IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v411y2001i6834d10.1038_35075590.html
   My bibliography  Save this article

Linkage disequilibrium in the human genome

Author

Listed:
  • David E. Reich

    (Whitehead Institute / MIT Center for Genome Research)

  • Michele Cargill

    (Whitehead Institute / MIT Center for Genome Research
    Celera Genomics)

  • Stacey Bolk

    (Whitehead Institute / MIT Center for Genome Research)

  • James Ireland

    (Whitehead Institute / MIT Center for Genome Research)

  • Pardis C. Sabeti

    (Institute of Biological Anthropology, University of Oxford)

  • Daniel J. Richter

    (Whitehead Institute / MIT Center for Genome Research)

  • Thomas Lavery

    (Whitehead Institute / MIT Center for Genome Research)

  • Rose Kouyoumjian

    (Whitehead Institute / MIT Center for Genome Research)

  • Shelli F. Farhadian

    (Whitehead Institute / MIT Center for Genome Research)

  • Ryk Ward

    (Institute of Biological Anthropology, University of Oxford)

  • Eric S. Lander

    (Whitehead Institute / MIT Center for Genome Research
    MIT)

Abstract

With the availability of a dense genome-wide map of single nucleotide polymorphisms (SNPs)1, a central issue in human genetics is whether it is now possible to use linkage disequilibrium (LD) to map genes that cause disease. LD refers to correlations among neighbouring alleles, reflecting ‘haplotypes’ descended from single, ancestral chromosomes. The size of LD blocks has been the subject of considerable debate. Computer simulations2 and empirical data3 have suggested that LD extends only a few kilobases (kb) around common SNPs, whereas other data have suggested that it can extend much further, in some cases greater than 100 kb4,5,6. It has been difficult to obtain a systematic picture of LD because past studies have been based on only a few (1–3) loci and different populations. Here, we report a large-scale experiment using a uniform protocol to examine 19 randomly selected genomic regions. LD in a United States population of north-European descent typically extends 60 kb from common alleles, implying that LD mapping is likely to be practical in this population. By contrast, LD in a Nigerian population extends markedly less far. The results illuminate human history, suggesting that LD in northern Europeans is shaped by a marked demographic event about 27,000–53,000 years ago.

Suggested Citation

  • David E. Reich & Michele Cargill & Stacey Bolk & James Ireland & Pardis C. Sabeti & Daniel J. Richter & Thomas Lavery & Rose Kouyoumjian & Shelli F. Farhadian & Ryk Ward & Eric S. Lander, 2001. "Linkage disequilibrium in the human genome," Nature, Nature, vol. 411(6834), pages 199-204, May.
    • Handle: RePEc:nat:nature:v:411:y:2001:i:6834:d:10.1038_35075590
    DOI: 10.1038/35075590
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/35075590
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/35075590?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.

    Citations

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


    Cited by:

    1. Pietro Biroli & Titus J. Galama & Stephanie von Hinke & Hans van Kippersluis & Cornelius A. Rietveld & Kevin Thom, 2022. "The Economics and Econometrics of Gene-Environment Interplay," Papers 2203.00729, arXiv.org.
    2. Chung-Feng Kao & Jia-Rou Liu & Hung Hung & Po-Hsiu Kuo, 2015. "A Robust GWSS Method to Simultaneously Detect Rare and Common Variants for Complex Disease," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-14, April.
    3. Haipeng Li & Thomas Wiehe, 2013. "Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation," PLOS Computational Biology, Public Library of Science, vol. 9(5), pages 1-14, May.
    4. Shuo Jiao & Li Hsu & Sonja Berndt & Stéphane Bézieau & Hermann Brenner & Daniel Buchanan & Bette J Caan & Peter T Campbell & Christopher S Carlson & Graham Casey & Andrew T Chan & Jenny Chang-Claude &, 2012. "Genome-Wide Search for Gene-Gene Interactions in Colorectal Cancer," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-14, December.
    5. Konstantin Schildknecht & Sven Olek & Thorsten Dickhaus, 2015. "Simultaneous Statistical Inference for Epigenetic Data," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-15, May.
    6. Shuxia Guo & Yunhua Hu & Yusong Ding & Jiaming Liu & Mei Zhang & Rulin Ma & Heng Guo & Kui Wang & Jia He & Yizhong Yan & Dongsheng Rui & Feng Sun & Lati Mu & Qiang Niu & Jingyu Zhang & Shugang Li, 2015. "Association between Eight Functional Polymorphisms and Haplotypes in the Cholesterol Ester Transfer Protein (CETP) Gene and Dyslipidemia in National Minority Adults in the Far West Region of China," IJERPH, MDPI, vol. 12(12), pages 1-14, December.
    7. Li Qin & Wu Rongling, 2009. "A Multilocus Model for Constructing a Linkage Disequilibrium Map in Human Populations," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-25, February.
    8. Shpak, Max & Ni, Yang & Lu, Jie & Müller, Peter, 2017. "Variance in estimated pairwise genetic distance under high versus low coverage sequencing: The contribution of linkage disequilibrium," Theoretical Population Biology, Elsevier, vol. 117(C), pages 51-63.
    9. Zhang, Hong & Wu, Zheyang, 2022. "The general goodness-of-fit tests for correlated data," Computational Statistics & Data Analysis, Elsevier, vol. 167(C).
    10. Wei Zhao & Erin B. Ware & Zihuai He & Sharon L. R. Kardia & Jessica D. Faul & Jennifer A. Smith, 2017. "Interaction between Social/Psychosocial Factors and Genetic Variants on Body Mass Index: A Gene-Environment Interaction Analysis in a Longitudinal Setting," IJERPH, MDPI, vol. 14(10), pages 1-17, September.
    11. Zhuling Yu & Wei Li & Deren Hou & Lin Zhou & Yanyao Deng & Mi Tian & Xialu Feng, 2015. "Relationship between Adiponectin Gene Polymorphisms and Late-Onset Alzheimer’s Disease," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-11, April.
    12. Hou, Wei & Liu, Tian & Li, Yao & Li, Qin & Li, Jiahan & Das, Kiranmoy & Berg, Arthur & Wu, Rongling, 2009. "Multilocus genomics of outcrossing plant populations," Theoretical Population Biology, Elsevier, vol. 76(1), pages 68-76.
    13. Kari E. North & Lisa J. Martin, 2008. "The Importance of Gene—Environment Interaction," Sociological Methods & Research, , vol. 37(2), pages 164-200, November.
    14. Xiaoshuai Zhang & Xiaowei Yang & Zhongshang Yuan & Yanxun Liu & Fangyu Li & Bin Peng & Dianwen Zhu & Jinghua Zhao & Fuzhong Xue, 2013. "A PLSPM-Based Test Statistic for Detecting Gene-Gene Co-Association in Genome-Wide Association Study with Case-Control Design," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-8, April.
    15. Hu, Xin-Sheng & Hu, Yang & Chen, Xiaoyang, 2016. "Testing neutrality at copy-number-variable loci under the finite-allele and finite-site models," Theoretical Population Biology, Elsevier, vol. 112(C), pages 1-13.

    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:nat:nature:v:411:y:2001:i:6834:d:10.1038_35075590. 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.

    We have no bibliographic references for this item. You can help adding them by using 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: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.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.