Haplotype Inference from Pedigree Data and Population Data

Haplotype Inference from Pedigree Data and Population Data

Bibliographic Details
Main Author: Li, Xin
Language:English
Published: Case Western Reserve University School of Graduate Studies / OhioLINK 2010
Subjects:
Bioinformatics
Computer Science
haplotype inference
genetic linkage
recombination
pedigree
SNP
human genetic variation
linear systems
Online Access:http://rave.ohiolink.edu/etdc/view?acc_num=case1259867573
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spelling ndltd-OhioLink-oai-etd.ohiolink.edu-case12598675732021-08-03T05:33:33Z Haplotype Inference from Pedigree Data and Population Data Li, Xin Bioinformatics Computer Science haplotype inference genetic linkage recombination pedigree SNP human genetic variation linear systems 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 10<sup>5</sup>-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. 2010 English text Case Western Reserve University School of Graduate Studies / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=case1259867573 http://rave.ohiolink.edu/etdc/view?acc_num=case1259867573 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws.
collection NDLTD
language English
sources NDLTD
topic Bioinformatics
Computer Science
haplotype inference
genetic linkage
recombination
pedigree
SNP
human genetic variation
linear systems
spellingShingle Bioinformatics
Computer Science
haplotype inference
genetic linkage
recombination
pedigree
SNP
human genetic variation
linear systems
Li, Xin
Haplotype Inference from Pedigree Data and Population Data
author Li, Xin
author_facet Li, Xin
author_sort Li, Xin
title Haplotype Inference from Pedigree Data and Population Data
title_short Haplotype Inference from Pedigree Data and Population Data
title_full Haplotype Inference from Pedigree Data and Population Data
title_fullStr Haplotype Inference from Pedigree Data and Population Data
title_full_unstemmed Haplotype Inference from Pedigree Data and Population Data
title_sort haplotype inference from pedigree data and population data
publisher Case Western Reserve University School of Graduate Studies / OhioLINK
publishDate 2010
url http://rave.ohiolink.edu/etdc/view?acc_num=case1259867573
work_keys_str_mv AT lixin haplotypeinferencefrompedigreedataandpopulationdata
_version_ 1719421688390615040

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