IDEAS home Printed from https://ideas.repec.org/a/spr/jcomop/v19y2010i2d10.1007_s10878-008-9180-y.html
   My bibliography  Save this article

A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on pedigrees without mating loops

Author

Listed:
  • Lan Liu

    (University of California
    Google Inc.)

  • Tao Jiang

    (University of California)

Abstract

With the launch of the international HapMap project, the haplotype inference problem has attracted a great deal of attention in the computational biology community recently. In this paper, we study the question of how to efficiently infer haplotypes from genotypes of individuals related by a pedigree without mating loops, assuming that the hereditary process was free of mutations (i.e. the Mendelian law of inheritance) and recombinants. We model the haplotype inference problem as a system of linear equations as in (Xiao et al. in Proceedings of the 18th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA’07), pp. 655–664, 2007) and present an (optimal) linear-time (i.e. O(mn) time) algorithm to generate a particular solution to the haplotype inference problem, where m is the number of loci (or markers) in a genotype and n is the number of individuals in the pedigree. Moreover, the algorithm also provides a general solution in O(mn 2) time, which is optimal because the descriptive size of a general solution could be as large as Θ(mn 2). The key ingredients of our construction are (i) a fast consistency checking procedure for the system of linear equations introduced in (Xiao et al. 2007) based on a careful investigation of the relationship between the equations (ii) a novel linear-time method for solving linear equations without invoking the Gaussian elimination method. Although such a fast method for solving equations is not known for general systems of linear equations, we take advantage of the underlying loop-free pedigree graph and some special properties of the linear equations.

Suggested Citation

  • Lan Liu & Tao Jiang, 2010. "A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on pedigrees without mating loops," Journal of Combinatorial Optimization, Springer, vol. 19(2), pages 217-240, February.
    • Handle: RePEc:spr:jcomop:v:19:y:2010:i:2:d:10.1007_s10878-008-9180-y
    DOI: 10.1007/s10878-008-9180-y
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s10878-008-9180-y
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1007/s10878-008-9180-y?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. Yongxi Cheng & Guohui Lin, 2012. "Solving haplotype inference problem with non-genotyped founders via integer linear programming," Journal of Combinatorial Optimization, Springer, vol. 23(1), pages 50-60, January.

    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:spr:jcomop:v:19:y:2010:i:2:d:10.1007_s10878-008-9180-y. 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.springer.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.