IDEAS home Printed from https://ideas.repec.org/a/plo/pgen00/1004517.html
   My bibliography  Save this article

Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes

Author

Listed:
  • Maggie C Y Ng
  • Daniel Shriner
  • Brian H Chen
  • Jiang Li
  • Wei-Min Chen
  • Xiuqing Guo
  • Jiankang Liu
  • Suzette J Bielinski
  • Lisa R Yanek
  • Michael A Nalls
  • Mary E Comeau
  • Laura J Rasmussen-Torvik
  • Richard A Jensen
  • Daniel S Evans
  • Yan V Sun
  • Ping An
  • Sanjay R Patel
  • Yingchang Lu
  • Jirong Long
  • Loren L Armstrong
  • Lynne Wagenknecht
  • Lingyao Yang
  • Beverly M Snively
  • Nicholette D Palmer
  • Poorva Mudgal
  • Carl D Langefeld
  • Keith L Keene
  • Barry I Freedman
  • Josyf C Mychaleckyj
  • Uma Nayak
  • Leslie J Raffel
  • Mark O Goodarzi
  • Y-D Ida Chen
  • Herman A Taylor Jr.
  • Adolfo Correa
  • Mario Sims
  • David Couper
  • James S Pankow
  • Eric Boerwinkle
  • Adebowale Adeyemo
  • Ayo Doumatey
  • Guanjie Chen
  • Rasika A Mathias
  • Dhananjay Vaidya
  • Andrew B Singleton
  • Alan B Zonderman
  • Robert P Igo Jr.
  • John R Sedor
  • the FIND Consortium
  • Edmond K Kabagambe
  • David S Siscovick
  • Barbara McKnight
  • Kenneth Rice
  • Yongmei Liu
  • Wen-Chi Hsueh
  • Wei Zhao
  • Lawrence F Bielak
  • Aldi Kraja
  • Michael A Province
  • Erwin P Bottinger
  • Omri Gottesman
  • Qiuyin Cai
  • Wei Zheng
  • William J Blot
  • William L Lowe
  • Jennifer A Pacheco
  • Dana C Crawford
  • the eMERGE Consortium
  • the DIAGRAM Consortium
  • Elin Grundberg
  • the MuTHER Consortium
  • Stephen S Rich
  • M Geoffrey Hayes
  • Xiao-Ou Shu
  • Ruth J F Loos
  • Ingrid B Borecki
  • Patricia A Peyser
  • Steven R Cummings
  • Bruce M Psaty
  • Myriam Fornage
  • Sudha K Iyengar
  • Michele K Evans
  • Diane M Becker
  • W H Linda Kao
  • James G Wilson
  • Jerome I Rotter
  • Michèle M Sale
  • Simin Liu
  • Charles N Rotimi
  • Donald W Bowden
  • for the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium

Abstract

Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS) in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs) association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications were performed to follow up 21 loci in up to 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry. We identified three known loci (TCF7L2, HMGA2 and KCNQ1) and two novel loci (HLA-B and INS-IGF2) at genome-wide significance (4.15×10−94

Suggested Citation

  • Maggie C Y Ng & Daniel Shriner & Brian H Chen & Jiang Li & Wei-Min Chen & Xiuqing Guo & Jiankang Liu & Suzette J Bielinski & Lisa R Yanek & Michael A Nalls & Mary E Comeau & Laura J Rasmussen-Torvik &, 2014. "Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes," PLOS Genetics, Public Library of Science, vol. 10(8), pages 1-14, August.
    • Handle: RePEc:plo:pgen00:1004517
    DOI: 10.1371/journal.pgen.1004517
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004517
    Download Restriction: no
    File URL: https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1004517&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pgen.1004517?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Vincent Plagnol & Joanna M M Howson & Deborah J Smyth & Neil Walker & Jason P Hafler & Chris Wallace & Helen Stevens & Laura Jackson & Matthew J Simmonds & Type 1 Diabetes Genetics Consortium & Polly , 2011. "Genome-Wide Association Analysis of Autoantibody Positivity in Type 1 Diabetes Cases," PLOS Genetics, Public Library of Science, vol. 7(8), pages 1-9, August.
    2. B. Devlin & Kathryn Roeder, 1999. "Genomic Control for Association Studies," Biometrics, The International Biometric Society, vol. 55(4), pages 997-1004, December.
    3. Bryan N Howie & Peter Donnelly & Jonathan Marchini, 2009. "A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies," PLOS Genetics, Public Library of Science, vol. 5(6), pages 1-15, June.
    4. Hakon Hakonarson & Struan F. A. Grant & Jonathan P. Bradfield & Luc Marchand & Cecilia E. Kim & Joseph T. Glessner & Rosemarie Grabs & Tracy Casalunovo & Shayne P. Taback & Edward C. Frackelton & Marg, 2007. "A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene," Nature, Nature, vol. 448(7153), pages 591-594, August.
    5. Alexandra C Nica & Leopold Parts & Daniel Glass & James Nisbet & Amy Barrett & Magdalena Sekowska & Mary Travers & Simon Potter & Elin Grundberg & Kerrin Small & Åsa K Hedman & Veronique Bataille & Jo, 2011. "The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study," PLOS Genetics, Public Library of Science, vol. 7(2), pages 1-9, February.
    6. Adam C. Bell & Gary Felsenfeld, 2000. "Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene," Nature, Nature, vol. 405(6785), pages 482-485, May.
    7. Nicholette D Palmer & Caitrin W McDonough & Pamela J Hicks & Bong H Roh & Maria R Wing & S Sandy An & Jessica M Hester & Jessica N Cooke & Meredith A Bostrom & Megan E Rudock & Matthew E Talbert & Jos, 2012. "A Genome-Wide Association Search for Type 2 Diabetes Genes in African Americans," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-14, January.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Jiajin Li & Brandon Jew & Lingyu Zhan & Sungoo Hwang & Giovanni Coppola & Nelson B Freimer & Jae Hoon Sul, 2019. "ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest," PLOS Computational Biology, Public Library of Science, vol. 15(12), pages 1-30, December.
    2. Nicole A Restrepo & Eric Farber-Eger & Robert Goodloe & Jonathan L Haines & Dana C Crawford, 2015. "Extracting Primary Open-Angle Glaucoma from Electronic Medical Records for Genetic Association Studies," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-15, June.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Peng Chen & Rick Twee-Hee Ong & Wan-Ting Tay & Xueling Sim & Mohammad Ali & Haiyan Xu & Chen Suo & Jianjun Liu & Kee-Seng Chia & Eranga Vithana & Terri L Young & Tin Aung & Wei-Yen Lim & Chiea-Chuen K, 2013. "A Study Assessing the Association of Glycated Hemoglobin A1C (HbA1C) Associated Variants with HbA1C, Chronic Kidney Disease and Diabetic Retinopathy in Populations of Asian Ancestry," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-1, November.
    2. Peristera Paschou & Petros Drineas & Jamey Lewis & Caroline M Nievergelt & Deborah A Nickerson & Joshua D Smith & Paul M Ridker & Daniel I Chasman & Ronald M Krauss & Elad Ziv, 2008. "Tracing Sub-Structure in the European American Population with PCA-Informative Markers," PLOS Genetics, Public Library of Science, vol. 4(7), pages 1-13, July.
    3. Gabriel E Hoffman & Benjamin A Logsdon & Jason G Mezey, 2013. "PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data," PLOS Computational Biology, Public Library of Science, vol. 9(6), pages 1-19, June.
    4. Qiliang Ding & Matthew M. Edwards & Ning Wang & Xiang Zhu & Alexa N. Bracci & Michelle L. Hulke & Ya Hu & Yao Tong & Joyce Hsiao & Christine J. Charvet & Sulagna Ghosh & Robert E. Handsaker & Kevin Eg, 2021. "The genetic architecture of DNA replication timing in human pluripotent stem cells," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    5. Susanna Lemmelä & Svetlana Solovieva & Rahman Shiri & Christian Benner & Markku Heliövaara & Johannes Kettunen & Verneri Anttila & Samuli Ripatti & Markus Perola & Ilkka Seppälä & Markus Juonala & Mik, 2016. "Genome-Wide Meta-Analysis of Sciatica in Finnish Population," PLOS ONE, Public Library of Science, vol. 11(10), pages 1-18, October.
    6. Lei Zhang & Yu-Fang Pei & Jian Li & Christopher J Papasian & Hong-Wen Deng, 2009. "Univariate/Multivariate Genome-Wide Association Scans Using Data from Families and Unrelated Samples," PLOS ONE, Public Library of Science, vol. 4(8), pages 1-12, August.
    7. Dominic Holland & Oleksandr Frei & Rahul Desikan & Chun-Chieh Fan & Alexey A Shadrin & Olav B Smeland & V S Sundar & Paul Thompson & Ole A Andreassen & Anders M Dale, 2020. "Beyond SNP heritability: Polygenicity and discoverability of phenotypes estimated with a univariate Gaussian mixture model," PLOS Genetics, Public Library of Science, vol. 16(5), pages 1-30, May.
    8. Vincent Michaud & Eulalie Lasseaux & David J. Green & Dave T. Gerrard & Claudio Plaisant & Tomas Fitzgerald & Ewan Birney & Benoît Arveiler & Graeme C. Black & Panagiotis I. Sergouniotis, 2022. "The contribution of common regulatory and protein-coding TYR variants to the genetic architecture of albinism," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    9. Daniel Svensson & Matilda Rentoft & Anna M Dahlin & Emma Lundholm & Pall I Olason & Andreas Sjödin & Carin Nylander & Beatrice S Melin & Johan Trygg & Erik Johansson, 2020. "A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences," PLOS ONE, Public Library of Science, vol. 15(9), pages 1-18, September.
    10. Joan Costa-Font & Cristina Vilaplana-Prieto, 2022. "Biased survival expectations and behaviours: Does domain specific information matter?," Journal of Risk and Uncertainty, Springer, vol. 65(3), pages 285-317, December.
    11. Natalie DeForest & Yuqi Wang & Zhiyi Zhu & Jacqueline S. Dron & Ryan Koesterer & Pradeep Natarajan & Jason Flannick & Tiffany Amariuta & Gina M. Peloso & Amit R. Majithia, 2024. "Genome-wide discovery and integrative genomic characterization of insulin resistance loci using serum triglycerides to HDL-cholesterol ratio as a proxy," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    12. Chuan Gao & Nan Wang & Xiuqing Guo & Julie T Ziegler & Kent D Taylor & Anny H Xiang & Yang Hai & Steven J Kridel & Jerry L Nadler & Fouad Kandeel & Leslie J Raffel & Yii-Der I Chen & Jill M Norris & J, 2015. "A Comprehensive Analysis of Common and Rare Variants to Identify Adiposity Loci in Hispanic Americans: The IRAS Family Study (IRASFS)," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-17, November.
    13. Parsa Akbari & Dragana Vuckovic & Luca Stefanucci & Tao Jiang & Kousik Kundu & Roman Kreuzhuber & Erik L. Bao & Janine H. Collins & Kate Downes & Luigi Grassi & Jose A. Guerrero & Stephen Kaptoge & Ju, 2023. "A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    14. Anna L Mitchell & Anette Bøe Wolff & Katie MacArthur & Jolanta U Weaver & Bijay Vaidya & Sophie Bensing on behalf of The Swedish Addison Registry Study Group & Martina M Erichsen & Rebecca Darlay & Ey, 2015. "Linkage Analysis in Autoimmune Addison’s Disease: NFATC1 as a Potential Novel Susceptibility Locus," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-13, June.
    15. Gang Zheng & Zhaohai Li & Mitchell H. Gail & Joseph L. Gastwirth, 2010. "Impact of Population Substructure on Trend Tests for Genetic Case–Control Association Studies," Biometrics, The International Biometric Society, vol. 66(1), pages 196-204, March.
    16. Sandosh Padmanabhan & Olle Melander & Toby Johnson & Anna Maria Di Blasio & Wai K Lee & Davide Gentilini & Claire E Hastie & Cristina Menni & Maria Cristina Monti & Christian Delles & Stewart Laing & , 2010. "Genome-Wide Association Study of Blood Pressure Extremes Identifies Variant near UMOD Associated with Hypertension," PLOS Genetics, Public Library of Science, vol. 6(10), pages 1-11, October.
    17. Mathias Seviiri & Matthew H. Law & Jue-Sheng Ong & Puya Gharahkhani & Pierre Fontanillas & Catherine M. Olsen & David C. Whiteman & Stuart MacGregor, 2022. "A multi-phenotype analysis reveals 19 susceptibility loci for basal cell carcinoma and 15 for squamous cell carcinoma," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    18. Jakris Eu-ahsunthornwattana & E Nancy Miller & Michaela Fakiola & Wellcome Trust Case Control Consortium 2 & Selma M B Jeronimo & Jenefer M Blackwell & Heather J Cordell, 2014. "Comparison of Methods to Account for Relatedness in Genome-Wide Association Studies with Family-Based Data," PLOS Genetics, Public Library of Science, vol. 10(7), pages 1-20, July.
    19. Zari Dastani & Marie-France Hivert & Nicholas Timpson & John R B Perry & Xin Yuan & Robert A Scott & Peter Henneman & Iris M Heid & Jorge R Kizer & Leo-Pekka Lyytikäinen & Christian Fuchsberger & Tosh, 2012. "Novel Loci for Adiponectin Levels and Their Influence on Type 2 Diabetes and Metabolic Traits: A Multi-Ethnic Meta-Analysis of 45,891 Individuals," PLOS Genetics, Public Library of Science, vol. 8(3), pages 1-23, March.
    20. Jianzhong Ma & Christopher I Amos, 2010. "Theoretical Formulation of Principal Components Analysis to Detect and Correct for Population Stratification," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-14, September.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pgen00:1004517. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosgenetics (email available below). General contact details of provider: https://journals.plos.org/plosgenetics/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.