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Haplotype Inference from Pedigree Data and Population Data

Li, Xin
http://rave.ohiolink.edu/etdc/view?acc_num=case1259867573

Abstract Details

2010, Doctor of Philosophy, Case Western Reserve University, EECS - Computer and Information Sciences.
Haplotype is an important representation of human genetic variation and is thus valuable for investigating the genetics behind diseases.However, humans are diploid and in practice, genotype data instead of haplotype data are collected directly. Consequently, there are great demands for efficient and accurate computational methods to reconstruct haplotypes from genotype data. Our project started with the development of a rule-based haplotyping method for pedigree data with tightly linked markers. We formulate Mendelian constraints as a linear system of inheritance variables and solve the linear system using disjoint-set data structures. Our algorithm achieved the lowest time complexity among all existing methods. Comparisons with two popular algorithms showed that this algorithm made 10 to 105-fold improvements on a variety of parameter settings. Based on the zero-recombinant haplotype inference, we went on to construct a general framework for haplotyping population and pedigree mixed data that consist of many families with unrelated founders, by combining novel techniques of recombination event detection and maximum likelihood optimization. This method makes it possible to do the genome-wide haplotype inference on pedigree and population mixed data.
Jing Li (Committee Chair)
Xiaofeng Zhu (Committee Member)
Mehmet Koyuturk (Committee Member)
Soumya Ray (Committee Member)
79 p.
Bioinformatics; Computer Science
haplotype inference; genetic linkage; recombination; pedigree; SNP; human genetic variation; linear systems

Recommended Citations

Citations

  • Li, X. (2010). Haplotype Inference from Pedigree Data and Population Data [Doctoral dissertation, Case Western Reserve University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=case1259867573

    APA Style (7th edition)

  • Li, Xin. Haplotype Inference from Pedigree Data and Population Data. 2010. Case Western Reserve University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=case1259867573.

    MLA Style (8th edition)

  • Li, Xin. "Haplotype Inference from Pedigree Data and Population Data." Doctoral dissertation, Case Western Reserve University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1259867573

    Chicago Manual of Style (17th edition)

case1259867573
913
© 2009, all rights reserved.
This open access ETD is published by Case Western Reserve University School of Graduate Studies and OhioLINK.