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An Investigation of Personal Ancestry Using Haplotypes

Brennan, Patrick J
http://rave.ohiolink.edu/etdc/view?acc_num=toledo1501705310326744

Abstract Details

2017, Master of Science, University of Toledo, Biology (Cell-Molecular Biology).
Several companies over the past decade have started to offer ancestry analysis, the most notable company being 23andMe. For a relatively low price, 23andMe will sequence select variants in a person’s genome to determine where their ancestors came from. Since 23andMe is a private company, the exact techniques and algorithms it uses to determine ancestry are proprietary. Many customers have wondered about the accuracy of these results, often citing their own genealogical research of recent ancestors. To bridge the gap between 23andMe and the public, we sought to provide a tool that could assess the ancestry results of 23andMe. Using publicly available 23andMe genotype files, we constructed a program pipeline that takes these files and compares them against genomes from the 1000 Genomes Project. We constructed haplotypes from the 23andMe file by converting 50 adjacent SNPs (single nucleotide polymorphisms) into haplotypes and comparing them against the haplotypes of 2504 individuals in the Phase 3 data from the 1000 Genome Project. To smooth the data, we bundled together six of our haplotype segments to form an “IBD segment” (Identity-by-descent segment) and used a point scoring system to calculate the highest matching population. Our pipeline determined ancestry results for 57 individuals with similar results to 23andMe. Fifty of our subjects showed European ancestry, while the other seven subjects showed ancestry from East Asia, Africa, America, and South Asia. Of our 5 geographic categories (South Asia, Africa, America, Europe, East Asia), 98% of our subjects showed ancestral representation from 4 of the 5 categories. In addition to ancestry, we also investigated IBD sharing across populations, particularly IBD segments in the Human Leukocyte Antigen (HLA) region on chromosome 6. We hope this tool will help 23andMe customers and those of similar genotyping companies understand the methods used to determine ancestry and verify their results.
Alexei Fedorov (Committee Chair)
Robert Blumenthal (Committee Member)
Sadik Khuder (Committee Member)
53 p.
Bioinformatics
haplotypes; population; 1000 genomes; genomes; ancestry; 23andMe; perl; bioinformatics; SNP

Recommended Citations

Citations

  • Brennan, P. J. (2017). An Investigation of Personal Ancestry Using Haplotypes [Master's thesis, University of Toledo]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1501705310326744

    APA Style (7th edition)

  • Brennan, Patrick. An Investigation of Personal Ancestry Using Haplotypes. 2017. University of Toledo, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=toledo1501705310326744.

    MLA Style (8th edition)

  • Brennan, Patrick. "An Investigation of Personal Ancestry Using Haplotypes." Master's thesis, University of Toledo, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1501705310326744

    Chicago Manual of Style (17th edition)

toledo1501705310326744
938
© 2017, all rights reserved.
This open access ETD is published by University of Toledo and OhioLINK.