Haploblock Detection Based on Reads and Population Structure

Please enable javascript in your browser.

Akbari, Elahe | 2022

129 Viewed

Type of Document: M.Sc. Thesis
Language: Farsi
Document No: 55233 (19)
University: Sharif University of Technology
Department: Computer Engineering
Advisor(s): Motahari, Abolfazl
Abstract:
Human is diploid specie that inherits a set of chromosomes from their mother and a set from their father. The process of separating the nucleotide content of a set of extracted maternal and paternal chromosomes for an individual or a population is called phasing the genome of the individual or the population. The placement of any two variants relative to each other in diploid species is possible in two forms: cis (placement of both variants on one chromosome), and trans (placement of variants on different chromosomes). Each of these conditions leads to different phenotypes. Thus, understanding how variants are placed relative to each other is a crucial problem in human biology which is solved by phasing methods. In this project we phase genotypes of a whole population simultaneously based on reads and population structure. The main challenge we face is how to model the problem given that the reads are short and insular and do not cover the whole genome, and the find an optimal or suboptimal algorithm to phase the genotypes based on this model. To assess the results we used both real and simulated data which is generated based on the population structure.
Keywords:
Genome Sequencing ; Phasing ; Phasing Haploblocks ; Haploblocks ; Population Genetics

No TOC