IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v8y2009i1n17.html
   My bibliography  Save this article

Impact of Population Stratification on Family-Based Association Tests with Longitudinal Measurements

Author

Listed:
  • Ding Xiao

    (Harvard School of Public Health)

  • Weiss Scott

    (Harvard Medical School)

  • Raby Benjamin

    (Harvard Medical School)

  • Lange Christoph

    (Harvard School of Public Health)

  • Laird Nan M

    (Harvard School of Public Health)

Abstract

Several family-based approaches for testing genetic association with traits obtained from longitudinal or repeated measurement studies have been previously proposed. These approaches utilize the multivariate data more efficiently by using estimated optimal weights to combine univariate tests. We show that these FBAT approaches are still robust against hidden population stratification, but their power can be heavily affected since the estimated weights might provide poor approximation of the true theoretical optimal weights with the presence of population stratification. We introduce a permutation-based approach FBAT-MinP and an equal combination approach FBAT-EW, both of which do not involve the use of estimated weights. Through simulation studies, FBAT-MinP and FBAT-EW are shown to be powerful even in the presence of population stratification, when other approaches may substantially lose their power. An application of these approaches to the Childhood Asthma Management Program (CAMP) study data for testing an association between body mass index and a previously reported candidate SNP is given as an example.

Suggested Citation

  • Ding Xiao & Weiss Scott & Raby Benjamin & Lange Christoph & Laird Nan M, 2009. "Impact of Population Stratification on Family-Based Association Tests with Longitudinal Measurements," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-19, February.
    • Handle: RePEc:bpj:sagmbi:v:8:y:2009:i:1:n:17
    DOI: 10.2202/1544-6115.1398
    as

    Download full text from publisher

    File URL: https://doi.org/10.2202/1544-6115.1398
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.2202/1544-6115.1398?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Neil J. Risch, 2000. "Searching for genetic determinants in the new millennium," Nature, Nature, vol. 405(6788), pages 847-856, June.
    2. Lange Christoph & van Steen Kristel & Andrew Toby & Lyon Helen & DeMeo Dawn L & Raby Benjamin & Murphy Amy & Silverman Edwin K & MacGregor Alex & Weiss Scott T & Laird Nan M, 2004. "A Family-Based Association Test for Repeatedly Measured Quantitative Traits Adjusting for Unknown Environmental and/or Polygenic Effects," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 3(1), pages 1-29, August.
    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. Wanwan Tang & Xuebing Wu & Rui Jiang & Yanda Li, 2009. "Epistatic Module Detection for Case-Control Studies: A Bayesian Model with a Gibbs Sampling Strategy," PLOS Genetics, Public Library of Science, vol. 5(5), pages 1-18, May.
    2. Jungnam Joo & Minjung Kwak & Gang Zheng, 2010. "Improving Power for Testing Genetic Association in Case–Control Studies by Reducing the Alternative Space," Biometrics, The International Biometric Society, vol. 66(1), pages 266-276, March.
    3. Lei Zhang & Aaron J Bonham & Jian Li & Yu-Fang Pei & Jie Chen & Christopher J Papasian & Hong-Wen Deng, 2009. "Family-Based Bivariate Association Tests for Quantitative Traits," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-9, December.
    4. Minjung Kwak & Jungnam Joo & Gang Zheng, 2009. "A Robust Test for Two-Stage Design in Genome-Wide Association Studies," Biometrics, The International Biometric Society, vol. 65(4), pages 1288-1295, December.
    5. H. Zhang & G. Zheng & Z. Li, 2006. "Statistical Analysis for Haplotype-Based Matched Case–Control Studies," Biometrics, The International Biometric Society, vol. 62(4), pages 1124-1131, December.
    6. Ning Jiang & Minghui Wang & Tianye Jia & Lin Wang & Lindsey Leach & Christine Hackett & David Marshall & Zewei Luo, 2011. "A Robust Statistical Method for Association-Based eQTL Analysis," PLOS ONE, Public Library of Science, vol. 6(8), pages 1-11, August.
    7. Kari E. North & Lisa J. Martin, 2008. "The Importance of Gene—Environment Interaction," Sociological Methods & Research, , vol. 37(2), pages 164-200, November.
    8. Xiaofeng Zhu & Richard S Cooper, 2007. "Admixture Mapping Provides Evidence of Association of the VNN1 Gene with Hypertension," PLOS ONE, Public Library of Science, vol. 2(11), pages 1-10, November.
    9. Jaya M. Satagopan & E. S. Venkatraman & Colin B. Begg, 2004. "Two-Stage Designs for Gene–Disease Association Studies with Sample Size Constraints," Biometrics, The International Biometric Society, vol. 60(3), pages 589-597, September.
    10. Li, Zhaohai & Zhang, Hong & Zheng, Gang & Gastwirth, Joseph L. & Gail, Mitchell H., 2009. "Excess false positive rate caused by population stratification and disease rate heterogeneity in case-control association studies," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1767-1781, March.
    11. Zhenchuan Wang & Qiuying Sha & Shuanglin Zhang, 2016. "Joint Analysis of Multiple Traits Using "Optimal" Maximum Heritability Test," PLOS ONE, Public Library of Science, vol. 11(3), pages 1-12, March.
    12. Sirkku Karinen & Tuomas Heikkinen & Heli Nevanlinna & Sampsa Hautaniemi, 2011. "Data Integration Workflow for Search of Disease Driving Genes and Genetic Variants," PLOS ONE, Public Library of Science, vol. 6(4), pages 1-8, April.
    13. Frank, Reanne, 2007. "What to make of it? The (Re)emergence of a biological conceptualization of race in health disparities research," Social Science & Medicine, Elsevier, vol. 64(10), pages 1977-1983, May.

    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:bpj:sagmbi:v:8:y:2009:i:1:n:17. 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: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    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.