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INCLUSION OF CUSTOM MARKERS DOES NOT IMPROVE GENOTYPE IMPUTATION ACCURACY IN A POPULATION ISOLATE

Dikec, Devin (2022) INCLUSION OF CUSTOM MARKERS DOES NOT IMPROVE GENOTYPE IMPUTATION ACCURACY IN A POPULATION ISOLATE. Master's Thesis, University of Pittsburgh. (Unpublished)

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Abstract

The field of genetics has been expanding as researchers can now study the entire genome to observe associations between diseases and specific allele markers. Due to the expensive nature of genotyping, an important set of markers can instead be genotyped so the remainder of the genome can be inferred from patterns computationally. This process of genotype imputation significantly reduces costs, but references patterns from mainly European populations when making computational predictions. The island nation of Samoa shows significant genetic differences as a population isolate with bottleneck effects, so little data shows how well these selected markers predict the Samoan genome. I aim to compare a standardized scaffold of allele markers using an Illumina chip against an enhanced scaffold with an additional 5,000 custom Samoan markers added for associations with traits of interest. I will be imputing the missing genotypes from each scaffold using a master reference panel of Samoan individuals with additional 1000 Genomes individuals sequenced by TopMed. The imputations are run for chromosome 21 as a test set for its smaller size, followed by chromosome 5 for its connection to Samoan specific traits of higher BMI and HDL levels. The generated results provided minor allele frequency (MAF) and two measures of imputation accuracy, r2 and empirical r2, to observe from each imputation using the unique scaffolds. These outputs were compared by various graphical representations. While the output values were not identical, their comparisons showed no discernable difference by scaffold. Most outputs by scaffold were similar but a unique result of interest is r2 comparison on chromosome 5. The custom Samoan markers showed unusual clumps in r2 value outputs by scaffold. This change could show an improvement from the inclusion of the new markers but is the only significant result of difference from all comparisons. Therefore, the main conclusion seems to be that these included markers do not significantly alter imputation, but if available may be helpful for future accuracy in Samoan data.


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Details

Item Type: University of Pittsburgh ETD
Status: Unpublished
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Dikec, Devindad165@pitt.edudad165
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Thesis AdvisorMinster, Ryanrminster@pitt.edurminster0000-0001-7382-6717
Committee MemberWeeks, Danielweeks@pitt.eduweeks0000-0001-9410-7228
Committee MemberCarlson, Jennajnc35@pitt.edujnc350000-0001-5483-0833
Date: 11 May 2022
Date Type: Publication
Defense Date: 22 April 2022
Approval Date: 11 May 2022
Submission Date: 29 April 2022
Access Restriction: 2 year -- Restrict access to University of Pittsburgh for a period of 2 years.
Number of Pages: 42
Institution: University of Pittsburgh
Schools and Programs: Graduate School of Public Health > Human Genetics
Degree: MS - Master of Science
Thesis Type: Master's Thesis
Refereed: Yes
Uncontrolled Keywords: imputation, scaffolds, Samoa, custom markers
Date Deposited: 11 May 2022 19:53
Last Modified: 30 Jun 2022 15:13
URI: http://d-scholarship.pitt.edu/id/eprint/42893

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