IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0172880.html
   My bibliography  Save this article

Admixture mapping in two Mexican samples identifies significant associations of locus ancestry with triglyceride levels in the BUD13/ZNF259/APOA5 region and fine mapping points to rs964184 as the main driver of the association signal

Author

Listed:
  • Esteban J Parra
  • Andrew Mazurek
  • Christopher R Gignoux
  • Alexandra Sockell
  • Michael Agostino
  • Andrew P Morris
  • Lauren E Petty
  • Craig L Hanis
  • Nancy J Cox
  • Adan Valladares-Salgado
  • Jennifer E Below
  • Miguel Cruz

Abstract

We carried out an admixture mapping study of lipid traits in two samples from Mexico City. Native American locus ancestry was significantly associated with triglyceride levels in a broad region of chromosome 11 overlapping the BUD13, ZNF259 and APOA5 genes. In our fine-mapping analysis of this region using dense genome-wide data, rs964184 is the only marker included in the 99% credible set of SNPs, providing strong support for rs964184 as the causal variant within this region. The frequency of the allele associated with increased triglyceride concentrations (rs964184-G) is between 30–40% higher in Native American populations from Mexico than in European populations. The evidence currently available for this variant indicates that it may be exerting its effect through three potential mechanisms: 1) modification of enhancer activity, 2) regulation of the expression of several genes in cis and/or trans, or 3) modification of the methylation patterns of the promoter of the APOA5 gene.

Suggested Citation

  • Esteban J Parra & Andrew Mazurek & Christopher R Gignoux & Alexandra Sockell & Michael Agostino & Andrew P Morris & Lauren E Petty & Craig L Hanis & Nancy J Cox & Adan Valladares-Salgado & Jennifer E , 2017. "Admixture mapping in two Mexican samples identifies significant associations of locus ancestry with triglyceride levels in the BUD13/ZNF259/APOA5 region and fine mapping points to rs964184 as the main," PLOS ONE, Public Library of Science, vol. 12(2), pages 1-16, February.
    • Handle: RePEc:plo:pone00:0172880
    DOI: 10.1371/journal.pone.0172880
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0172880
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0172880&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0172880?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. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    2. Carlos D. Bustamante & Francisco M. De La Vega & Esteban G. Burchard, 2011. "Genomics for the world," Nature, Nature, vol. 475(7355), pages 163-165, July.
    Full references (including those not matched with items on IDEAS)

    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. Gyaneshwer Chaubey & Anurag Kadian & Saroj Bala & Vadlamudi Raghavendra Rao, 2015. "Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-11, June.
    2. 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.
    3. Estavoyer, Maxime & François, Olivier, 2022. "Theoretical analysis of principal components in an umbrella model of intraspecific evolution," Theoretical Population Biology, Elsevier, vol. 148(C), pages 11-21.
    4. Felsenstein, Joseph, 2015. "Covariation of gene frequencies in a stepping-stone lattice of populations," Theoretical Population Biology, Elsevier, vol. 100(C), pages 88-97.
    5. Nadine R. Caron & Wilf Adam & Kate Anderson & Brooke T. Boswell & Meck Chongo & Viktor Deineko & Alexanne Dick & Shannon E. Hall & Jessica T. Hatcher & Patricia Howard & Megan Hunt & Kevin Linn & Ashl, 2023. "Partnering with First Nations in Northern British Columbia Canada to Reduce Inequity in Access to Genomic Research," IJERPH, MDPI, vol. 20(10), pages 1-31, May.
    6. Julian R Homburger & Andrés Moreno-Estrada & Christopher R Gignoux & Dominic Nelson & Elena Sanchez & Patricia Ortiz-Tello & Bernardo A Pons-Estel & Eduardo Acevedo-Vasquez & Pedro Miranda & Carl D La, 2015. "Genomic Insights into the Ancestry and Demographic History of South America," PLOS Genetics, Public Library of Science, vol. 11(12), pages 1-26, December.
    7. Yaron Granot & Omri Tal & Saharon Rosset & Karl Skorecki, 2016. "On the Apportionment of Population Structure," PLOS ONE, Public Library of Science, vol. 11(8), pages 1-24, August.
    8. Hyosik Jang & Ian M Ehrenreich, 2012. "Genome-Wide Characterization of Genetic Variation in the Unicellular, Green Alga Chlamydomonas reinhardtii," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-9, July.
    9. Mathieu Gautier & Denis Laloë & Katayoun Moazami-Goudarzi, 2010. "Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-11, September.
    10. Xiaofeng Cai & Xuepeng Sun & Chenxi Xu & Honghe Sun & Xiaoli Wang & Chenhui Ge & Zhonghua Zhang & Quanxi Wang & Zhangjun Fei & Chen Jiao & Quanhua Wang, 2021. "Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    11. Lee, Anthony J. & Hibbs, Courtney & Wright, Margaret J. & Martin, Nicholas G. & Keller, Matthew C. & Zietsch, Brendan P., 2017. "Assessing the accuracy of perceptions of intelligence based on heritable facial features," Intelligence, Elsevier, vol. 64(C), pages 1-8.
    12. Thompson Katherine L. & Linnen Catherine R. & Kubatko Laura, 2016. "Tree-based quantitative trait mapping in the presence of external covariates," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(6), pages 473-490, December.
    13. Matthieu Bouaziz & Caroline Paccard & Mickael Guedj & Christophe Ambroise, 2012. "SHIPS: Spectral Hierarchical Clustering for the Inference of Population Structure in Genetic Studies," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-17, October.
    14. Jacobo Pardo-Seco & Alberto Gómez-Carballa & Jorge Amigo & Federico Martinón-Torres & Antonio Salas, 2014. "A Genome-Wide Study of Modern-Day Tuscans: Revisiting Herodotus's Theory on the Origin of the Etruscans," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-11, September.
    15. Andrey V Khrunin & Denis V Khokhrin & Irina N Filippova & Tõnu Esko & Mari Nelis & Natalia A Bebyakova & Natalia L Bolotova & Janis Klovins & Liene Nikitina-Zake & Karola Rehnström & Samuli Ripatti & , 2013. "A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-9, March.
    16. Ilja M Nolte & Chris Wallace & Stephen J Newhouse & Daryl Waggott & Jingyuan Fu & Nicole Soranzo & Rhian Gwilliam & Panos Deloukas & Irina Savelieva & Dongling Zheng & Chrysoula Dalageorgou & Martin F, 2009. "Common Genetic Variation Near the Phospholamban Gene Is Associated with Cardiac Repolarisation: Meta-Analysis of Three Genome-Wide Association Studies," PLOS ONE, Public Library of Science, vol. 4(7), pages 1-10, July.
    17. Hoicheong Siu & Li Jin & Momiao Xiong, 2012. "Manifold Learning for Human Population Structure Studies," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-18, January.
    18. Elodie Persyn & Richard Redon & Lise Bellanger & Christian Dina, 2018. "The impact of a fine-scale population stratification on rare variant association test results," PLOS ONE, Public Library of Science, vol. 13(12), pages 1-17, December.
    19. Andre Krumel Portella & Afroditi Papantoni & Catherine Paquet & Spencer Moore & Keri Shiels Rosch & Stewart Mostofsky & Richard S Lee & Kimberly R Smith & Robert Levitan & Patricia Pelufo Silveira & S, 2020. "Predicted DRD4 prefrontal gene expression moderates snack intake and stress perception in response to the environment in adolescents," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-20, June.
    20. Jonathon P. Schuldt & Adam R. Pearson & Neil A. Lewis jr. & Ashley Jardina & Peter K. Enns, 2022. "Inequality and Misperceptions of Group Concerns Threaten the Integrity and Societal Impact of Science," The ANNALS of the American Academy of Political and Social Science, , vol. 700(1), pages 195-207, March.

    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:pone00:0172880. 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: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    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.