Algorithms towards haplotype-sharing based association studies of case-control traits on pedigree data

  • Author / Creator
    Sabaa, Hadi
  • Association studies that attempt to link genes with traits are expected to unearth various genomic roots for various diseases. Recently, haplotype based association studies have become popular due to the inheritance information innate to haplotypes. In this work, we provide a summary of recent works that focus on haplotyping and those focusing on association studies. We show that haplotyping is a very promising technique for case−control association studies on pedigree data. We also present a novel haplotyping algorithm that relaxes the assumption of many previous rule based algorithms. We extend the algorithm to compute and enumerate all possible identity-by-state and identity-by-descent sharings. The algorithm is also able to calculate LOD scores, a metric to measure linkage, for every chromosomal region that is free of breakpoints. Our algorithm is implemented in iBDD, which we believe will be highly useful in downstream case−control association studies on pedigree data.

  • Subjects / Keywords
  • Graduation date
  • Type of Item
  • Degree
    Doctor of Philosophy
  • DOI
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
  • Institution
    University of Alberta
  • Degree level
  • Department
    • Department of Computing Science
  • Supervisor / co-supervisor and their department(s)
    • Guohui Lin (Computing Science)
  • Examining committee members and their departments
    • Randy Goebel (Computing Science)
    • Zhiquan Wang (Agricultural, Food and Nutritional Science)
    • Boting Yang (Computer Science)
    • Osmar Zaiane (Computing Science)