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1. Migraine-Associated Common Genetic Variants Confer Greater Risk of Posterior vs. Anterior Circulation Ischemic Stroke☆

Author

Frid, P., Xu, H., Mitchell, B.D., Drake, M., Wasselius, J., Gaynor, B., Ryan, K., Giese, A.K., Schirmer, M., Donahue, K.L., Irie, R., Bouts, M.J.R.J., McIntosh, E.C., Mocking, S.J.T., Dalca, A.V., Giralt-Steinhauer, E., Holmegaard, L., Jood, K., Roquer, J., Cole, J.W., McArdle, P.F., Broderick, J.P., Jimenez-Conde, J., Jern, C., Kissela, B.M., Kleindorfer, D.O., Lemmens, R., Meschia, J.F., Rosand, J., Rundek, T., Sacco, R.L., Schmidt, R., Sharma, P., Slowik, A., Thijs, V., Woo, D., Worrall, B.B., Kittner, S.J., Petersson, J., Golland, P., Wu, O., Rost, N.S., and Lindgren, A.

Published
2022
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4. Genome-wide association study of circulating interleukin 6 levels identifies novel loci

Author

Ahluwalia, T.S., Prins, B.P., Abdollahi, M., Armstrong, N.J., Aslibekyan, S., Bain, L., Jefferis, B., Baumert, J., Beekman, M., Ben-Shlomo, Y., Bis, J.C., Mitchell, B.D., Geus, E. de, Delgado, G.E., Marek, D., Eriksson, J., Kajantie, E., Kanoni, S., Kemp, J.P., Lu, C., Marioni, R.E., McLachlan, S., Milaneschi, Y., Nolte, I.M., Petrelis, A.M., Porcu, E., Sabater-Lleal, M., Naderi, E., Seppala, I., Shah, T., Singhal, G., Standl, M., Teumer, A., Thalamuthu, A., Thiering, E., Trompet, S., Ballantyne, C.M., Benjamin, E.J., Casas, J.P., Toben, C., Dedoussis, G., Deelen, J., Durda, P., Engmann, J., Feitosa, M.F., Grallert, H., Hammarstedt, A., Harris, S.E., Homuth, G., Hottenga, J.J., Jalkanen, S., Jamshidi, Y., Jawahar, M.C., Jess, T., Kivimaki, M., Kleber, M.E., Lahti, J., Liu, Y., Marques-Vidal, P., Mellstrom, D., Mooijaart, S.P., Muller-Nurasyid, M., Penninx, B., Revez, J.A., Rossing, P., Raikkonen, K., Sattar, N., Scharnagl, H., Sennblad, B., Silveira, A., St Pourcain, B., Timpson, N.J., Trollor, J., Dongen, J. van, Heemst, D. van, Visvikis-Siest, S., Vollenweider, P., Volker, U., Waldenberger, M., Willemsen, G., Zabaneh, D., Morris, R.W., Arnett, D.K., Baune, B.T., Boomsma, D.I., Chang, Y.P.C., Deary, I.J., Deloukas, P., Eriksson, J.G., Evans, D.M., Ferreira, M.A., Gaunt, T., Gudnason, V., Hamsten, A., Heinrich, J., Hingorani, A., Humphries, S.E., Jukema, J.W., Koenig, W., Kumari, M., Kutalik, Z., Lawlor, D.A., Lehtimaki, T., Marz, W., Mather, K.A., Naitza, S., Nauck, M., Ohlsson, C., Price, J.F., Raitakari, O., Rice, K., Sachdev, P.S., Slagboom, E., Sorensen, T.I.A., Spector, T., Stacey, D., Stathopoulou, M.G., Tanaka, T., Wannamethee, S.G., Whincup, P., Rotter, J.I., Dehghan, A., Boerwinkle, E., Psaty, B.M., Snieder, H., Alizadeh, B.Z., and CHARGE Inflammation Working Grp

Abstract

Interleukin 6 (IL-6) is a multifunctional cytokine with both pro- and anti-inflammatory properties with a heritability estimate of up to 61%. The circulating levels of IL-6 in blood have been associated with an increased risk of complex disease pathogenesis. We conducted a two-staged, discovery and replication meta genome-wide association study (GWAS) of circulating serum IL-6 levels comprising up to 67428 (n(discovery)=52654 and n(replication)=14774) individuals of European ancestry. The inverse variance fixed effects based discovery meta-analysis, followed by replication led to the identification of two independent loci, IL1F10/IL1RN rs6734238 on chromosome (Chr) 2q14, (P-combined=1.8x10(-11)), HLA-DRB1/DRB5 rs660895 on Chr6p21 (P-combined=1.5x10(-10)) in the combined meta-analyses of all samples. We also replicated the IL6R rs4537545 locus on Chr1q21 (P-combined=1.2x10(-122)). Our study identifies novel loci for circulating IL-6 levels uncovering new immunological and inflammatory pathways that may influence IL-6 pathobiology.

Published
2021

6. Allelic Heterogeneity at the CRP Locus Identified by Whole-Genome Sequencing in Multi-ancestry Cohorts

Author

Gaynor, S.M., Lee, S., Lee, J., Yanek, L.R., Correa, A., Metcalf, G.A., Rotter, J.I., TOPMed Inflammation Working Group, Kowalski, M.H., Mohlke, K.L., Kral, B.G., Seo, D., Rockville, MD 20850, United States, Dupuis, J., Cruz, P., Bis, J.C., Tracy, R.P., Lange, L.A., Park, C.J., Comellas, A.P., Larson, M.G., Raffield, L.M., Lin, X., Pankratz, N., Polfus, L.M., Jain, D., Gogarten, S.M., Benjamin, E.J., Muzny, D.M., Kim, R.W., Rockville, MD 20850, United States, Zhong, X., Durda, P., Choi, W.J., Mitchell, B.D., Iyengar, A.K., Zhao, L.P., Bowler, R., Rich, S.S., Reiner, A.P., Ryan, K., Spracklen, C.N., Doddapaneni, H., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Viaud-Martinez, K.A., Wang, B., Momin, Z., Li, B., Laurie, C., Salimi, S., Cade, B.E., Li, Y., Lewis, J.P., and Auer, P.L.

Subjects
Black People, Medical and Health Sciences, Linkage Disequilibrium, White People, Cohort Studies, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Gene Frequency, Asian People, c-reactive protein, Clinical Research, Genetics, Humans, 2.1 Biological and endogenous factors, Genetic Predisposition to Disease, Polymorphism, Aetiology, Genetics & Heredity, Whole Genome Sequencing, TOPMed Inflammation Working Group, Human Genome, Single Nucleotide, Biological Sciences, Good Health and Well Being, whole-genome sequencing, Genome-Wide Association Study, Biotechnology
Abstract

Whole-genome sequencing (WGS) can improve assessment of low-frequency and rare variants, particularly in non-European populations that have been underrepresented in existing genomic studies. The genetic determinants of C-reactive protein (CRP), a biomarker of chronic inflammation, have been extensively studied, with existing genome-wide association studies (GWASs) conducted in >200,000 individuals of European ancestry. In order to discover novel loci associated with CRP levels, we examined a multi-ancestry population (n = 23,279) with WGS (∼38× coverage) from the Trans-Omics for Precision Medicine (TOPMed) program. We found evidence for eight distinct associations at the CRP locus, including two variants that have not been identified previously (rs11265259 and rs181704186), both of which are non-coding and more common in individuals of African ancestry (∼10% and ∼1% minor allele frequency, respectively, and rare or monomorphic in 1000 Genomes populations of East Asian, South Asian, and European ancestry). We show that the minor (G) allele of rs181704186 is associated with lower CRP levels and decreased transcriptional activity and protein binding invitro, providing a plausible molecular mechanism for this African ancestry-specific signal. The individuals homozygous for rs181704186-G have a mean CRP level of 0.23mg/L, in contrast to individuals heterozygous for rs181704186 with mean CRP of 2.97mg/L and major allele homozygotes with mean CRP of 4.11mg/L. This study demonstrates the utility of WGS in multi-ethnic populations to drive discovery of complex trait associations of large effect and to identify functional alleles in noncoding regulatory regions.

Published
2020

7. Genomewide Association Study of Platelet Reactivity and Cardiovascular Response in Patients Treated With Clopidogrel: A Study by the International Clopidogrel Pharmacogenomics Consortium

Author

Verma, S.S. Bergmeijer, T.O. Gong, L. Reny, J.-L. Lewis, J.P. Mitchell, B.D. Alexopoulos, D. Aradi, D. Altman, R.B. Bliden, K. Bradford, Y. Campo, G. Chang, K. Cleator, J.H. Déry, J.-P. Dridi, N.P. Fernandez-Cadenas, I. Fontana, P. Gawaz, M. Geisler, T. Gensini, G.F. Giusti, B. Gurbel, P.A. Hochholzer, W. Holmvang, L. Kim, E.-Y. Kim, H.-S. Marcucci, R. Montaner, J. Backman, J.D. Pakyz, R.E. Roden, D.M. Schaeffeler, E. Schwab, M. Shin, J.G. Siller-Matula, J.M. ten Berg, J.M. Trenk, D. Valgimigli, M. Wallace, J. Wen, M.-S. Kubo, M. Lee, M.T.M. Whaley, R. Winter, S. Klein, T.E. Shuldiner, A.R. Ritchie, M.D. for the ICPC Investigators

Subjects
cardiovascular diseases
Abstract

Antiplatelet response to clopidogrel shows wide variation, and poor response is correlated with adverse clinical outcomes. CYP2C19 loss-of-function alleles play an important role in this response, but account for only a small proportion of variability in response to clopidogrel. An aim of the International Clopidogrel Pharmacogenomics Consortium (ICPC) is to identify other genetic determinants of clopidogrel pharmacodynamics and clinical response. A genomewide association study (GWAS) was performed using DNA from 2,750 European ancestry individuals, using adenosine diphosphate-induced platelet reactivity and major cardiovascular and cerebrovascular events as outcome parameters. GWAS for platelet reactivity revealed a strong signal for CYP2C19*2 (P value = 1.67e−33). After correction for CYP2C19*2 no other single-nucleotide polymorphism reached genomewide significance. GWAS for a combined clinical end point of cardiovascular death, myocardial infarction, or stroke (5.0% event rate), or a combined end point of cardiovascular death or myocardial infarction (4.7% event rate) showed no significant results, although in coronary artery disease, percutaneous coronary intervention, and acute coronary syndrome subgroups, mutations in SCOS5P1, CDC42BPA, and CTRAC1 showed genomewide significance (lowest P values: 1.07e−09, 4.53e−08, and 2.60e−10, respectively). CYP2C19*2 is the strongest genetic determinant of on-clopidogrel platelet reactivity. We identified three novel associations in clinical outcome subgroups, suggestive for each of these outcomes. © 2020 The Authors. Clinical Pharmacology & Therapeutics published by Wiley Periodicals LLC on behalf of American Society for Clinical Pharmacology and Therapeutics.

Published
2020

9. Genetic and lifestyle risk factors for MRI-defined brain infarcts in a population-based setting

Author

Chauhan, G., Adams, H.H.H., Satizabal, C.L., Bis, J.C., Teumer, A., Sargurupremraj, M., Hofer, E., Trompet, S., Hilal, S., Smith, A.V., Jian, X.Q., Malik, R., Traylor, M., Pulit, S.L., Amouyel, P., Mazoyer, B., Zhu, Y.C., Kaffashian, S., Schilling, S., Beecham, G.W., Montine, T.J., Schellenberg, G.D., Kjartansson, O., Gudnason, V., Knopman, D.S., Griswold, M.E., Windham, B.G., Gottesman, R.F., Mosley, T.H., Schmidt, R., Saba, Y., Schmidt, H., Takeuchi, F., Yamaguchi, S., Nabika, T., Kato, N., Rajan, K.B., Aggarwal, N.T., Jager, P.L. de, Evans, D.A., Psaty, B.M., Rotter, J.I., Rice, K., Lopez, O.L., Liao, J.M., Chen, C., Cheng, C.Y., Wong, T.Y., Ikram, M.K., Lee, S.J. van der, Amin, N., Chouraki, V., DeStefano, A.L., Aparicio, H.J., Romero, J.R., Maillard, P., DeCarli, C., Wardlaw, J.M., Hernandez, M.D.V., Luciano, M., Liewald, D., Deary, I.J., Starr, J.M., Bastin, M.E., Maniega, S.M., Slagboom, P.E., Beekman, M., Deelen, J., Uh, H.W., Lemmens, R., Brodaty, H., Wright, M.J., Ames, D., Boncoraglio, G.B., Hopewell, J.C., Beecham, A.H., Blanton, S.H., Wright, C.B., Sacco, R.L., Wen, W., Thalamuthu, A., Armstrong, N.J., Chong, E., Schofield, P.R., Kwok, J.B., Grond, J. van der, Stott, D.J., Ford, I., Jukema, J.W., Vernooij, M.W., Hofman, A., Uitterlinden, A.G., Lugt, A. van der, Wittfeld, K., Grabe, H.J., Hosten, N., Sarnowski, B. von, Volker, U., Levi, C., Jimenez-Conde, J., Sharma, P., Sudlow, C.L.M., Rosand, J., Woo, D., Cole, J.W., Meschia, J.F., Slowik, A., Thijs, V., Lindgren, A., Melander, O., Grewal, R.P., Rundek, T., Rexrode, K., Rothwell, P.M., Arnett, D.K., Jern, C., Johnson, J.A., Benavente, O.R., Wasssertheil-Smoller, S., Lee, J.M., Wong, Q., Mitchell, B.D., Rich, S.S., McArdle, P.F., Geerlings, M.I., Graaf, Y. van der, Bakker, P.I.W. de, Asselbergs, F.W., Srikanth, V., Thomson, R., McWhirter, R., Moran, C., Callisaya, M., Phan, T., Rutten-Jacobs, L.C.A., Bevan, S., Tzourio, C., Mather, K.A., Sachdev, P.S., Duijn, C.M. van, Worrall, B.B., Dichgans, M., Kittner, S.J., Markus, H.S., Ikram, M.A., Fornage, M., Launer, L.J., Seshadri, S., Longstreth, W.T., Debette, S., Stroke Genetics Network SiGN, ISGC, METASTROKE, ADGC, and CHARGE Consortium

Subjects
Meta-analysis, Mendelian Randomization, Blood Pressure, Polymorphisms, Genome-wide Association, Silent, Insights, Small Vessel Disease, Matter Hyperintensity Volume, Ischemic Stroke, Doenças Cardio e Cérebro-vasculares
Abstract

Collaborators (845): Astrid M. Vicente Free PMC article:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369905/ Objective: To explore genetic and lifestyle risk factors of MRI-defined brain infarcts (BI) in large population-based cohorts. Methods: We performed meta-analyses of genome-wide association studies (GWAS) and examined associations of vascular risk factors and their genetic risk scores (GRS) with MRI-defined BI and a subset of BI, namely, small subcortical BI (SSBI), in 18 population-based cohorts (n = 20,949) from 5 ethnicities (3,726 with BI, 2,021 with SSBI). Top loci were followed up in 7 population-based cohorts (n = 6,862; 1,483 with BI, 630 with SBBI), and we tested associations with related phenotypes including ischemic stroke and pathologically defined BI. Results: The mean prevalence was 17.7% for BI and 10.5% for SSBI, steeply rising after age 65. Two loci showed genome-wide significant association with BI: FBN2, p = 1.77 × 10-8; and LINC00539/ZDHHC20, p = 5.82 × 10-9. Both have been associated with blood pressure (BP)-related phenotypes, but did not replicate in the smaller follow-up sample or show associations with related phenotypes. Age- and sex-adjusted associations with BI and SSBI were observed for BP traits (p value for BI, p [BI] = 9.38 × 10-25; p [SSBI] = 5.23 × 10-14 for hypertension), smoking (p [BI] = 4.4 × 10-10; p [SSBI] = 1.2 × 10-4), diabetes (p [BI] = 1.7 × 10-8; p [SSBI] = 2.8 × 10-3), previous cardiovascular disease (p [BI] = 1.0 × 10-18; p [SSBI] = 2.3 × 10-7), stroke (p [BI] = 3.9 × 10-69; p [SSBI] = 3.2 × 10-24), and MRI-defined white matter hyperintensity burden (p [BI] = 1.43 × 10-157; p [SSBI] = 3.16 × 10-106), but not with body mass index or cholesterol. GRS of BP traits were associated with BI and SSBI (p ≤ 0.0022), without indication of directional pleiotropy. Conclusion: In this multiethnic GWAS meta-analysis, including over 20,000 population-based participants, we identified genetic risk loci for BI requiring validation once additional large datasets become available. High BP, including genetically determined, was the most significant modifiable, causal risk factor for BI. info:eu-repo/semantics/publishedVersion

Published
2019

10. Low-frequency and common genetic variation in ischemic stroke : the METASTROKE collaboration

Author

Malik, R., Traylor, M., Pulit, S.L., Bevan, S., Hopewell, J.C., Holliday, E.G., Zhao, W., Abrantes, P., Amouyel, P., Attia, J.R., Battey, T.W., Berger, K., Boncoraglio, G.B., Chauhan, G., Cheng, Y.C., Chen, W.M., Clarke, R., Cotlarciuc, I., Debette, S., Falcone, G.J., Ferro, J.M., Gamble, D.M., Ilinca, A., Kittner, S.J., Kourkoulis, C.E., Lemmens, R., Levi, C.R., Lichtner, P., Lindgren, A., Liu, J., Meschia, J.F., Mitchell, B.D., Oliveira, S.A., Pera, J., Reiner, A.P., Rothwell, P.M., Sharma, P., Slowik, A., Sudlow, C.L., Tatlisumak, T., Thijs, V., Vicente, A.M., Woo, D., Seshadri, S., Saleheen, D., Rosand, J., Markus, H.S., Worrall, B.B., Dichgans, M., ISGC Analysis Group, METASTROKE collaboration, Wellcome Trust Case Control Consortium 2 (WTCCC2), and NINDS Stroke Genetics Network (SiGN)

Subjects
0301 basic medicine, medicine.medical_specialty, Genome-wide association study, Polymorphism, Single Nucleotide, Gastroenterology, Article, Brain Ischemia, Doenças Cardio e Cérebro-vasculares, 03 medical and health sciences, 0302 clinical medicine, Missing heritability problem, Internal medicine, ABO blood group system, Genetic variation, Humans, Medicine, Cooperative Behavior, 1000 Genomes Project, Allele frequency, Stroke, Ischemic Stroke, Genetic association, Genetics, business.industry, Genetic Variation, Correction, medicine.disease, 030104 developmental biology, Case-Control Studies, Ischemic stroke, Cardiology, Neurology (clinical), business, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Erratum in: Low-frequency and common genetic variation in ischemic stroke: The METASTROKE collaboration. [Neurology. 2016] Objective: To investigate the influence of common and low-frequency genetic variants on the risk of ischemic stroke (all IS) and etiologic stroke subtypes. Methods: We meta-analyzed 12 individual genome-wide association studies comprising 10,307 cases and 19,326 controls imputed to the 1000 Genomes (1 KG) phase I reference panel. We selected variants showing the highest degree of association (p , 1E-5) in the discovery phase for replication in Caucasian (13,435 cases and 29,269 controls) and South Asian (2,385 cases and 5,193 controls) samples followed by a transethnic meta-analysis. We further investigated the p value distribution for different bins of allele frequencies for all IS and stroke subtypes. Results: We showed genome-wide significance for 4 loci: ABO for all IS, HDAC9 for large vessel disease (LVD), and both PITX2 and ZFHX3 for cardioembolic stroke (CE). We further refined the association peaks for ABO and PITX2. Analyzing different allele frequency bins, we showed significant enrichment in low-frequency variants (allele frequency ,5%) for both LVD and small vessel disease, and an enrichment of higher frequency variants (allele frequency 10% and 30%) for CE (all p , 1E-5). Conclusions: Our findings suggest that the missing heritability in IS subtypes can in part be attributed to low-frequency and rare variants. Larger sample sizes are needed to identify the variants associated with all IS and stroke subtypes.

Published
2016

12. CPT1A methylation is associated with plasma adiponectin

Author

Aslibekyan, S., primary, Do, A.N., additional, Xu, H., additional, Li, S., additional, Irvin, M.R., additional, Zhi, D., additional, Tiwari, H.K., additional, Absher, D.M., additional, Shuldiner, A.R., additional, Zhang, T., additional, Chen, W., additional, Tanner, K., additional, Hong, C., additional, Mitchell, B.D., additional, Berenson, G., additional, and Arnett, D.K., additional

Published
2017
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13. Genetic sharing with cardiovascular disease risk factors and diabetes reveals novel bone mineral density loci

Author

Reppe, S. Wang, Y. Thompson, W.K. McEvoy, L.K. Schork, A.J. Zuber, V. LeBlanc, M. Bettella, F. Mills, I.G. Desikan, R.S. Djurovic, S. Gautvik, K.M. Dale, A.M. Andreassen, O.A. Estrada, K. Styrkarsdottir, U. Evangelou, E. Hsu, Y.-H. Duncan, E.L. Ntzani, E.E. Oei, L. Albagha, O.M.E. Amin, N. Kemp, J.P. Koller, D.L. Li, G. Liu, C.-T. Minster, R.L. Moayyeri, A. Vandenput, L. Willner, D. Xiao, S.-M. Yerges-Armstrong, L.M. Zheng, H.-F. Alonso, N. Eriksson, J. Kammerer, C.M. Kaptoge, S.K. Leo, P.J. Thorleifsson, G. Wilson, S.G. Wilson, J.F. Aalto, V. Alen, M. Aragaki, A.K. Aspelund, T. Center, J.R. Dailiana, Z. Duggan, D.J. Garcia, M. Garcia-Giralt, N. Giroux, S. Hallmans, G. Hocking, L.J. Husted, L.B. Jameson, K.A. Khusainova, R. Kim, G.S. Kooperberg, C. Koromila, T. Kruk, M. Laaksonen, M. Lacroix, A.Z. Lee, S.H. Leung, P.C. Lewis, J.R. Masi, L. Mencej-Bedrac, S. Nguyen, T.V. Nogues, X. Patel, M.S. Prezelj, J. Rose, L.M. Scollen, S. Siggeirsdottir, K. Smith, A.V. Svensson, O. Trompet, S. Trummer, O. Van Schoor, N.M. Woo, J. Zhu, K. Balcells, S. Brandi, M.L. Buckley, B.M. Cheng, S. Christiansen, C. Cooper, C. Dedoussis, G. Ford, I. Frost, M. Goltzman, D. González-Macías, J. Kähönen, M. Karlsson, M. Khusnutdinova, E. Koh, J.-M. Kollia, P. Langdahl, B.L. Leslie, W.D. Lips, P. Ljunggren, Ö. Lorenc, R.S. Marc, J. Mellström, D. Obermayer-Pietsch, B. Olmos, J.M. Pettersson-Kymmer, U. Reid, D.M. Riancho, J.A. Ridker, P.M. Rousseau, F. Slagboom, P.E. Tang, N.L.S. Urreizti, R. Van Hul, W. Viikari, J. Zarrabeitia, M.T. Aulchenko, Y.S. Castano-Betancourt, M. Grundberg, E. Herrera, L. Ingvarsson, T. Johannsdottir, H. Kwan, T. Li, R. Luben, R. Medina-Gómez, C. Palsson, S.Th. Rotter, J.I. Sigurdsson, G. Van Meurs, J.B.J. Verlaan, D. Williams, F.M.K. Wood, A.R. Zhou, Y. Pastinen, T. Raychaudhuri, S. Cauley, J.A. Chasman, D.I. Clark, G.R. Cummings, S.R. Danoy, P. Dennison, E.M. Eastell, R. Eisman, J.A. Gudnason, V. Hofman, A. Jackson, R.D. Jones, G. Jukema, J.W. Khaw, K.-T. Lehtimäki, T. Liu, Y. Lorentzon, M. McCloskey, E. Mitchell, B.D. Nandakumar, K. Nicholson, G.C. Oostra, B.A. Peacock, M. Pols, H.A.P. Prince, R.L. Raitakari, O. Reid, I.R. Robbins, J. Sambrook, P.N. Sham, P.C. Shuldiner, A.R. Tylavsky, F.A. Van Duijn, C.M. Wareham, N.J. Cupples, L.A. Econs, M.J. Evans, D.M. Harris, T.B. Kung, A.W.C. Psaty, B.M. Reeve, J. Spector, T.D. Streeten, E.A. Zillikens, M.C. Thorsteinsdottir, U. Ohlsson, C. Karasik, D. Richards, J.B. Brown, M.A. Stefansson, K. Uitterlinden, A.G. Ralston, S.H. Ioannidis, J.P.A. Kiel, D.P. Rivadeneira, F. GEFOS Consortium

Subjects
musculoskeletal diseases
Abstract

Bone Mineral Density (BMD) is a highly heritable trait, but genome-wide association studies have identified few genetic risk factors. Epidemiological studies suggest associations between BMD and several traits and diseases, but the nature of the suggestive comorbidity is still unknown. We used a novel genetic pleiotropy-informed conditional False Discovery Rate (FDR) method to identify single nucleotide polymorphisms (SNPs) associated with BMD by leveraging cardiovascular disease (CVD) associated disorders and metabolic traits. By conditioning on SNPs associated with the CVD-related phenotypes, type 1 diabetes, type 2 diabetes, systolic blood pressure, diastolic blood pressure, high density lipoprotein, low density lipoprotein, triglycerides and waist hip ratio, we identified 65 novel independent BMD loci (26 with femoral neck BMD and 47 with lumbar spine BMD) at conditional FDR < 0.01. Many of the loci were confirmed in genetic expression studies. Genes validated at the mRNA levels were characteristic for the osteoblast/osteocyte lineage, Wnt signaling pathway and bone metabolism. The results provide new insight into genetic mechanisms of variability in BMD, and a better understanding of the genetic underpinnings of clinical comorbidity. © 2015 Reppe et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Published
2015

14. Seasonality shows evidence for polygenic architecture and genetic correlation with schizophrenia and bipolar disorder

Author

Byrne, E.M., Boomsma, D.I., Martin, N.G., Penninx, B.W.J.H., de Geus, E.J.C., Hoogendijk, W.J.G., Hottenga, J.J., Middeldorp, C.M., Nyholt, DR, Smit, J.H., van den Oord, E.J., Grootheest, G., Willemsen, G., Zitman, F.G., Neale, B.M., Sullivan, P.F., Raheja, U.K., Stephens, S.H., Heath, A.C., Madden, P.A.F., Vaswani, D., Nijjar, G.V., Ryan, K.A., Youssufi, H., Gehrman, P.R., Shuldiner, A.R., Montgomery, G.W., Wray, N.R., Nelson, E.C., Mitchell, B.D., Postolache, T.T., Biological Psychology, Neuroscience Campus Amsterdam - Neurobiology of Mental Health, EMGO+ - Mental Health, Psychiatry, NCA - Neurobiology of mental health, and EMGO - Mental health

Subjects
Adult, Male, Netherlands Twin Register (NTR), Multifactorial Inheritance, Bipolar Disorder, Genotype, Genome-wide association study, Single-nucleotide polymorphism, Genetic correlation, Life Change Events, Young Adult, mental disorders, medicine, Diseases in Twins, Humans, Bipolar disorder, Genetic association, Aged, Psychiatric Status Rating Scales, Depressive Disorder, Major, Middle Aged, medicine.disease, United States, Psychiatry and Mental health, Alcoholism, Mood, Schizophrenia, Major depressive disorder, Female, Schizophrenic Psychology, Queensland, Psychology, Amish, Clinical psychology
Abstract

OBJECTIVE: To test common genetic variants for association with seasonality (seasonal changes in mood and behavior) and to investigate whether there are shared genetic risk factors between psychiatric disorders and seasonality. METHOD: Genome-wide association studies (GWASs) were conducted in Australian (between 1988 and 1990 and between 2010 and 2013) and Amish (between May 2010 and December 2011) samples in whom the Seasonal Pattern Assessment Questionnaire (SPAQ) had been administered, and the results were meta-analyzed in a total sample of 4,156 individuals. Genetic risk scores based on results from prior large GWAS studies of bipolar disorder, major depressive disorder (MDD), and schizophrenia were calculated to test for overlap in risk between psychiatric disorders and seasonality. RESULTS: The most significant association was with rs11825064 (P = 1.7 × 10⁻⁶, β = 0.64, standard error = 0.13), an intergenic single nucleotide polymorphism (SNP) found on chromosome 11. The evidence for overlap in risk factors was strongest for schizophrenia and seasonality, with the schizophrenia genetic profile scores explaining 3% of the variance in log-transformed global seasonality scores. Bipolar disorder genetic profile scores were also associated with seasonality, although at much weaker levels (minimum P value = 3.4 × 10⁻³), and no evidence for overlap in risk was detected between MDD and seasonality. CONCLUSIONS: Common SNPs of large effect most likely do not exist for seasonality in the populations examined. As expected, there were overlapping genetic risk factors for bipolar disorder (but not MDD) with seasonality. Unexpectedly, the risk for schizophrenia and seasonality had the largest overlap, an unprecedented finding that requires replication in other populations and has potential clinical implications considering overlapping cognitive deficits in seasonal affective disorders and schizophrenia.

Published
2015

15. Polygenic Overlap Between Kidney Function and Large Artery Atherosclerotic Stroke

Author

Holliday, E.G., Traylor, M., Malik, R., Bevan, S., Maguire, J., Koblar, S.A., Sturm, J., Hankey, G.J., Oldmeadow, C., McEvoy, M., Sudlow, C., Rothwell, P.M., Coresh, J., Hamet, P., Tremblay, J., Turner, S.T., Andrade, M. de, Rao, M., Schmidt, R., Crick, P.A., Robino, A., Peralta, C.A., Jukema, J.W., Mitchell, P., Rosas, S.E., Wang, J.J., Scott, R.J., Dichgans, M., Mitchell, B.D., Kao, W.H.L., Fox, C.S., Levi, C., Attia, J., Markus, H.S., CKDGen Consortium, and Int Stroke Genetics Consortium

Subjects
medicine.medical_specialty, kidney, genetic epidemiology, Genotype, Renal function, Single-nucleotide polymorphism, Gastroenterology, Polymorphism, Single Nucleotide, Article, chemistry.chemical_compound, Internal medicine, medicine, Humans, Albuminuria, Genetic Predisposition to Disease, Stroke, Advanced and Specialized Nursing, Creatinine, Neurology & Neurosurgery, biology, business.industry, medicine.disease, stroke, Endocrinology, Cystatin C, chemistry, Intima-media thickness, biology.protein, Kidney Diseases, Neurology (clinical), medicine.symptom, Cardiology and Cardiovascular Medicine, business, Kidney disease, Genome-Wide Association Study
Abstract

Background and Purpose— Epidemiological studies show strong associations between kidney dysfunction and risk of ischemic stroke (IS), the mechanisms of which are incompletely understood. We investigated whether these associations may reflect shared heritability because of a common polygenic basis and whether this differed for IS subtypes. Methods— Polygenic models were derived using genome-wide association studies meta-analysis results for 3 kidney traits: estimated glomerular filtration rate using serum creatinine (eGFRcrea: n=73 998), eGFR using cystatin C (eGFRcys: n=22 937), and urinary albumin to creatinine ratio (n=31 580). For each, single nucleotide polymorphisms passing 10 P value thresholds were used to form profile scores in 4561 IS cases and 7094 controls from the United Kingdom, Germany, and Australia. Scores were tested for association with IS and its 3 aetiological subtypes: large artery atherosclerosis, cardioembolism, and small vessel disease. Results— Polygenic scores correlating with higher eGFRcrea were associated with reduced risk of large artery atherosclerosis, with 5 scores reaching P P =0.004) and all showing the epidemiologically expected direction of effect. A similar pattern was observed for polygenic scores reflecting higher urinary albumin to creatinine ratio, of which 3 associated with large artery atherosclerosis (peak P =0.01) and all showed the expected directional association. One urinary albumin to creatinine ratio–based score also associated with small vessel disease ( P =0.03). The global pattern of results was unlikely to have occurred by chance ( P =0.02). Conclusions— This study suggests possible polygenic correlation between renal dysfunction and IS. The shared genetic components may be specific to stroke subtypes, particularly large artery atherosclerotic stroke. Further study of the genetic relationships between these disorders seems merited.

Published
2014

16. Fecundity is a familial trait in the Old Order Amish

Author

Pollin, T.I., Agarwala, R., Schaffer, A.A., Lodge, A.L., King, T.M., Shuldiner, A.R., and Mitchell, B.D.

Subjects
Human genetics -- Research, Fertility -- Genetic aspects, Amish -- Statistics, Quantitative genetics -- Research, Biological sciences
Published
2001

19. Heritability of age at death in the Old Order Amish

Author

Mitchell, B.D., Hsueh, W.-C., King, T.M., Pollin, T.I., Sorkin, J., and Shuldiner, A.R.

Subjects
Genetic research -- Analysis, Human genetics -- Research, Longevity -- Genetic aspects, Amish -- Health aspects, Biological sciences
Published
2000

21. A Meta-Analysis of Thyroid-Related Traits Reveals Novel Loci and Gender-Specific Differences in the Regulation of Thyroid Function

Author

McCarthy, M.I., Porcu, E., Medici, M., Pistis, G., Volpato, C.B., Wilson, S.G., Cappola, A.R., Bos, S.D., Deelen, J., den Heijer, M., Freathy, R.M., Lahti, J., Liu, C., Lopez, L.M., Nolte, I.M., O'Connell, J.R., Tanaka, T., Trompet, S., Arnold, A., Bandinelli, S., Beekman, M., Böhringer, S., Brown, S.J., Buckley, B.M., Camaschella, C., de Craen, A.J.M., Davies, G., de Visser, M.C.H., Ford, I., Forsen, T., Frayling, T.M., Fugazzola, L., Gögele, M., Hattersley, A.T., Hermus, A.R., Hofman, A., Houwing-Duistermaat, J.J., Jensen, R.A., Kajantie, E., Kloppenburg, M., Lim, E.M., Masciullo, C., Mariotti, S., Minelli, C., Mitchell, B.D., Nagaraja, R., Netea-Maier, R.T., Palotie, A., Persani, L., Piras, M.G., Psaty, B.M., Räikkönen, K., Richards, J.B., Rivadeneira, F., Sala, C., Sabra, M.M., Sattar, N., Shields, B.M., Soranzo, N., Starr, J.M., Stott, D.J., Sweep, F.C.G.J., Usala, G., van der Klauw, M.M., van Heemst, D., van Mullem, A., H.Vermeulen, S., Visser, W.E., Walsh, J.P., Westendorp, R.G.J., Widen, E., Zhai, G., Cucca, F., Deary, I.J., Eriksson, J.G., Ferrucci, L., Fox, C.S., Jukema, J.W., Kiemeney, L.A., Pramstaller, P.P., Schlessinger, D., Shuldiner, A.R., Slagboom, E.P., Uitterlinden, A.G., Vaidya, B., Visser, T.J., Wolffenbuttel, B.H.R., Meulenbelt, I., Rotter, J.I., Spector, T.D., Hicks, A.A., Toniolo, D., Sanna, S., Peeters, R.P., Naitza, S., Internal Medicine, Clinical Genetics, Public Health, Epidemiology, Internal medicine, ICaR - Circulation and metabolism, Behavioural Sciences, Clinicum, Department of General Practice and Primary Health Care, Children's Hospital, Lastentautien yksikkö, Institute for Molecular Medicine Finland, Haartman Institute (-2014), Department of Medical and Clinical Genetics, Diabetes and Obesity Research Program, Developmental Psychology Research Group, Genomics of Neurological and Neuropsychiatric Disorders, Genomic Discoveries and Clinical Translation, Life Course Epidemiology (LCE), Lifestyle Medicine (LM), Center for Liver, Digestive and Metabolic Diseases (CLDM), Porcu, E, Medici, M, Pistis, G, Volpato, Cb, Wilson, Sg, Cappola, Ar, Bos, Sd, Deelen, J, DEN HEIJER, M, Freathy, Rm, Lahti, J, Liu, C, Lopez, Lm, Nolte, Im, O'Connell, Jr, Tanaka, T, Trompet, S, Arnold, A, Bandinelli, S, Beekman, M, Böhringer, S, Brown, Sj, Buckley, Bm, Camaschella, Clara, DE CRAEN, Aj, Davies, G, DE VISSER, Mc, Ford, I, Forsen, T, Frayling, Tm, Fugazzola, L, Gögele, M, Hattersley, At, Hermus, Ar, Hofman, A, HOUWING DUISTERMAAT, Jj, Jensen, Ra, Kajantie, E, Kloppenburg, M, Lim, Em, Masciullo, C, Mariotti, S, Minelli, C, Mitchell, Bd, Nagaraja, R, NETEA MAIER, Rt, Palotie, A, Persani, L, Piras, Mg, Psaty, Bm, Räikkönen, K, Richards, Jb, Rivadeneira, F, Sala, C, Sabra, Mm, Sattar, N, Shields, Bm, Soranzo, N, Starr, Jm, Stott, Dj, Sweep, Fc, Usala, G, VAN DER KLAUW, Mm, VAN HEEMST, D, VAN MULLEM, A, Vermeulen, Sh, Visser, We, Walsh, Jp, Westendorp, Rg, Widen, E, Zhai, G, Cucca, F, Deary, Ij, Eriksson, Jg, Ferrucci, L, Fox, C, Jukema, Jw, Kiemeney, La, Pramstaller, Pp, Schlessinger, D, Shuldiner, Ar, Slagboom, Ep, Uitterlinden, Ag, Vaidya, B, Visser, Tj, Wolffenbuttel, Bh, Meulenbelt, I, Rotter, Ji, Spector, Td, Hicks, Aa, Toniolo, D, Sanna, S, Peeters, Rp, and Naitza, S.

Subjects
Male, Cancer Research, endocrine system diseases, Factor binding protein 5, Thyroid Gland, FACTOR BINDING PROTEIN-5, Thyrotropin, Genome-wide association study, Expression, Aetiology, screening and detection [ONCOL 5], Growth, Hyperthyroidism, CLEFT-PALATE, Serum TSH, 0302 clinical medicine, Euthyroid, Genetics (clinical), 0303 health sciences, Sex Characteristics, factor binding protein-S, Thyroid, 3. Good health, medicine.anatomical_structure, Phenotype, NFIA, Cleft palate, GROWTH, Genome wide Association, Female, Thyroid function, hormones, hormone substitutes, and hormone antagonists, Research Article, Signal Transduction, EXPRESSION, medicine.medical_specialty, endocrine system, lcsh:QH426-470, cleft-palate, 515 Psychology, education, 030209 endocrinology & metabolism, Biology, Polymorphism, Single Nucleotide, Molecular epidemiology [NCEBP 1], 03 medical and health sciences, Thyroid-stimulating hormone, Hypothyroidism, SERUM TSH, Internal medicine, medicine, Genetics, Humans, Hormonal regulation Translational research [IGMD 6], GENOME-WIDE ASSOCIATION, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Health aging / healthy living Cardiovascular diseases [IGMD 5], 030304 developmental biology, Molecular epidemiology Aetiology, screening and detection [NCEBP 1], Polymorphism, Genetic, THYROTROPIN, HORMONE PATHWAY GENES, Hormonal regulation [IGMD 6], R1, Thyroxine, Common variation, lcsh:Genetics, Endocrinology, HYPOTHYROIDISM, Hormone pathway genes, genome-wide association, Hormonal regulation Aetiology, screening and detection [IGMD 6], 3111 Biomedicine, COMMON VARIATION, Hormone, FOXE1, Genome-Wide Association Study, Developmental Biology
Abstract

Thyroid hormone is essential for normal metabolism and development, and overt abnormalities in thyroid function lead to common endocrine disorders affecting approximately 10% of individuals over their life span. In addition, even mild alterations in thyroid function are associated with weight changes, atrial fibrillation, osteoporosis, and psychiatric disorders. To identify novel variants underlying thyroid function, we performed a large meta-analysis of genome-wide association studies for serum levels of the highly heritable thyroid function markers TSH and FT4, in up to 26,420 and 17,520 euthyroid subjects, respectively. Here we report 26 independent associations, including several novel loci for TSH (PDE10A, VEGFA, IGFBP5, NFIA, SOX9, PRDM11, FGF7, INSR, ABO, MIR1179, NRG1, MBIP, ITPK1, SASH1, GLIS3) and FT4 (LHX3, FOXE1, AADAT, NETO1/FBXO15, LPCAT2/CAPNS2). Notably, only limited overlap was detected between TSH and FT4 associated signals, in spite of the feedback regulation of their circulating levels by the hypothalamic-pituitary-thyroid axis. Five of the reported loci (PDE8B, PDE10A, MAF/LOC440389, NETO1/FBXO15, and LPCAT2/CAPNS2) show strong gender-specific differences, which offer clues for the known sexual dimorphism in thyroid function and related pathologies. Importantly, the TSH-associated loci contribute not only to variation within the normal range, but also to TSH values outside the reference range, suggesting that they may be involved in thyroid dysfunction. Overall, our findings explain, respectively, 5.64% and 2.30% of total TSH and FT4 trait variance, and they improve the current knowledge of the regulation of hypothalamic-pituitary-thyroid axis function and the consequences of genetic variation for hypo- or hyperthyroidism., Author Summary Levels of thyroid hormones are tightly regulated by TSH produced in the pituitary, and even mild alterations in their concentrations are strong indicators of thyroid pathologies, which are very common worldwide. To identify common genetic variants associated with the highly heritable markers of thyroid function, TSH and FT4, we conducted a meta-analysis of genome-wide association studies in 26,420 and 17,520 individuals, respectively, of European ancestry with normal thyroid function. Our analysis identified 26 independent genetic variants regulating these traits, several of which are new, and confirmed previously detected polymorphisms affecting TSH (within the PDE8B gene and near CAPZB, MAF/LOC440389, and NR3C2) and FT4 (within DIO1) levels. Gender-specific differences in the genetic effects of several variants for TSH and FT4 levels were identified at several loci, which offer clues to understand the known sexual dimorphism in thyroid function and pathology. Of particular clinical interest, we show that TSH-associated loci contribute not only to normal variation, but also to TSH values outside reference range, suggesting that they may be involved in thyroid dysfunction. Overall, our findings add to the developing landscape of the regulation of thyroid homeostasis and the consequences of genetic variation for thyroid related diseases.

Published
2013

22. Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture

Author

Estrada, K. Styrkarsdottir, U. Evangelou, E. Hsu, Y.-H. Duncan, E.L. Ntzani, E.E. Oei, L. Albagha, O.M.E. Amin, N. Kemp, J.P. Koller, D.L. Li, G. Liu, C.-T. Minster, R.L. Moayyeri, A. Vandenput, L. Willner, D. Xiao, S.-M. Yerges-Armstrong, L.M. Zheng, H.-F. Alonso, N. Eriksson, J. Kammerer, C.M. Kaptoge, S.K. Leo, P.J. Thorleifsson, G. Wilson, S.G. Wilson, J.F. Aalto, V. Alen, M. Aragaki, A.K. Aspelund, T. Center, J.R. Dailiana, Z. Duggan, D.J. Garcia, M. Garcia-Giralt, N. Giroux, S. Hallmans, G. Hocking, L.J. Husted, L.B. Jameson, K.A. Khusainova, R. Kim, G.S. Kooperberg, C. Koromila, T. Kruk, M. Laaksonen, M. Lacroix, A.Z. Lee, S.H. Leung, P.C. Lewis, J.R. Masi, L. Mencej-Bedrac, S. Nguyen, T.V. Nogues, X. Patel, M.S. Prezelj, J. Rose, L.M. Scollen, S. Siggeirsdottir, K. Smith, A.V. Svensson, O. Trompet, S. Trummer, O. Van Schoor, N.M. Woo, J. Zhu, K. Balcells, S. Brandi, M.L. Buckley, B.M. Cheng, S. Christiansen, C. Cooper, C. Dedoussis, G. Ford, I. Frost, M. Goltzman, D. González-Macías, J. Kähönen, M. Karlsson, M. Khusnutdinova, E. Koh, J.-M. Kollia, P. Langdahl, B.L. Leslie, W.D. Lips, P. Ljunggren, O. Lorenc, R.S. Marc, J. Mellström, D. Obermayer-Pietsch, B. Olmos, J.M. Pettersson-Kymmer, U. Reid, D.M. Riancho, J.A. Ridker, P.M. Rousseau, F. Lagboom, P.E.S. Tang, N.L.S. Urreizti, R. Van Hul, W. Viikari, J. Zarrabeitia, M.T. Aulchenko, Y.S. Castano-Betancourt, M. Grundberg, E. Herrera, L. Ingvarsson, T. Johannsdottir, H. Kwan, T. Li, R. Luben, R. Medina-Gómez, C. Th Palsson, S. Reppe, S. Rotter, J.I. Sigurdsson, G. Van Meurs, J.B.J. Verlaan, D. Williams, F.M.K. Wood, A.R. Zhou, Y. Gautvik, K.M. Pastinen, T. Raychaudhuri, S. Cauley, J.A. Chasman, D.I. Clark, G.R. Cummings, S.R. Danoy, P. Dennison, E.M. Eastell, R. Eisman, J.A. Gudnason, V. Hofman, A. Jackson, R.D. Jones, G. Jukema, J.W. Khaw, K.-T. Lehtimäki, T. Liu, Y. Lorentzon, M. Mccloskey, E. Mitchell, B.D. Nandakumar, K. Nicholson, G.C. Oostra, B.A. Peacock, M. Pols, H.A.P. Prince, R.L. Raitakari, O. Reid, I.R. Robbins, J. Sambrook, P.N. Sham, P.C. Shuldiner, A.R. Tylavsky, F.A. Van Duijn, C.M. Wareham, N.J. Cupples, L.A. Econs, M.J. Evans, D.M. Harris, T.B. Kung, A.W.C. Psaty, B.M. Reeve, J. Spector, T.D. Streeten, E.A. Zillikens, M.C. Thorsteinsdottir, U. Ohlsson, C. Karasik, D. Richards, J.B. Brown, M.A. Stefansson, K. Uitterlinden, A.G. Ralston, S.H. Ioannidis, J.P.A. Kiel, D.P. Rivadeneira, F.

Subjects
musculoskeletal diseases
Abstract

Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top BMD-associated markers for replication in 50,933 independent subjects and for association with risk of low-trauma fracture in 31,016 individuals with a history of fracture (cases) and 102,444 controls. We identified 56 loci (32 new) associated with BMD at genome-wide significance (P < 5 × 10 -8). Several of these factors cluster within the RANK-RANKL-OPG, mesenchymal stem cell differentiation, endochondral ossification and Wnt signaling pathways. However, we also discovered loci that were localized to genes not known to have a role in bone biology. Fourteen BMD-associated loci were also associated with fracture risk (P < 5 × 10 -4, Bonferroni corrected), of which six reached P < 5 × 10 -8, including at 18p11.21 (FAM210A), 7q21.3 (SLC25A13), 11q13.2 (LRP5), 4q22.1 (MEPE), 2p16.2 (SPTBN1) and 10q21.1 (DKK1). These findings shed light on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility. © 2012 Nature America, Inc. All rights reserved.

Published
2012

23. Elevated peripheral blood leukocyte inflammatory gene expression in radiographic progressors with symptomatic knee osteoarthritis: NYU and OAI cohorts

Author

Attur, M., primary, Statnikov, A., additional, Krasnokutsky, S., additional, Kraus, V., additional, Jordan, J.M., additional, Mitchell, B.D., additional, Yau, M., additional, Patel, J., additional, Aliferis, C.F., additional, Hochberg, M., additional, Samuels, J., additional, and Abramson, S.B., additional

Published
2015
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30. Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits

Author

Speliotes, E.K., Yerges-Armstrong, L.M., Wu, J., Hernaez, R., Kim, L.J., Palmer, C.D., Gudnason, V., Eiriksdottir, G., Garcia, M.E., Launer, L.J., Nalls, M.A., Clark, J.M., Mitchell, B.D., Shuldiner, A.R., Butler, J.L., Tomas, M., Hoffmann, U., Hwang, S.J., Massaro, J.M., O'Donnell, C.J., Sahani, D.V., Salomaa, V., Schadt, E.E., Schwartz, S.M., Siscovick, D.S., Voight, B.F., Carr, J.J., Feitosa, M.F., Harris, T.B., Fox, C.S., Smith, A.V., Kao, W.H., Hirschhorn, J.N., Borecki, I.B., and Heijer, M. den

Subjects
Molecular epidemiology [NCEBP 1], Hormonal regulation [IGMD 6]
Abstract

Contains fulltext : 95930.pdf (Author’s version postprint ) (Open Access) Nonalcoholic fatty liver disease (NAFLD) clusters in families, but the only known common genetic variants influencing risk are near PNPLA3. We sought to identify additional genetic variants influencing NAFLD using genome-wide association (GWA) analysis of computed tomography (CT) measured hepatic steatosis, a non-invasive measure of NAFLD, in large population based samples. Using variance components methods, we show that CT hepatic steatosis is heritable ( approximately 26%-27%) in family-based Amish, Family Heart, and Framingham Heart Studies (n = 880 to 3,070). By carrying out a fixed-effects meta-analysis of genome-wide association (GWA) results between CT hepatic steatosis and approximately 2.4 million imputed or genotyped SNPs in 7,176 individuals from the Old Order Amish, Age, Gene/Environment Susceptibility-Reykjavik study (AGES), Family Heart, and Framingham Heart Studies, we identify variants associated at genome-wide significant levels (p

Published
2011

31. Reducing feed costs in semi-intensive finfish culture: an update on mixed feeding schedules and an idea for enhancing endogenous food supply in ponds

Author

De Silva, S.S., Mitchell, B.D., and Nandeesha, M.C.

Subjects
Fish culture, Feed, jel:Q00, Feeding, Cost analysis, Aquaculture, Pond culture, Fish culture, Feed, Cost analysis, Feeding, Pond culture
Abstract

Some interesting ideas on improving the cost-effectiveness of feeding in semi-intensive finfish aquaculture are presented.

Published
1993

35. Constitutive and Induced Neurogenesis in the Adult Mammalian Brain: Manipulation of Endogenous Precursors toward CNS Repair

Author

Mitchell, B.D., Emsley, J.G., Magavi, S.S.P., Arlotta, P., and Macklis, J.D.

Abstract

AbstractOver most of the past century of modern neuroscience, it was thought that the adult brain was completely incapable of generating new neurons. During the past 3 decades, research exploring potential neuronal replacement therapies has focused on replacing lost neurons by transplanting cells or grafting tissue into diseased regions of the brain. However, in the last decade, the development of new techniques has resulted in an explosion of new research showing that neurogenesis, the birth of new neurons, normally occurs in two limited and specific regions of the adult mammalian brain and that there are significant numbers of multipotent neural precursors in many parts of the adult mammalian brain. Recent advances in our understanding of related events of neural development and plasticity, including the role of radial glia in developmental neurogenesis and the ability of endogenous precursors present in the adult brain to be induced to produce neurons and partially repopulate brain regions affected by neurodegenerative processes, have led to fundamental changes in the views about how the brain develops as well as to approaches by which endogenous precursors might be recruited to repair the adult brain. Recruitment of new neurons can be induced in a region-specific, layer-specific and neuronal-type-specific manner, and, in some cases, newly recruited neurons can form long-distance connections to appropriate targets. Elucidation of the relevant molecular controls may both allow control over transplanted precursor cells and potentially allow the development of neuronal replacement therapies for neurodegenerative disease and other CNS injuries that do not require transplantation of exogenous cells.Copyright © 2004 S. Karger AG, Basel

Published
2004

36. The Application of Alkali Dissolution Techniques in the Study of Aluminium Hydroxides and Oxyhydroxides

Author

Storgaard Jørgensen, S. and Mitchell, B.D.

Abstract

The effect of treatment with 5% sodium carbonate solution on aluminium hydroxides and oxyhydroxides likely to occur in soils has been investigated. Ultrasonic pretreatment, sample to solution ratio and temperature were factors studied. It is shown that particle size and degree of order of the sample influence the amount of alumina dissolved in 5% sodium carbonate solution in a fixed time; it is apparent, however, that both dissolution rate and solubility can be determining factors. Consequently, extraction with alkali at a low temperature and with a low solid: solution ratio is desirable for the preferential dissolution of poorly‐ordered aluminous material from soil clays.

Published
1970
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45. Rare variant in scavenger receptor BI raises HDL cholesterol and increases risk of coronary heart disease

Author

Zanoni, P., Khetarpal, S.A., Larach, D.B., Hancock-Cerutti, W.F., Millar, J.S., Cuchel, M., Derohannessian, S.L., Kontush, A., Surendran, P., Saleheen, D., Trompet, S., Jukema, J.W., de Craen, A.J., Deloukas, P., Sattar, N., Ford, I., Packard, C., Al Shafi Majumder, A., Alam, D.S., di Angelantonio, E., Abecasis, G., Chowdhury, R., Erdmann, J., Nørdestgaard, B.G., Nielsen, S.F., Tybjærg-Hansen, A., Schmidt, R.F., Kuulasmaa, K., Liu, D.J., Perola, M., Blankenberg, S., Salomaa, V., Männistö, S., Amouyel, P., Arveiler, D., Ferrieres, J., Müller-Nurasyid, M., Ferrario, M., Kee, F., Willer, C.J., Samani, N., Schunkert, H., Butterworth, A.S., Howson, J.M.M., Peloso, G.M., Stitziel, N.O., Danesh, J., Kathiresan, S., Rader, D.J., CHD Exome Consortium (), CARDIoGRAM Exome Consortium (), Global Lipids Genetics Consortium (), CHD Exome+ Consortium, CARDIoGRAM Exome Consortium, Global Lipids Genetics Consortium, Watson, S., Schmidt, E.M., Sengupta, S., Gustafsson, S., Kanoni, S., Ganna, A., Chen, J., Buchkovich, M.L., Mora, S., Beckmann, J.S., Bragg-Gresham, J.L., Chang, H.Y., Demirkan, A., Den Hertog, H.M., Do, R., Donnelly, L.A., Ehret, G.B., Esko, T., Feitosa, M.F., Ferreira, T., Fischer, K., Fontanillas, P., Fraser, R.M., Freitag, D.F., Gurdasani, D., Heikkilä, K., Hyppönen, E., Isaacs, A., Jackson, A.U., Johansson, Å., Johnson, T., Kaakinen, M., Kettunen, J., Kleber, M.E., Li, X., Luan, J., Lyytikäinen, L.P., Magnusson, P.K., Mangino, M., Mihailov, E., Montasser, M.E., Nolte, I.M., O'Connell, J.R., Palmer, C.D., Petersen, A.K., Sanna, S., Saxena, R., Service, S.K., Shah, S., Shungin, D., Sidore, C., Song, C., Strawbridge, R.J., Surakka, I., Tanaka, T., Teslovich, T.M., Thorleifsson, G., Van den Herik, E.G., Voight, B.F., Volcik, K.A., Waite, L.L., Wong, A., Wu, Y., Zhang, W., Absher, D., Asiki, G., Barroso, I., Been, L.F., Bolton, J.L., Bonnycastle, L.L., Brambilla, P., Burnett, M.S., Cesana, G., Dimitriou, M., Doney, A.S., Döring, A., Elliott, P., Epstein, S.E., Eyjolfsson, G.I., Gigante, B., Goodarzi, M.O., Grallert, H., Gravito, M.L., Groves, C.J., Hallmans, G., Hartikainen, A.L., Hayward, C., Hernandez, D., Hicks, A.A., Holm, H., Hung, Y.J., Illig, T., Jones, M.R., Kaleebu, P., Kastelein, J.J., Khaw, K.T., Kim, E., Klopp, N., Komulainen, P., Kumari, M., Langenberg, C., Lehtimäki, T., Lin, S.Y., Lindström, J., Loos, R.J., Mach, F., McArdle, W.L., Meisinger, C., Mitchell, B.D., Müller, G., Nagaraja, R., Narisu, N., Nieminen, T.V., Nsubuga, R.N., Olafsson, I., Ong, K.K., Palotie, A., Papamarkou, T., Pomilla, C., Pouta, A., Reilly, M.P., Ridker, P.M., Rivadeneira, F., Rudan, I., Ruokonen, A., Scharnagl, H., Seeley, J., Silander, K., Stancáková, A., Stirrups, K., Swift, A.J., Tiret, L., Uitterlinden, A.G., van Pelt, L.J., Vedantam, S., Wainwright, N., Wijmenga, C., Wild, S.H., Willemsen, G., Wilsgaard, T., Wilson, J.F., Young, E.H., Zhao, J.H., Adair, L.S., Arveiler, D., Assimes, T.L., Bandinelli, S., Bennett, F., Bochud, M., Boehm, B.O., Boomsma, D.I., Borecki, I.B., Bornstein, S.R., Bovet, P., Burnier, M., Campbell, H., Chakravarti, A., Chambers, J.C., Chen, Y.D., Collins, F.S., Cooper, R.S., Dedoussis, G., de Faire, U., Feranil, A.B., Ferrucci, L., Freimer, N.B., Gieger, C., Groop, L.C., Gudnason, V., Gyllensten, U., Hamsten, A., Harris, T.B., Hingorani, A., Hirschhorn, J.N., Hofman, A., Hovingh, G.K., Hsiung, C.A., Humphries, S.E., Hunt, S.C., Hveem, K., Iribarren, C., Järvelin, M.R., Jula, A., Kähönen, M., Kaprio, J., Kesäniemi, A., Kivimaki, M., Kooner, J.S., Koudstaal, P.J., Krauss, R.M., Kuh, D., Kuusisto, J., Kyvik, K.O., Laakso, M., Lakka, T.A., Lind, L., Lindgren, C.M., Martin, N.G., März, W., McCarthy, M.I., McKenzie, C.A., Meneton, P., Metspalu, A., Moilanen, L., Morris, A.D., Munroe, P.B., Njølstad, I., Pedersen, N.L., Power, C., Pramstaller, P.P., Price, J.F., Psaty, B.M., Quertermous, T., Rauramaa, R., Salomaa, V., Sanghera, D.K., Saramies, J., Schwarz, P.E., Sheu, W.H., Shuldiner, A.R., Siegbahn, A., Spector, T.D., Stefansson, K., Strachan, D.P., Tayo, B.O., Tremoli, E., Tuomilehto, J., Uusitupa, M., van Duijn, C.M., Vollenweider, P., Wallentin, L., Wareham, N.J., Whitfield, J.B., Wolffenbuttel, B.H., Ordovas, J.M., Boerwinkle, E., Palmer, C.N., Thorsteinsdottir, U., Chasman, D.I., Rotter, J.I., Franks, P.W., Riatti, S., Cupples, L.A., Sandhu, M.S., Rich, S.S., Boehnke, M., Deloukas, P., Mohlke, K.L., Ingelsson, E., Gu, D., Roberts, R., Watkins, H., Blankenberg, S., Clarke, R., Collins, R., Kim, B.J., McPherson, R., Nieminen, M.S., O'Donnell, C., Schreiber, S., Zalloua, P.A., Zanoni, P, Khetarpal, SA, Larach, DB, Hancock-Cerutti, WF, Rader, DJ, Hypponen, Elina, Biological Psychology, Khetarpal, S, Larach, D, Hancock Cerutti, W, Millar, J, Cuchel, M, Derohannessian, S, Kontush, A, Surendran, P, Saleheen, D, Trompet, S, Wouter Jukema, J, De Craen, A, Deloukas, P, Sattar, N, Ford, I, Packard, C, Majumder, A, Alam, D, Di Angelantonio, E, Abecasis, G, Chowdhury, R, Erdmann, J, Nordestgaard, B, Nielsen, S, Tybjærg Hansen, A, Ruth Frikke Schmidt, N, Kuulasmaa, K, Liu, D, Perola, M, Blankenberg, S, Salomaa, V, Männistö, S, Amouyel, P, Arveiler, D, Ferrieres, J, Möller Nurasyid, M, Ferrario, M, Kee, F, Willer, C, Samani, N, Schunkert, H, Butterworth, A, Howson, J, Peloso, G, Stitziel, N, Danesh, J, Kathiresan, S, Rader, D, Brambilla, P, ACS - Amsterdam Cardiovascular Sciences, and Vascular Medicine

Subjects
Netherlands Twin Register (NTR), 0301 basic medicine, Male, BIO/12 - BIOCHIMICA CLINICA E BIOLOGIA MOLECOLARE CLINICA, Scavenger Receptors, DNA Mutational Analysis, Coronary Disease, 030204 cardiovascular system & hematology, scavenger receptor, chemistry.chemical_compound, Mice, 0302 clinical medicine, High-density lipoprotein, Receptor, increased atherosclerosis, levels of plasma, Multidisciplinary, Medicine (all), Homozygote, Scavenger Receptors, Class B, Middle Aged, 3. Good health, Cholesterol, Knockout mouse, Female, lipids (amino acids, peptides, and proteins), Human, Risk, medicine.medical_specialty, Heterozygote, HDL, Proline, Aged, Amino Acid Substitution, Animals, Cholesterol, HDL, Genetic Variation, Humans, Leucine, Protein Processing, Post-Translational, Article, DNA Mutational Analysi, Cholesterol, HDL/blood, Coronary Disease/blood, Coronary Disease/genetics, Leucine/genetics, Proline/genetics, Scavenger Receptors, Class B/genetics, Scavenger Receptors, Class B/metabolism, 03 medical and health sciences, Internal medicine, medicine, Scavenger receptor, Protein Processing, Animal, business.industry, Post-Translational, Heterozygote advantage, SCARB1, 030104 developmental biology, Endocrinology, chemistry, Class B, business, Lipoprotein
Abstract

Scavenger receptor BI (SR-BI) is the major receptor for high-density lipoprotein (HDL) cholesterol (HDL-C). In humans, high amounts of HDL-C in plasma are associated with a lower risk of coronary heart disease (CHD). Mice that have depleted Scarb1 (SR-BI knockout mice) have markedly elevated HDL-C levels but, paradoxically, increased atherosclerosis. The impact of SR-BI on HDL metabolism and CHD risk in humans remains unclear. Through targeted sequencing of coding regions of lipid-modifying genes in 328 individuals with extremely high plasma HDL-C levels, we identified a homozygote for a lossof-function variant, in which leucine replaces proline 376 (P376L), in SCARB1, the gene encoding SR-BI. The P376L variant impairs posttranslational processing of SR-BI and abrogates selective HDL cholesterol uptake in transfected cells, in hepatocyte-like cells derived from induced pluripotent stem cells from the homozygous subject, and in mice. Large population-based studies revealed that subjects who are heterozygous carriers of the P376L variant have significantly increased levels of plasma HDL-C. P376L carriers have a profound HDL-related phenotype and an increased risk of CHD (odds ratio = 1.79, which is statistically significant). Zanoni P, Khetarpal SA, Larach DB, Hancock-Cerutti WF, Millar JS, Cuchel M, DerOhannessian S, Kontush A, Surendran P, Saleheen D, Trompet S, Jukema JW, De Craen A, Deloukas P, Sattar N, Ford I, Packard C, Majumder Aa, Alam DS, Di Angelantonio E, Science (New York, N.Y.), 2016, vol. 351, no. 6278, pp. 1166-1171, 2016 Refereed/Peer-reviewed

Published
2016

46. Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations

Author

Okada, Y, Sim, X, Go, Mj, Wu, Jy, Gu, D, Takeuchi, F, Takahashi, A, Maeda, S, Tsunoda, T, Chen, P, Lim, Sc, Wong, Ty, Liu, J, Young, Tl, Aung, T, Seielstad, M, Teo, Yy, Kim, Yj, Lee, Jy, Han, Bg, Kang, D, Chen, Ch, Tsai, Fj, Chang, Lc, Fann, Sj, Mei, H, Rao, Dc, Hixson, Je, Chen, S, Katsuya, T, Isono, M, Ogihara, T, Chambers, Jc, Zhang, W, Kooner, Js, Kidneygen, Consortium, Ckdgen, Consortium, Albrecht, E, Gugc, Consortium, Yamamoto, K, Kubo, M, Nakamura, Y, Kamatani, N, Kato, N, He, J, Chen, Yt, Cho, Ys, Tai, Es, Tanaka, T., Lord, Gm, van der Harst, P, Lawlor, Da, Sehmi, Js, Gale, Dp, Wass, Mn, Ahmadi, Kr, Bakker, Sj, Beckmann, J, Bilo, Hj, Bochud, M, Brown, Mj, Caulfield, Mj, Connell, Jm, Cook, Ht, Cotlarciuc, I, Smith, Gd, de Silva, R, Deng, G, Devuyst, O, Dikkeschei, Ld, Dimkovic, N, Dockrell, M, Dominiczak, A, Ebrahim, S, Eggermann, T, Farrall, M, Ferrucci, L, Floege, J, Forouhi, Ng, Gansevoort, Rt, Han, X, Hedblad, B, van der Heide JJ, Hepkema, Bg, Hernandez Fuentes, M, Hypponen, E, Johnson, T, de Jong PE, Kleefstra, N, Lagou, V, Lapsley, M, Li, Y, Loos, Rj, Luan, J, Luttropp, K, Maréchal, C, Melander, O, Munroe, Pb, Nordfors, L, Parsa, A, Peltonen, L, Penninx, Bw, Perucha, E, Pouta, A, Prokopenko, I, Roderick, Pj, Ruokonen, A, Samani, Nj, Sanna, S, Schalling, M, Schlessinger, D, Schlieper, G, Seelen, Ma, Shuldiner, Ar, Sjögren, M, Smit, Jh, Snieder, H, Soranzo, N, Spector, Td, Stenvinkel, P, Sternberg, Mj, Swaminathan, R, Tanaka, T, Ubink Veltmaat LJ, Uda, M, Vollenweider, P, Wallace, C, Waterworth, D, Zerres, K, Waeber, G, Wareham, Nj, Maxwell, Ph, Mccarthy, Mi, Jarvelin, Mr, Mooser, V, Abecasis, Gr, Lightstone, L, Scott, J, Navis, G, Elliott, P, Köttgen, A, Pattaro, C, Böger, Ca, Fuchsberger, C, Olden, M, Glazer, Nl, Gao, X, Yang, Q, Smith, Av, O'Connell, Jr, Li, M, Schmidt, H, Isaacs, A, Ketkar, S, Hwang, Sj, Johnson, Ad, Dehghan, A, Teumer, A, Paré, G, Atkinson, Ej, Zeller, T, Lohman, K, Cornelis, Mc, Probst Hensch NM, Kronenberg, F, Tönjes, A, Hayward, C, 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D.P., Wass, M.N., Ahmadi, K.R., Bakker, S.J., Beckmann, J., Bilo, H.J., Bochud, M., Brown, M.J., Caulfield, M.J., Connell, J.M., Cook, H.T., Cotlarciuc, I., Smith, G.D., de Silva, R., Deng, G., Devuyst, O., Dikkeschei, L.D., Dimkovic, N., Dockrell, M., Dominiczak, A., Ebrahim, S., Eggermann, T., Farrall, M., Ferrucci, L., Floege, J., Forouhi, N.G., Gansevoort, R.T., Han, X., Hedblad, B., van der Heide, J.J., Hepkema, B.G., Hernandez-Fuentes, M., Hypponen, E., Johnson, T., de Jong, P.E., Kleefstra, N., Lagou, V., Lapsley, M., Li, Y., Loos, R.J., Luan, J., Luttropp, K., Maréchal, C., Melander, O., Munroe, P.B., Nordfors, L., Parsa, A., Peltonen, L., Penninx, B.W., Perucha, E., Pouta, A., Prokopenko, I., Roderick, P.J., Ruokonen, A., Samani, N.J., Sanna, S., Schalling, M., Schlessinger, D., Schlieper, G., Seelen, M.A., Shuldiner, A.R., Sjögren, M., Smit, J.H., Snieder, H., Soranzo, N., Spector, T.D., Stenvinkel, P., Sternberg, M.J., Swaminathan, R., Tanaka, T., Ubink-Veltmaat, L.J., Uda, M., Vollenweider, P., Wallace, C., Waterworth, D., Zerres, K., Waeber, G., Wareham, N.J., Maxwell, P.H., McCarthy, M.I., Jarvelin, M.R., Mooser, V., Abecasis, G.R., Lightstone, L., Scott, J., Navis, G., Elliott, P., Kooner, J.S., Köttgen, A., Pattaro, C., Böger, C.A., Fuchsberger, C., Olden, M., Glazer, N.L., Gao, X., Yang, Q., Smith, A.V., O'Connell, J.R., Li, M., Schmidt, H., Isaacs, A., Ketkar, S., Hwang, S.J., Johnson, A.D., Dehghan, A., Teumer, A., Paré, G., Atkinson, E.J., Zeller, T., Lohman, K., Cornelis, M.C., Probst-Hensch, N.M., Kronenberg, F., Tönjes, A., Hayward, C., Aspelund, T., Eiriksdottir, G., Launer, L.J., Harris, T.B., Rampersaud, E., Mitchell, B.D., Arking, D.E., Boerwinkle, E., Struchalin, M., Cavalieri, M., Singleton, A., Giallauria, F., Metter, J., de Boer, I.H., Haritunians, T., Lumley, T., Siscovick, D., Psaty, B.M., Zillikens, M.C., Oostra, B.A., Feitosa, M., Province, M., de Andrade, M., Turner, S.T., Schillert, A., Ziegler, A., Wild, P.S., Schnabel, R.B., Wilde, S., Munzel, T.F., Leak, T.S., Illig, T., Klopp, N., Meisinger, C., Wichmann, H.E., Koenig, W., Zgaga, L., Zemunik, T., Kolcic, I., Minelli, C., Hu, F.B., Johansson, Å., Igl, W., Zaboli, G., Wild, S.H., Wright, A.F., Campbell, H., Ellinghaus, D., Schreiber, S., Aulchenko, Y.S., Felix, J.F., Rivadeneira, F., Uitterlinden, A.G., Hofman, A., Imboden, M., Nitsch, D., Brandstätter, A., Kollerits, B., Kedenko, L., Mägi, R., Stumvoll, M., Kovacs, P., Boban, M., Campbell, S., Endlich, K., Völzke, H., Kroemer, H.K., Nauck, M., Völker, U., Polasek, O., Vitart, V., Badola, S., Parker, A.N., Ridker, P.M., Kardia, S.L., Blankenberg, S., Liu, Y., Curhan, G.C., Franke, A., Rochat, T., Paulweber, B., Wang, W., Gudnason, V., Coresh, J., Schmidt, R., Shlipak, M.G., van Duijn, C.M., Borecki, I., Krämer, B.K., Rudan, I., Gyllensten, U., Wilson, J.F., Witteman, J.C., Pramstaller, P.P., Rettig, R., Hastie, N., Chasman, D.I., Kao, W.H., Heid, I.M., Fox, C.S., Albrecht, E., Krumsiek, J., Hundertmark, C., Pistis, G., Ruggiero, D., O'Seaghdha, M., Haller, T., Kutalik, Z., Shi, J., Middelberg, P.S., Gaffo, A.L., Pirastu, N., Li, G., Huffman, J., Yengo, L., Zhao, J.H., Demirkan, A., Feitosa, M.F., Liu, X., Malerba, G., Lopez, L.M., Li, X., Kleber, M.E., Hicks, A.A., Nolte, I.M., Johansson, A., Murgia, F., Peden, J.F., Steri, M., Tenesa, A., Salo, P., Mangino, M., Rose, L.M., Lehtimäki, T., Woodward, O.M., Okada, Y., Tin, A., Müller, C., Oldmeadow, C., Putku, M., Czamara, D., Kraft, P., Frogheri, L., Thun, G.A., Grotevendt, A., Gislason, G.K., McArdle, P., Schallert, M., Martin, N.G., Montgomery, G.W., Kubo, M., Nakamura, Y., Jacobs, D.R., Liu, K., D'Adamo, P., Ulivi, S., Rotter, J.I., Navaro, P., Balkau, B., Froguel, P., Esko, T., Salumets, A., Khaw, K.T., Langenberg, C., Kraja, A., Zhang, Q., Scott, R.J., Holliday, E.G., Org, E., Viigimaa, M., Bandinelli, S., Metter, J.E., Lupo, A., Trabetti, E., Sorice, R., Döring, A., Lattka, E., Strauch, K., Theis, F., Waldenberger, M., Davies, G., Gow, A.J., Bruinenberg, M., Stolk, R.P., Winkelmann, B.R., Boehm, B.O., Lucae, S., Curhan, G., Mudgal, P., Plenge, R.M., Portas, L., Persico, I., Kirin, M., Mateo Leach, I., van Gilst, W.H., Goel, A., Ongen, H., von Eckardstein, A., Cucca, F., Nagaraja, R., Piras, M.G., Schurmann, C., Budde, K., Ernst, F., Farrington, S.M., Theodoratou, E., Jula, A., Perola, M., Salomaa, V., Shin, S.Y., Sala, C., Kähönen, M., Viikari, J., Hengstenberg, C., Nelson, C.P., Meschia, J.F., Nalls, M.A., Sharma, P., Singleton, A.B., Kamatani, N., Burnier, M., Attia, J., Laan, M., Hillege, H.L., Kloiber, S., Choi, H., Pirastu, M., Tore, S., Whitfield, J.B., Fornage, M., Gasparini, P., Siscovick, D.S., Bouatia-Naji, N., Metspalu, A., Borecki, I.B., Gambaro, G., Deary, I.J., Wolffenbuttel, B.H., März, W., Watkins, H., Schipf, S., Dunlop, M.G., Ripatti, S., Toniolo, D., Raitakari, O., Ciullo, M., Caulfield, M., Obstetrics & Gynecology, Medical Informatics, Okada, Yukinori, Sim, Xueling, Go, Min Jin, Wu, Jer-Yuarn, Gu, Dongfeng, Takeuchi, Fumihiko, Takahashi, Atsushi, Maeda, Shiro, Tsunoda, Tatsuhiko, Chen, Peng, Lim, Su-Chi, Wong, Tien-Yin, Liu, Jianjun, Young, Terri L., Aung, Tin, Seielstad, Mark, Teo, Yik-Ying, Kim, Young Jin, Lee, Jong-Young, Han, Bok-Ghee, Kang, Daehee, Chen, Chien-Hsiun, Tsai, Fuu-Jen, Chang, Li-Ching, Cathy Fann, S. -J. C., Mei, Hao, Rao, Dabeeru C., Hixson, James E., Chen, Shufeng, Katsuya, Tomohiro, Isono, Masato, Ogihara, Toshio, Chambers, John C., Zhang, Weihua, Kooner, Jaspal S., Albrecht, Eva, Yamamoto, Kazuhiko, Kubo, Michiaki, Nakamura, Yusuke, Kamatani, Naoyuki, Kato, Norihiro, He, Jiang, Chen, Yuan-Tsong, Cho, Yoon Shin, Tai, E-Shyong, Tanaka, Toshihiro, de Silva, R Deng G, Hernandez-Fuentes, M, Ubink-Veltmaat, Lj, Probst-Hensch, Nm, Giallauria, Francesco, Pirastu, N, D'Adamo, P, Gasparini, P, and Bouatia-Naji, N

Subjects
Asian Continental Ancestry Group, kidney, Population, Renal function, Genome-wide association study, Biology, Kidney, Polymorphism, Single Nucleotide, Article, Blood Urea Nitrogen, Cohort Studies, chemistry.chemical_compound, SDG 3 - Good Health and Well-being, Asian People, loci, Asian, medicine, Humans, genetics, Genetic Predisposition to Disease, Renal Insufficiency, Chronic, education, meta-analysis, Genome-Wide Association Study, Genetic association, Genetics, Creatinine, education.field_of_study, ta3121, medicine.disease, Uric Acid, Asian Continental Ancestry Group/genetics, Creatinine/blood, Glomerular Filtration Rate/genetics, Kidney/physiology, Renal Insufficiency, Chronic/genetics, Uric Acid/blood, medicine.anatomical_structure, chemistry, Genetic epidemiology, Cohort Studie, Human, Kidney disease, Glomerular Filtration Rate
Abstract

Chronic kidney disease (CKD), impairment of kidney function, is a serious public health problem, and the assessment of genetic factors influencing kidney function has substantial clinical relevance. Here, we report a meta-analysis of genomewide association studies for kidney function-related traits, including 71,149 east Asian individuals from 18 studies in 11 population-, hospital- or family-based cohorts, conducted as part of the Asian Genetic Epidemiology Network (AGEN). Our meta-analysis identified 17 loci newly associated with kidney function-related traits, including the concentrations of blood urea nitrogen, uric acid and serum creatinine and estimated glomerular filtration rate based on serum creatinine levels (eGFRcrea) (P < 5.0 x 10(-8)). We further examined these loci with in silico replication in individuals of European ancestry from the KidneyGen, CKDGen and GUGC consortia, including a combined total of similar to 110,347 individuals. We identify pleiotropic associations among these loci with kidney function-related traits and risk of CKD. These findings provide new insights into the genetics of kidney function.

Published
2012

47. Interactions of dietary whole-grain intake with fasting glucose- and insulin-related genetic loci in individuals of European descent: a meta-analysis of 14 cohort studies

Author

Nettleton, J.A., McKeown, N.M., Kanoni, S., Lemaitre, R.N., Hivert, M.F., Ngwa, J., van Rooij, F.J., Sonestedt, E., Wojczynski, M.K., Ye, Z., Tanaka, T., Garcia, M., Anderson, J.S., Follis, J.L., Djousse, L., Mukamal, K., Papoutsakis, C., Mozaffarian, D., Zillikens, M.C., Bandinelli, S., Bennett, A.J., Borecki, I.B., Feitosa, M.F., Ferrucci, L., Forouhi, N.G., Groves, C.J., Hallmans, G., Harris, T., Hofman, A., Houston, D.K., Hu, F.B., Johansson, I., Kritchevsky, S.B., Langenberg, C., Launer, L., Liu, Y., Loos, R.J., Nalls, M., Orho-Melander, M., Renstrom, F., Rice, K., Riserus, U., Rolandsson, O., Rotter, J.I., Saylor, G., Sijbrands, E.J., Sjogren, P., Smith, A., Steingrímsdóttir, L., Uitterlinden, A.G., Wareham, N.J., Prokopenko, I., Pankow, J.S., van Duijn, C.M., Florez, J.C., Witteman, J.C., Dupuis, J., Dedoussis, G.V., Ordovas, J.M., Ingelsson, E., Cupples, L., Siscovick, D.S., Franks, P.W., Meigs, J.B., MAGIC Investigators, Dupuis, J., Claudia, L., Prokopenko, I., Saxena, R., Soranzo, N., Jackson, A.U., Wheeler, E., Glazer, N.L., Bouatia-Naji, N., Lindgren, C.M., Mägi, R., Morris, A.P., Randal, J., Rybin, D., Johnson, T., Henneman, P., Gieger, C., Thorleifsson, G., Steinthorsdottir, V., Dehghan, A., Hottenga, J.J., Franklin, C.S., Navarro, P., Song, K., Goe, A., Perry, J.R., Lajunen, T., Grallert, H., Li, M., Stringham, H.M., Kumari, M., Timpson, N.J., Shrader, P., Ingelsson, E., Zabena, C., O'Connell, J., Cavalcanti-Proença, C., Luan, J., Elliott, A., McCarroll, S.A., Payne, F., Roccasecca, R.M., Sethupathy, P., Andrew, T., Ariyurek, Y., Balkau, B., Barter, P., Bennett, A.J., Ben-Shlomo, Y., Bergmann, S., Bochud, M., Boerwinkle, E., Bonnefond, A., Bonnycastle, L.L., Böttcher, Y., Brunner, E., Bumpstead, S.J., Chen, Y.D., Chines, P., Clarke, R., Coin, L.J., Crawford, G.J., Crisponi, L., Day, I.N., Geus, Ed, Dina, C., Doney, A., Egan, J.M., Elliott, P., Erdos, M.R., Fischer-Rosinsky, A., Forouhi, N.G., Fox, C.S., Frants, R., Franzosi, M.G., Galan, P., Goodarzi, M.O., Graessler, J., Groves, C.J., Grundy, S., Gwilliam, R., Hallmans, G., Hammond, N., Han, X., Hartikainen, A.L., Hayward, C., Heath, S.C., Hercberg, S., Herder, C., Hicks, A.A., Hingorani, A.D., Hofman, A., Isomaa, B., Jula, A., Kaakinen, M., Kanoni, S., Kesaniemi, Y.A., Kivimaki, M., Knight, B., Koskinen, S., Kovacs, P., Lathrop, G.M., Lawlor, D.A., Li, Y., Lyssenko, V., Mahley, R., Mangino, M., Manning, A.K., Martínez-Larrad, M.T., McAteer, J.B., McPherson, R., Meisinger, C., Melzer, D., Meyre, D., Mitchell, B.D., Morken, M.A., Naitza, S., Narisu, N., Neville, M.J., Oostra, B.A., Orrù, M., Pakyz, R., Palmer, C.N., Paolisso, G., Pattaro, C., Pearson, D., Peden, J.F., Perola, M., Pfeiffer, A.F., Pichler, I., Polasek, O., Posthuma, D., Potter, S.C., Pouta, A., Psaty, B.M., Rathmann, W., Rayner, N.W., Rice, K., Ripatti, S., Rivadeneira, F., Rolandsson, O., Sandhu, M., Sanna, S., Sayer, A.A., Scheet, P., Scott, L.J., Seedorf, U., Sharp, S.J., Shields, B., Sijbrands, E.J., Silveira, A., Singleton, A., Smith, N.L., Sovio, U., Swift, A., Syddall, H., Syvänen, A.C., Tanaka, T., Tönjes, A., Tuomi, T., Uitterlinden, A.G., van Dijk, K.W., Varma, D., Visvikis-Siest, S., Vitart, V., Vogelzangs, N., Waeber, G., Wagner, P.J., Watkins, H., Weedon, M.N., Wild, S.H., Willemsen, G., Witteman, J.C., Yarnell, J.W., Zelenika, D., Zethelius, B., Zhai, G., Zhao, J.H., Zillikens, M.C., GIANT Consortium, X., Global BPgen Consortium, X., Loos, R.J., Meneton, P., Nathan, D.M., Williams, G.H., Hattersley, A.T., Silander, K., Salomaa, V., Smith, G.D., Bornstein, S.R., Schwarz, P., Spranger, J., Karpe, F., Shuldiner, A.R., Cooper, C., Dedoussis, G.V., Serrano-Ríos, M., Morris, A.D., Lind, L., Franks, P.W., Ebrahim, S., Marmot, M., Kuusisto, J., Laakso, M., Kao, W.H., Pankow, J.S., Pramstaller, P.P., Wichmann, H.E., Illig, T., Rudan, I., Wright, A., Stumvoll, M., Campbell, H., Wilson, J.F., Hamsten, A., Bergman, R.N., Buchanan, T.A., Collins, F.S., Mohlke, K.L., Tuomilehto, J., Valle, T.T., Altshuler, D., Rotter, J.I., Siscovick, D.S., Penninx, B.W., Boomsma, D., Deloukas, P., Spector, T.D., Frayling, T.M., Ferrucci, L., Kong, A., Thorsteinsdottir, U., Stefansson, K., van Duijn, C.M., Aulchenko, Y.S., Cao, A., Scuteri, A., Schlessinger, D., Uda, M., Ruokonen, A., Jarvelin, M.R., Waterworth, D.M., Vollenweider, P., Peltonen, L., Mooser, V., Abecasis, G.R., Wareham, N.J., Sladek, R., Froguel, P., Watanabe, R.M., Meigs, J.B., Groop, L., Boehnke, M., McCarthy, M.I., Florez, J.C., and Barroso, I.

Subjects
Adult, Blood Glucose, Male, Genotype, Reviews/Commentaries/ADA Statements, Fasting, Middle Aged, Polymorphism, Single Nucleotide, White People, Genetic Loci, Humans, Insulin, Female, Aged, Blood Glucose/genetics, Blood Glucose/metabolism, Edible Grain, European Continental Ancestry Group, Fasting/blood, Genetic Loci/genetics, Genome-Wide Association Study, Insulin/blood, Insulin/genetics, Polymorphism, Single Nucleotide/genetics, Meta-Analysis
Abstract

OBJECTIVE Whole-grain foods are touted for multiple health benefits, including enhancing insulin sensitivity and reducing type 2 diabetes risk. Recent genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs) associated with fasting glucose and insulin concentrations in individuals free of diabetes. We tested the hypothesis that whole-grain food intake and genetic variation interact to influence concentrations of fasting glucose and insulin. RESEARCH DESIGN AND METHODS Via meta-analysis of data from 14 cohorts comprising ∼48,000 participants of European descent, we studied interactions of whole-grain intake with loci previously associated in GWAS with fasting glucose (16 loci) and/or insulin (2 loci) concentrations. For tests of interaction, we considered a P value

Published
2010

48. A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

Author

Adolfo Correa, Kotaro Ogawa, Yukinori Okada, Paul J. McLaren, Philip E. Stuart, Kenichi Yamamoto, Peter K. Gregersen, Saori Sakaue, David W Haas, Tõnu Esko, Michael H. Cho, Albert V. Smith, Wanson Choi, Sebastian Schönherr, Yii-Der Ida Chen, James T. Elder, Soumya Raychaudhuri, Maria Gutierrez-Arcelus, Lukas Forer, Kent D. Taylor, Yang Luo, Xiuqing Guo, Jerome I. Rotter, Stephen S. Rich, Nicholette D. Palmer, Mary Carrington, Masahiro Kanai, Christian Fuchsberger, Buhm Han, Andres Metspalu, Xinyi Li, Sekar Kathiresan, James G. Wilson, Jacques Fellay, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Abe, N., Abecasis, G., Aguet, F., Albert, C., Almasy, L., Alonso, A., Ament, S., Anderson, P., Anugu, P., Applebaum-Bowden, D., Ardlie, K., Dan Arking, X., Arnett, D.K., Ashley-Koch, A., Aslibekyan, S., Assimes, T., Auer, P., Avramopoulos, D., Ayas, N., Balasubramanian, A., Barnard, J., Barnes, K., Barr, R.G., Barron-Casella, E., Barwick, L., Beaty, T., Beck, G., Becker, D., Becker, L., Beer, R., Beitelshees, A., Benjamin, E., Benos, T., Bezerra, M., Bielak, L., Bis, J., Blackwell, T., Blangero, J., Boerwinkle, E., Bowden, D.W., Bowler, R., Brody, J., Broeckel, U., Broome, J., Brown, D., Bunting, K., Burchard, E., Bustamante, C., Buth, E., Cade, B., Cardwell, J., Carey, V., Carrier, J., Carty, C., Casaburi, R., Romero, JPC, Casella, J., Castaldi, P., Chaffin, M., Chang, C., Chang, Y.C., Chasman, D., Chavan, S., Chen, B.J., Chen, W.M., Choi, S.H., Chuang, L.M., Chung, M., Chung, R.H., Clish, C., Comhair, S., Conomos, M., Cornell, E., Crandall, C., Crapo, J., Cupples, L.A., Curran, J., Curtis, J., Custer, B., Damcott, C., Darbar, D., David, S., Davis, C., Daya, M., de Andrade, M., Fuentes, L.L., de Vries, P., DeBaun, M., Deka, R., DeMeo, D., Devine, S., Dinh, H., Doddapaneni, H., Duan, Q., Dugan-Perez, S., Duggirala, R., Durda, J.P., Dutcher, S.K., Eaton, C., Ekunwe, L., Boueiz, A.E., Ellinor, P., Emery, L., Erzurum, S., Farber, C., Farek, J., Fingerlin, T., Flickinger, M., Fornage, M., Franceschini, N., Frazar, C., Fu, M., Fullerton, S.M., Fulton, L., Gabriel, S., Gan, W., Gao, S., Gao, Y., Gass, M., Geiger, H., Gelb, B., Geraci, M., Germer, S., Gerszten, R., Ghosh, A., Gibbs, R., Gignoux, C., Gladwin, M., Glahn, D., Gogarten, S., Gong, D.W., Goring, H., Graw, S., Gray, K.J., Grine, D., Gross, C., Gu, C.C., Guan, Y., Gupta, N., Haas, D.M., Haessler, J., Hall, M., Han, Y., Hanly, P., Harris, D., Hawley, N.L., He, J., Heavner, B., Heckbert, S., Hernandez, R., Herrington, D., Hersh, C., Hidalgo, B., Hixson, J., Hobbs, B., Hokanson, J., Hong, E., Hoth, K., Hsiung, C.A., Hu, J., Hung, Y.J., Huston, H., Hwu, C.M., Irvin, M.R., Jackson, R., Jain, D., Jaquish, C., Johnsen, J., Johnson, A., Johnson, C., Johnston, R., Jones, K., Kang, H.M., Kaplan, R., Kardia, S., Kelly, S., Kenny, E., Kessler, M., Khan, A., Khan, Z., Kim, W., Kimoff, J., Kinney, G., Konkle, B., Kooperberg, C., Kramer, H., Lange, C., Lange, E., Lange, L., Laurie, C., LeBoff, M., Lee, J., Lee, S., Lee, W.J., LeFaive, J., Levine, D., Dan Levy, X., Lewis, J., Li, X., Li, Y., Lin, H., Lin, X., Liu, S., Liu, Y., Loos, RJF, Lubitz, S., Lunetta, K., Luo, J., Magalang, U., Mahaney, M., Make, B., Manichaikul, A., Manning, A., Manson, J., Martin, L., Marton, M., Mathai, S., Mathias, R., May, S., McArdle, P., McDonald, M.L., McFarland, S., McGarvey, S., McGoldrick, D., McHugh, C., McNeil, B., Mei, H., Meigs, J., Menon, V., Mestroni, L., Metcalf, G., Meyers, D.A., Mignot, E., Mikulla, J., Min, N., Minear, M., 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Zoellner, S., and Consortium, NHLBI Trans-Omics for Precision Medicine (TOPMed)

Subjects
haplotypes, Population genetics, Alleles, Amino Acids/genetics, Gene Frequency/genetics, Genetic Variation, Genetics, Population, HIV Infections/genetics, HIV-1/genetics, HLA Antigens/genetics, Haplotypes/genetics, Host-Pathogen Interactions/genetics, Humans, Linkage Disequilibrium/genetics, Physical Chromosome Mapping, Reference Standards, Selection, Genetic, Viral Load, HIV Infections, Immunogenetics, Human leukocyte antigen, Major histocompatibility complex, Linkage Disequilibrium, Article, Gene Frequency, HLA Antigens, Genetics, mhc, Amino Acids, Allele, biology, Haplotype, association, genetic-basis, micropolymorphism, polygenic risk scores, Evolutionary biology, Host-Pathogen Interactions, alleles, loci, HIV-1, biology.protein, amino-acid, identification, Viral load, Imputation (genetics)
Abstract

A high-resolution reference panel based on whole-genome sequencing data enables accurate imputation of HLA alleles across diverse populations and fine-mapping of HLA association signals for HIV-1 host response., Fine-mapping to plausible causal variation may be more effective in multi-ancestry cohorts, particularly in the MHC, which has population-specific structure. To enable such studies, we constructed a large (n = 21,546) HLA reference panel spanning five global populations based on whole-genome sequences. Despite population-specific long-range haplotypes, we demonstrated accurate imputation at G-group resolution (94.2%, 93.7%, 97.8% and 93.7% in admixed African (AA), East Asian (EAS), European (EUR) and Latino (LAT) populations). Applying HLA imputation to genome-wide association study data for HIV-1 viral load in three populations (EUR, AA and LAT), we obviated effects of previously reported associations from population-specific HIV studies and discovered a novel association at position 156 in HLA-B. We pinpointed the MHC association to three amino acid positions (97, 67 and 156) marking three consecutive pockets (C, B and D) within the HLA-B peptide-binding groove, explaining 12.9% of trait variance.

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