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COMPARISON OF GENOTYPE IMPUTATION ON CHROMOSOME 5 IN A POPULATION ISOLATE USING HAPLOTYPES PHASED WITH AND WITHOUT TOPMED GENOTYPES

Witten, Joshua (2023) COMPARISON OF GENOTYPE IMPUTATION ON CHROMOSOME 5 IN A POPULATION ISOLATE USING HAPLOTYPES PHASED WITH AND WITHOUT TOPMED GENOTYPES. Master's Thesis, University of Pittsburgh. (Unpublished)

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Abstract

Imputation is a method of predicting unknown genotypes in a dataset by comparing measured genotypes to the patterns in a panel of reference haplotypes. The choice of reference panels matters, as does the phasing of the haplotypes in the chosen panel. Here I compared the imputa-tion accuracy of two reference panels: a panel of Samoan participants phased together with 1000 Genomes participants (“with-1000G”) and a panel of those participants phased together with the participants in the Trans-Omics in Precision Medicine (TOPMed) Program (“with-1000G+TOPMed”). I found no difference in the imputation accuracy between the panels. I also examined imputation quality statistics of variants in the 99th percentile of population branch statistics. They are the variants with allele frequencies most divergent from other populations and, therefore, might be most affected by differences in phasing. However, there was no differ-ence between the two panels in those results either. More accurate imputation improves the quality of genetic research, which should lead to an improved understanding of the biology of disease and improved information about efficacious public health interventions.

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Details

Item Type: University of Pittsburgh ETD
Status: Unpublished
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Witten, Joshuajow138@pitt.edujow1380009-0000-6284-9673
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Thesis AdvisorMinster, Ryanrminster@pitt.edurminster0000-0001-7382-6717
Committee MemberWeeks, Daniel Eweeks@pitt.eduweeks0000-0001-9410-7228
Committee MemberCarlson, Jenna Colavincenzojnc35@pitt.edujnc350000-0001-5483-0833
Date: 17 May 2023
Date Type: Publication
Defense Date: 28 April 2023
Approval Date: 17 May 2023
Submission Date: 11 May 2023
Access Restriction: 2 year -- Restrict access to University of Pittsburgh for a period of 2 years.
Number of Pages: 35
Institution: University of Pittsburgh
Schools and Programs: School of Public Health > Human Genetics
Degree: MS - Master of Science
Thesis Type: Master's Thesis
Refereed: Yes
Uncontrolled Keywords: Imputation, Soifua
Date Deposited: 17 May 2023 18:03
Last Modified: 17 May 2023 18:03
URI: http://d-scholarship.pitt.edu/id/eprint/44862

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