Gene 2018; 686:187-193. [PMID: 30468910 DOI: 10.1016/j.gene.2018.11.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/28/2018] [Accepted: 11/19/2018] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Large-scale association studies that mainly involve European populations identified many genetic loci related to high-density lipoprotein cholesterol (HDL-C) levels, one of the most important indicators of the risk for cardiovascular diseases. The question with intense speculation of whether the effect estimates obtained from European populations for different HDL-C level-related SNPs are applicable to the Roma ethnicity, the largest minority group in Europe with a South Asian origin, was addressed in the present study. DESIGN The associations between 21 SNPs (in the genes LIPC(G), CETP, GALNT2, HMGCP, ABCA1, KCTD10 and WWOX) and HDL-C levels were examined separately in adults of the Hungarian general (N = 1542) and Roma (N = 646) populations by linear regression. Individual effects (direction and size) of single SNPs on HDL-C levels were computed and compared between the study groups and with data published in the literature. RESULTS Significant associations between SNPs and HDL-C levels were more frequently found in general subjects than in Roma subjects (11 SNPs in general vs. 4 SNPs in Roma). The CETP gene variants rs1532624, rs708272 and rs7499892 consistently showed significant associations with HDL-C levels across the study groups (p ˂ 0.05), indicating a possible causal variant(s) in this region. Although nominally significant differences in effect size were found for three SNPs (rs693 in gene APOB, rs9989419 in gene CETP, and rs2548861 in gene WWOX) by comparing the general and Roma populations, most of these SNPs did not have a significant effect on HDL-C levels. The β coefficients for SNPs in the Roma population were found to be identical both in direction and magnitude to the effect obtained previously in large-scale studies on European populations. CONCLUSIONS The effect of the vast majority of the SNPs on HDL-C levels could be replicated in the Hungarian general and Roma populations, which indicates that the effect size measurements obtained from the literature can be used for risk estimation for both populations.
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Affiliation(s)
- Péter Pikó
- MTA-DE Public Health Research Group of the Hungarian Academy of Sciences, Faculty of Public Health, University of Debrecen, Debrecen 4028, Hungary; Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen 4028, Hungary
| | - Szilvia Fiatal
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen 4028, Hungary; WHO Collaborating Centre on Vulnerability and Health, Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen 4028, Hungary
| | - Zsigmond Kósa
- Department of Health Visitor Methodology and Public Health, Faculty of Health, University of Debrecen, Nyíregyháza 4400, Hungary
| | - János Sándor
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen 4028, Hungary; WHO Collaborating Centre on Vulnerability and Health, Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen 4028, Hungary
| | - Róza Ádány
- MTA-DE Public Health Research Group of the Hungarian Academy of Sciences, Faculty of Public Health, University of Debrecen, Debrecen 4028, Hungary; Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen 4028, Hungary; WHO Collaborating Centre on Vulnerability and Health, Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen 4028, Hungary.
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Pan L, Mo MQ, Miao L, Zhang QH, Yang S, Gao H, Huang F, Pan SL, Yin RX. Association of BDNF rs11030104 SNP and serum lipid levels in two Chinese ethnic groups. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:1466-1483. [PMID: 31938245 PMCID: PMC6958168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/08/2018] [Indexed: 06/10/2023]
Abstract
The correlation between the BDNF rs11030104 single nucleotide polymorphism (SNP) and serum lipid levels has been understudied. The present study was conducted to detect the association of the BDNF rs11030104 SNP and several environmental factors with serum lipid levels in the Jing and Han nationalities. Genotypes of the BDNF rs11030104 SNP in 709 unrelated subjects of Han and 706 unrelated participants of Jing populations were determined by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and further verified by direct sequencing. There was no significant difference in either genotypic or allelic frequencies between the Han and Jing populations. The genotypic and allelic frequencies of the SNP in Jing but not in Han populations were different between male and female subgroups (P<0.05 for each). The levels of serum total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) in the Jing population were different among the genotypes, the G allele carriers had lower TC and LDL-C levels than the G allele non-carriers. Subgroup analyses showed that the differences in serum TC and LDL-C levels among the genotypes were observed in the Jing males but not in females. Serum lipid profiles were also significantly associated with some environmental factors in the Han and Jing populations, or in male and female subgroups of the two ethnic groups (P<0.05 for all). Our study exhibited a correlation between the BDNF rs11030104 SNP and serum TC and LDL-C levels in the Jing males. These results indicate that there may be a racial/ethnic- and/or sex-specific association of the BDNF rs11030104 SNP and serum lipid parameters.
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Affiliation(s)
- Ling Pan
- Department of Nephrology, Institute of Urology, The First Affiliated Hospital, Guangxi Medical UniversityNanning, Guangxi, People’s Republic of China
| | - Man-Qiu Mo
- Department of Nephrology, Institute of Urology, The First Affiliated Hospital, Guangxi Medical UniversityNanning, Guangxi, People’s Republic of China
| | - Liu Miao
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning, Guangxi, People’s Republic of China
| | - Qing-Hui Zhang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning, Guangxi, People’s Republic of China
| | - Shuo Yang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning, Guangxi, People’s Republic of China
| | - Hui Gao
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning, Guangxi, People’s Republic of China
| | - Feng Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning, Guangxi, People’s Republic of China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Premedical Science, Guangxi Medical UniversityNanning, Guangxi, People’s Republic of China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical UniversityNanning, Guangxi, People’s Republic of China
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Liu H, Wang W, Zhang C, Xu C, Duan H, Tian X, Zhang D. Heritability and Genome-Wide Association Study of Plasma Cholesterol in Chinese Adult Twins. Front Endocrinol (Lausanne) 2018; 9:677. [PMID: 30498476 PMCID: PMC6249314 DOI: 10.3389/fendo.2018.00677] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
Dyslipidemia represents a strong and independent risk factor for cardiovascular disease. Plasma cholesterol, such as total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), and high density lipoprotein cholesterol (HDL-C), is the common indicator of diagnosing dyslipidemia. Here based on 382 Chinese twin pairs, we explored the magnitude of genetic impact on TC, HDL-C, LDL-C variation and further searched for genetic susceptibility loci for them using genome-wide association study (GWAS). The ACE model was the best fit model with additive genetic parameter (A) accounting for 26.6%, common or shared environmental parameter (C) accounting for 47.8%, unique/non-shared environmental parameter (E) accounting for 25.6% for the variance in HDL-C. The AE model was the best fit model for TC (A: 61.4%; E: 38.6%) and LDL-C (A: 65.5%; E: 34.5%). While no SNPs reached the genome-wide significance level (P < 5 × 10-8), 8, 14, 9 SNPs exceeded the suggestive significance level (P < 1 × 10-5) for TC, HDL-C, LDL-C, respectively. The promising genetic regions for TC, HDL-C, LDL-C were on chromosome 11 around rs7107698, chromosome 5 around rs12518218, chromosome 2 around rs10490120, respectively. Gene-based analysis found 1038, 1033 and 1090 genes nominally associated with TC, HDL-C, LDL-C (P < 0.05), especially FAF1, KLKB1 for TC, KLKB1 for HDL-C, and NTRK1, FAF1, SNTB2 for LDL-C, respectively. The number of common related genes among TC, HDL-C and LDL-C was 71, including FAF1, KLKB1, etc. Pathway enrichment analysis discovered known related pathways-zinc transporters, metal ion SLC transporters for TC, cell adhesion molecules CAMs, IL-6 signaling for HDL, FC epsilon RI signaling pathway, NFAT pathway for LDL, respectively. In conclusion, the TC and LDL-C level is moderately heritable and the HDL-C level is lowly heritable in Chinese population. The genomic loci, functional genes and pathways are identified to account for the heritability of plasma cholesterol level. Our findings provide important insights into plasma cholesterol molecular physiology and expect future research to replicate and validate our results.
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Affiliation(s)
- Hui Liu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Caixia Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Chunsheng Xu
- Qingdao Municipal Centre for Disease Control and Prevention, Qingdao, China
| | - Haiping Duan
- Qingdao Municipal Centre for Disease Control and Prevention, Qingdao, China
| | - Xiaocao Tian
- Qingdao Municipal Centre for Disease Control and Prevention, Qingdao, China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
- *Correspondence: Dongfeng Zhang
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The SRGAP2 SNPs, their haplotypes and G × E interactions on serum lipid traits. Sci Rep 2017; 7:11626. [PMID: 28912560 PMCID: PMC5599631 DOI: 10.1038/s41598-017-10950-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 08/18/2017] [Indexed: 12/14/2022] Open
Abstract
Maonan nationality is a relatively conservative and isolated minority in China. Little is known about the association of the Slit-Robo Rho GTPase activating protein 2 gene (SRGAP2) single nucleotide polymorphisms (SNPs) and serum lipid levels in the Chinese populations. This study was performed to clarify the association of the SRGAP2 rs2483058 and rs2580520 SNPs and their haplotypes with serum lipid traits in the Maonan and Han populations. Genotyping of the 2 SNPs was performed in 2444 unrelated subjects (Han, 1210 and Maonan, 1234) by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing. The allelic (rs2483058) and genotypic (rs2483058 and rs2580520) frequencies were different between the two ethnic groups. Four haplotypes were identified in our populations, and the rs2483058G-rs2580520C haplotype was the commonest one. The rs2483058C-rs2580520G haplotype was associated with an increased risk of dyslipidemia, and showed consistent association with serum total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), apolipoprotein (Apo) A1 levels, and the ApoA1/ApoB ratio. These results indicated that the SRGAP2 SNPs and their haplotypes were associated with serum lipid levels. Their haplotypes can explain much more serum lipid variation than any single SNP alone, especially for serum TC, HDL-C and ApoA1 levels.
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Haller T, Leitsalu L, Fischer K, Nuotio ML, Esko T, Boomsma DI, Kyvik KO, Spector TD, Perola M, Metspalu A. MixFit: Methodology for Computing Ancestry-Related Genetic Scores at the Individual Level and Its Application to the Estonian and Finnish Population Studies. PLoS One 2017; 12:e0170325. [PMID: 28107396 PMCID: PMC5249084 DOI: 10.1371/journal.pone.0170325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 01/03/2017] [Indexed: 01/05/2023] Open
Abstract
Ancestry information at the individual level can be a valuable resource for personalized medicine, medical, demographical and history research, as well as for tracing back personal history. We report a new method for quantitatively determining personal genetic ancestry based on genome-wide data. Numerical ancestry component scores are assigned to individuals based on comparisons with reference populations. These comparisons are conducted with an existing analytical pipeline making use of genotype phasing, similarity matrix computation and our addition-multidimensional best fitting by MixFit. The method is demonstrated by studying Estonian and Finnish populations in geographical context. We show the main differences in the genetic composition of these otherwise close European populations and how they have influenced each other. The components of our analytical pipeline are freely available computer programs and scripts one of which was developed in house (available at: www.geenivaramu.ee/en/tools/mixfit).
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Affiliation(s)
- Toomas Haller
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Liis Leitsalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Krista Fischer
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Marja-Liisa Nuotio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Dorothea Irene Boomsma
- Vrije University, Department of Biological Psychology, Netherlands Twin Register, Amsterdam, The Netherlands
| | - Kirsten Ohm Kyvik
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Tim D. Spector
- The Department of Twin Research & Genetic Epidemiology, TwinsUK Registry, Kings College London, London, United Kingdom
| | - Markus Perola
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helskinki, Finland
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The Concordance and Heritability of Type 2 Diabetes in 34,166 Twin Pairs From International Twin Registers: The Discordant Twin (DISCOTWIN) Consortium. Twin Res Hum Genet 2016; 18:762-71. [PMID: 26678054 DOI: 10.1017/thg.2015.83] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Twin pairs discordant for disease may help elucidate the epigenetic mechanisms and causal environmental factors in disease development and progression. To obtain the numbers of pairs, especially monozygotic (MZ) twin pairs, necessary for in-depth studies while also allowing for replication, twin studies worldwide need to pool their resources. The Discordant Twin (DISCOTWIN) consortium was established for this goal. Here, we describe the DISCOTWIN Consortium and present an analysis of type 2 diabetes (T2D) data in nearly 35,000 twin pairs. Seven twin cohorts from Europe (Denmark, Finland, Norway, the Netherlands, Spain, Sweden, and the United Kingdom) and one from Australia investigated the rate of discordance for T2D in same-sex twin pairs aged 45 years and older. Data were available for 34,166 same-sex twin pairs, of which 13,970 were MZ, with T2D diagnosis based on self-reported diagnosis and medication use, fasting glucose and insulin measures, or medical records. The prevalence of T2D ranged from 2.6% to 12.3% across the cohorts depending on age, body mass index (BMI), and national diabetes prevalence. T2D discordance rate was lower for MZ (5.1%, range 2.9-11.2%) than for same-sex dizygotic (DZ) (8.0%, range 4.9-13.5%) pairs. Across DISCOTWIN, 720 discordant MZ pairs were identified. Except for the oldest of the Danish cohorts (mean age 79), heritability estimates based on contingency tables were moderate to high (0.47-0.77). From a meta-analysis of all data, the heritability was estimated at 72% (95% confidence interval 61-78%). This study demonstrated high T2D prevalence and high heritability for T2D liability across twin cohorts. Therefore, the number of discordant MZ pairs for T2D is limited. By combining national resources, the DISCOTWIN Consortium maximizes the number of discordant MZ pairs needed for in-depth genotyping, multi-omics, and phenotyping studies, which may provide unique insights into the pathways linking genes to the development of many diseases.
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14
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Keers R, Coleman JR, Lester KJ, Roberts S, Breen G, Thastum M, Bögels S, Schneider S, Heiervang E, Meiser-Stedman R, Nauta M, Creswell C, Thirlwall K, Rapee RM, Hudson JL, Lewis C, Plomin R, Eley TC. A Genome-Wide Test of the Differential Susceptibility Hypothesis Reveals a Genetic Predictor of Differential Response to Psychological Treatments for Child Anxiety Disorders. PSYCHOTHERAPY AND PSYCHOSOMATICS 2016; 85:146-58. [PMID: 27043157 PMCID: PMC5079103 DOI: 10.1159/000444023] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 12/02/2015] [Indexed: 12/17/2022]
Abstract
BACKGROUND The differential susceptibly hypothesis suggests that certain genetic variants moderate the effects of both negative and positive environments on mental health and may therefore be important predictors of response to psychological treatments. Nevertheless, the identification of such variants has so far been limited to preselected candidate genes. In this study we extended the differential susceptibility hypothesis from a candidate gene to a genome-wide approach to test whether a polygenic score of environmental sensitivity predicted response to cognitive behavioural therapy (CBT) in children with anxiety disorders. METHODS We identified variants associated with environmental sensitivity using a novel method in which within-pair variability in emotional problems in 1,026 monozygotic twin pairs was examined as a function of the pairs' genotype. We created a polygenic score of environmental sensitivity based on the whole-genome findings and tested the score as a moderator of parenting on emotional problems in 1,406 children and response to individual, group and brief parent-led CBT in 973 children with anxiety disorders. RESULTS The polygenic score significantly moderated the effects of parenting on emotional problems and the effects of treatment. Individuals with a high score responded significantly better to individual CBT than group CBT or brief parent-led CBT (remission rates: 70.9, 55.5 and 41.6%, respectively). CONCLUSIONS Pending successful replication, our results should be considered exploratory. Nevertheless, if replicated, they suggest that individuals with the greatest environmental sensitivity may be more likely to develop emotional problems in adverse environments but also benefit more from the most intensive types of treatment.
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Affiliation(s)
- Robert Keers
- Department of Biological and Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, UK
- MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jonathan R.I. Coleman
- MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Kathryn J. Lester
- MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- University of Sussex, Brighton, UK
| | - Susanna Roberts
- MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Mikael Thastum
- Department of Psychology, University of Aarhus, Aarhus, Denmark
| | - Susan Bögels
- Research Institute of Child Development and Education, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Einar Heiervang
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Anxiety Research Network, Haukeland University Hospital, Bergen, Norway
| | | | - Maaike Nauta
- University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cathy Creswell
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
| | - Kerstin Thirlwall
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
| | - Ronald M. Rapee
- Centre for Emotional Health, Department of Psychology, Macquarie University, Sydney, N.S.W., Australia
| | - Jennifer L. Hudson
- Centre for Emotional Health, Department of Psychology, Macquarie University, Sydney, N.S.W., Australia
| | - Cathryn Lewis
- MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Robert Plomin
- MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Thalia C. Eley
- MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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15
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Deming Y, Xia J, Cai Y, Lord J, Del-Aguila JL, Fernandez MV, Carrell D, Black K, Budde J, Ma S, Saef B, Howells B, Bertelsen S, Bailey M, Ridge PG, Holtzman D, Morris JC, Bales K, Pickering EH, Lee JM, Heitsch L, Kauwe J, Goate A, Piccio L, Cruchaga C. Genetic studies of plasma analytes identify novel potential biomarkers for several complex traits. Sci Rep 2016; 6:18092. [PMID: 36647296 PMCID: PMC4698720 DOI: 10.1038/srep18092] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/11/2015] [Indexed: 01/23/2023] Open
Abstract
Genome-wide association studies of 146 plasma protein levels in 818 individuals revealed 56 genome-wide significant associations (28 novel) with 47 analytes. Loci associated with plasma levels of 39 proteins tested have been previously associated with various complex traits such as heart disease, inflammatory bowel disease, Type 2 diabetes and multiple sclerosis. These data suggest that these plasma protein levels may constitute informative endophenotypes for these complex traits. We found three potential pleiotropic genes: ABO for plasma SELE and ACE levels, FUT2 for CA19-9 and CEA plasma levels and APOE for ApoE and CRP levels. We also found multiple independent signals in loci associated with plasma levels of ApoH, CA19-9, FetuinA, IL6r and LPa. Our study highlights the power of biological traits for genetic studies to identify genetic variants influencing clinically relevant traits, potential pleiotropic effects and complex disease associations in the same locus.
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Affiliation(s)
- Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Jian Xia
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yefei Cai
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Jenny Lord
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Human Genetics Programme, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Jorge L. Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - David Carrell
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - ShengMei Ma
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Benjamin Saef
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Bill Howells
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Sarah Bertelsen
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Matthew Bailey
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Perry G. Ridge
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - David Holtzman
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, 4488 Forest Park Ave., St Louis, MO 63108, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - John C. Morris
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, 4488 Forest Park Ave., St Louis, MO 63108, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - Kelly Bales
- Neuroscience Research Unit, Worldwide Research and Development, Pfizer, Inc., Groton, CT, USA
| | - Eve H. Pickering
- Neuroscience Research Unit, Worldwide Research and Development, Pfizer, Inc., Groton, CT, USA
| | - Jin-Moo Lee
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Laura Heitsch
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - John Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Alison Goate
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, 4488 Forest Park Ave., St Louis, MO 63108, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - Laura Piccio
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
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16
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Reynolds CA, Gatz M, Christensen K, Christiansen L, Dahl Aslan AK, Kaprio J, Korhonen T, Kremen WS, Krueger R, McGue M, Neiderhiser JM, Pedersen NL. Gene-Environment Interplay in Physical, Psychological, and Cognitive Domains in Mid to Late Adulthood: Is APOE a Variability Gene? Behav Genet 2016; 46:4-19. [PMID: 26538244 PMCID: PMC4858319 DOI: 10.1007/s10519-015-9761-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 10/14/2015] [Indexed: 10/22/2022]
Abstract
Despite emerging interest in gene-environment interaction (GxE) effects, there is a dearth of studies evaluating its potential relevance apart from specific hypothesized environments and biometrical variance trends. Using a monozygotic within-pair approach, we evaluated evidence of G×E for body mass index (BMI), depressive symptoms, and cognition (verbal, spatial, attention, working memory, perceptual speed) in twin studies from four countries. We also evaluated whether APOE is a 'variability gene' across these measures and whether it partly represents the 'G' in G×E effects. In all three domains, G×E effects were pervasive across country and gender, with small-to-moderate effects. Age-cohort trends were generally stable for BMI and depressive symptoms; however, they were variable-with both increasing and decreasing age-cohort trends-for different cognitive measures. Results also suggested that APOE may represent a 'variability gene' for depressive symptoms and spatial reasoning, but not for BMI or other cognitive measures. Hence, additional genes are salient beyond APOE.
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Affiliation(s)
- Chandra A Reynolds
- Department of Psychology, University of California Riverside, 900 University Ave., Riverside, CA, 92521, USA.
| | - Margaret Gatz
- Department of Psychology, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 17177, Stockholm, Sweden
| | - Kaare Christensen
- Epidemiology, Biostatistics and Bio-demography, Institute of Public Health, University of Southern Denmark, 5000, Odense C, Denmark
- Department of Clinical Genetics and Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Bio-demography, Institute of Public Health, University of Southern Denmark, 5000, Odense C, Denmark
| | - Anna K Dahl Aslan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 17177, Stockholm, Sweden
- Institute of Gerontology, School of Health and Welfare, Jönköping University, Jönköping, Sweden
| | - Jaakko Kaprio
- Department of Public Health & Institute for Molecular Medicine FIMM, University of Helsinki, 00014, Helsinki, Finland
| | - Tellervo Korhonen
- Department of Public Health, University of Helsinki, 00014, Helsinki, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211, Kuopio, Finland
| | - William S Kremen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Robert Krueger
- Department of Psychology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Matt McGue
- Epidemiology, Biostatistics and Bio-demography, Institute of Public Health, University of Southern Denmark, 5000, Odense C, Denmark
- Department of Psychology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jenae M Neiderhiser
- Department of Psychology, The Pennsylvania State University, University Park, PA, USA
| | - Nancy L Pedersen
- Department of Psychology, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 17177, Stockholm, Sweden
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17
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Association of common variants in TOMM40/APOE/APOC1 region with human longevity in a Chinese population. J Hum Genet 2015; 61:323-8. [PMID: 26657933 DOI: 10.1038/jhg.2015.150] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/01/2015] [Accepted: 11/05/2015] [Indexed: 11/08/2022]
Abstract
Apolipoprotein E (APOE), translocase of outer mitochondrial membrane 40 homolog (TOMM40) and apolipoprotein C-I (APOC1) may extend lifespan by marked delay or escape from age-related diseases. This study aimed to elucidate the association of human longevity with genetic variations in TOMM40/APOE/APOC1 region in a Chinese population. Ten tag single-nucleotide polymorphisms (SNPs) in the TOMM40/APOE/APOC1 region were successfully genotyped in 616 unrelated long-lived individuals and 846 younger controls. Of the 10 SNPs, rs7254892 in 5' upstream of TOMM40 showed significant association with human longevity (G/A-A/A vs G/G: odds ratio (OR)=1.59, 95% confidence interval (CI)=1.20-2.09, P=0.0011, Bonferroni corrected P (Pc)=0.033). The haplotype analysis suggested that individuals carrying the haplotype A-A-A-A-T-A-T-G-C-A (rs7254892-rs157580-rs2075649-rs2075650-rs157582-rs8106922-rs1160985-rs405697-rs439401-rs445925) tended to have longer lifespan than those carrying the most common haplotype G-G-A-A-C-A-C-A-T-G (OR=1.59, 95% CI=1.19-2.12, P=0.0018, Pc=0.0216). These findings indicated that variants in TOMM40/APOE/APOC1 region might be associated with human longevity. Further studies are needed to identify the causal genetic variants influencing human longevity.
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18
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Wang B, Gao W, Yu C, Cao W, Lv J, Wang S, Pang Z, Cong L, Wang H, Wu X, Li L. Determination of Zygosity in Adult Chinese Twins Using the 450K Methylation Array versus Questionnaire Data. PLoS One 2015; 10:e0123992. [PMID: 25927701 PMCID: PMC4415785 DOI: 10.1371/journal.pone.0123992] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/25/2015] [Indexed: 11/19/2022] Open
Abstract
Previous studies have shown that both single nucleotide polymorphisms (SNPs) and questionnaires-based method can be used for twin zygosity determination, but few validation studies have been conducted using Chinese populations. In the current study, we recruited 192 same sex Chinese adult twin pairs to evaluate the validity of using genetic markers-based method and questionnaire-based method in zygosity determination. We considered the relatedness analysis based on more than 0.6 million SNPs genotyping as the golden standards for zygosity determination. After quality control, qualified twins were left for relatedness analysis based on identical by descent calculation. Then those same sex twin pairs were included in the zygosity questionnaire validation analysis. Logistic regression model was applied to assess the discriminant ability of age, sex and the three questions in zygosity determination. Leave one out cross-validation was used as a measurement of internal validation. The results of zygosity determination based on 65 SNPs in 450k methylation array were all consistent with genotyping. Age, gender, questions of appearance confused by strangers and previously perceived zygosity consisted of the most predictable model with a consistency rate of 0.8698, cross validation predictive error of 0.1347. For twin studies with genotyping and\or 450k methylation array, there would be no need to conduct other zygosity testing for the sake of costs consideration.
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Affiliation(s)
- Biqi Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Shengfeng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | - Zengchang Pang
- Qingdao Center for Diseases Control and Prevention, Qingdao, 266033, China
| | - Liming Cong
- Zhejiang Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Hua Wang
- Jiangsu Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Xianping Wu
- Sichuan Center for Disease Control and Prevention, Chengdu, 610041, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
- * E-mail:
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19
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Buil A, Brown AA, Lappalainen T, Viñuela A, Davies MN, Zheng H, Richards J, Glass D, Small KS, Durbin R, Spector TD, Dermitzakis ET. Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins. Nat Genet 2015; 47:88-91. [PMID: 25436857 PMCID: PMC4643454 DOI: 10.1038/ng.3162] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 11/06/2014] [Indexed: 12/18/2022]
Abstract
Understanding the genetic architecture of gene expression is an intermediate step in understanding the genetic architecture of complex diseases. RNA sequencing technologies have improved the quantification of gene expression and allow measurement of allele-specific expression (ASE). ASE is hypothesized to result from the direct effect of cis regulatory variants, but a proper estimation of the causes of ASE has not been performed thus far. In this study, we take advantage of a sample of twins to measure the relative contributions of genetic and environmental effects to ASE, and we find substantial effects from gene × gene (G×G) and gene × environment (G×E) interactions. We propose a model where ASE requires genetic variability in cis, a difference in the sequence of both alleles, but where the magnitude of the ASE effect depends on trans genetic and environmental factors that interact with the cis genetic variants.
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Affiliation(s)
- Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Tuuli Lappalainen
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Ana Viñuela
- Department of Twin Research, Kings College London, UK
| | | | - H.F Zheng
- Department of Medicine, Human Genetics, Epidemiology and Biostatistics McGill University, Canada
| | - J.B. Richards
- Department of Twin Research, Kings College London, UK
- Department of Medicine, Human Genetics, Epidemiology and Biostatistics McGill University, Canada
| | - Daniel Glass
- Department of Twin Research, Kings College London, UK
| | | | - Richard Durbin
- Department of Genetics, Stanford University, Stanford, California, USA
| | | | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
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20
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Hellwege JN, Palmer ND, Raffield LM, Ng MCY, Hawkins GA, Long J, Lorenzo C, Norris JM, Ida Chen YD, Speliotes EK, Rotter JI, Langefeld CD, Wagenknecht LE, Bowden DW. Genome-wide family-based linkage analysis of exome chip variants and cardiometabolic risk. Genet Epidemiol 2014; 38:345-52. [PMID: 24719370 DOI: 10.1002/gepi.21801] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/14/2014] [Accepted: 02/28/2014] [Indexed: 01/31/2023]
Abstract
Linkage analysis of complex traits has had limited success in identifying trait-influencing loci. Recently, coding variants have been implicated as the basis for some biomedical associations. We tested whether coding variants are the basis for linkage peaks of complex traits in 42 African-American (n = 596) and 90 Hispanic (n = 1,414) families in the Insulin Resistance Atherosclerosis Family Study (IRASFS) using Illumina HumanExome Beadchips. A total of 92,157 variants in African Americans (34%) and 81,559 (31%) in Hispanics were polymorphic and tested using two-point linkage and association analyses with 37 cardiometabolic phenotypes. In African Americans 77 LOD scores greater than 3 were observed. The highest LOD score was 4.91 with the APOE SNP rs7412 (MAF = 0.13) with plasma apolipoprotein B (ApoB). This SNP was associated with ApoB (P-value = 4 × 10(-19)) and accounted for 16.2% of the variance in African Americans. In Hispanic families, 104 LOD scores were greater than 3. The strongest evidence of linkage (LOD = 4.29) was with rs5882 (MAF = 0.46) in CETP with HDL. CETP variants were strongly associated with HDL (0.00049 < P-value <4.6 × 10(-12)), accounting for up to 4.5% of the variance. These loci have previously been shown to have effects on the biomedical traits evaluated here. Thus, evidence of strong linkage in this genome wide survey of primarily coding variants was uncommon. Loci with strong evidence of linkage was characterized by large contributions to the variance, and, in these cases, are common variants. Less compelling evidence of linkage and association was observed with additional loci that may require larger family sets to confirm.
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Affiliation(s)
- Jacklyn N Hellwege
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America; Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America; Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
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21
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Viktorin A, Frankowiack M, Padyukov L, Chang Z, Melén E, Sääf A, Kull I, Klareskog L, Hammarström L, Magnusson PKE. IgA measurements in over 12 000 Swedish twins reveal sex differential heritability and regulatory locus near CD30L. Hum Mol Genet 2014; 23:4177-84. [PMID: 24676358 DOI: 10.1093/hmg/ddu135] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In a broad attempt to improve the understanding of the genetic regulation of serum IgA levels, the heritability was estimated in over 12 000 Swedish twins, and a genome-wide association study was conducted in a subsample of 9617. Using the classical twin model the heritability was found to be significantly larger among females (61%) compared with males (21%), while contribution from shared environment (20%) was only seen for males. By modeling the genetic relationship matrix with IgA levels, we estimate that a substantial proportion (31%) of variance in IgA levels can ultimately be explained by the investigated SNPs. The genome-wide association study revealed significant association to two loci: (i) rs6928791 located on chromosome 6, 22 kb upstream of the gene SAM and SH3 domain containing 1 (SASH1) and (ii) rs13300483 on chromosome 9, situated 12 kb downstream the CD30 ligand (CD30L) encoding gene. The association to rs13300483 was replicated in two additional independent Swedish materials. The heritability of IgA levels is moderate and can partly be attributable to common variation in the CD30L locus.
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Affiliation(s)
| | | | | | - Zheng Chang
- Department of Medical Epidemiology and Biostatistics
| | - Erik Melén
- Institute of Environmental Medicine and Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden Sachś Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Annika Sääf
- Institute of Environmental Medicine and Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Inger Kull
- Institute of Environmental Medicine and Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden Sachś Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
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22
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Yu B, Zheng Y, Alexander D, Morrison AC, Coresh J, Boerwinkle E. Genetic determinants influencing human serum metabolome among African Americans. PLoS Genet 2014; 10:e1004212. [PMID: 24625756 PMCID: PMC3952826 DOI: 10.1371/journal.pgen.1004212] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 01/13/2014] [Indexed: 11/18/2022] Open
Abstract
Phenotypes proximal to gene action generally reflect larger genetic effect sizes than those that are distant. The human metabolome, a result of multiple cellular and biological processes, are functional intermediate phenotypes proximal to gene action. Here, we present a genome-wide association study of 308 untargeted metabolite levels among African Americans from the Atherosclerosis Risk in Communities (ARIC) Study. Nineteen significant common variant-metabolite associations were identified, including 13 novel loci (p<1.6×10−10). These loci were associated with 7–50% of the difference in metabolite levels per allele, and the variance explained ranged from 4% to 20%. Fourteen genes were identified within the nineteen loci, and four of them contained non-synonymous substitutions in four enzyme-encoding genes (KLKB1, SIAE, CPS1, and NAT8); the other significant loci consist of eight other enzyme-encoding genes (ACE, GATM, ACY3, ACSM2B, THEM4, ADH4, UGT1A, TREH), a transporter gene (SLC6A13) and a polycystin protein gene (PKD2L1). In addition, four potential disease-associated paths were identified, including two direct longitudinal predictive relationships: NAT8 with N-acetylornithine, N-acetyl-1-methylhistidine and incident chronic kidney disease, and TREH with trehalose and incident diabetes. These results highlight the value of using endophenotypes proximal to gene function to discover new insights into biology and disease pathology. Most contemporary GWAS studies have achieved increased power by increasing the size of the discovery sample to tens of thousands of individuals. An alternative approach for detecting the effects of novel loci is to measure phenotypes that more immediately reflect the effects of gene function. The metabolome consists of a collection of small molecules resulting from a variety of cellular and biologic processes, which can be considered intermediate phenotypes proximal to gene function. Here, we report a genome-wide association study identifying nineteen genetic loci influencing untargeted metabolomes traits among African Americans in the Atherosclerosis Risk in Communities (ARIC) Study. Fourteen genes mapped within nineteen loci, including twelve enzyme-encoding genes (KLKB1, SIAE, CPS1, NAT8, ACE, GATM, ACY3, ACSM2B, THEM4, ADH4, UGT1A and TREH), a transporter gene (SLC6A13) and a polycystin protein gene (PKD2L1). In addition, four potential disease-associated paths were identified, including two direct longitudinal predictive relationships: NAT8 with N-acetylornithine, N-acetyl-1-methylhistidine and incident chronic kidney disease, and TREH with trehalose and incident diabetes. These results highlight the value of using phenotypes proximal to gene function to promote novel gene discovery.
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Affiliation(s)
- Bing Yu
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Yan Zheng
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Danny Alexander
- Metabolon, Inc., Durham, North Carolina, United States of America
| | - Alanna C. Morrison
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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23
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Keller M, Schleinitz D, Förster J, Tönjes A, Böttcher Y, Fischer-Rosinsky A, Breitfeld J, Weidle K, Rayner NW, Burkhardt R, Enigk B, Müller I, Halbritter J, Koriath M, Pfeiffer A, Krohn K, Groop L, Spranger J, Stumvoll M, Kovacs P. THOC5: a novel gene involved in HDL-cholesterol metabolism. J Lipid Res 2013; 54:3170-6. [PMID: 24023261 DOI: 10.1194/jlr.m039420] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Although numerous genes are known to regulate serum lipid traits, identified variants explain only a small proportion of the expected heritability. We intended to identify further genetic variants associated with lipid phenotypes in a self-contained population of Sorbs in Germany. We performed a genome-wide association study (GWAS) on LDL-cholesterol, HDL-cholesterol (HDL-C), and triglyceride (TG) levels in 839 Sorbs. All single-nucleotide polymorphisms with a P value <0.01 were subjected to a meta-analysis, including an independent Swedish cohort (Diabetes Genetics Initiative; n = ∼3,100). Novel association signals with the strongest effects were subjected to replication studies in an additional German cohort (Berlin, n = 2,031). In the initial GWAS in the Sorbs, we identified 14 loci associated with lipid phenotypes reaching P values <10⁻⁵ and confirmed significant effects for 18 previously reported loci. The combined meta-analysis of the three study cohorts (n(HDL) = 6041; n(LDL) = 5,995; n(TG) = 6,087) revealed a novel association for a variant in THOC5 (rs8135828) with serum HDL-C levels (P = 1.78 × 10⁻⁷; Z-score = -5.221). Consistently, the variant was also associated with circulating APOA1 levels in Sorbs. The small interfering RNA-mediated mRNA silencing of THOC5 in HepG2 cells resulted in lower mRNA levels of APOA1, SCARB1, and ABCG8 (all P < 0.05). We propose THOC5 to be a novel gene involved in the regulation of serum HDL-C levels.
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Affiliation(s)
- Maria Keller
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
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