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Panel Construction and Haplotype Phasing of Iranian Genomes using Multimodal Genomics Data

Shadrooy Jadid, Mahdi | 2024

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 57583 (19)
  4. University: Sharif University of Technology
  5. Department: Computer Engineering
  6. Advisor(s): Motahari, Abolfazl
  7. Abstract:
  8. In recent decades, genetics has become one of the key pillars in medical and scientific research, and haplotype analysis plays a crucial role in understanding the genetic structure of populations. Haplotypes are specific combinations of alleles at different loci in the genome that are inherited together and provide valuable information about genetic history and intra-population diversity. One of the challenges in this field is the mismatch between the existing reference panels and the genetic characteristics of the Iranian population, as many of these panels have been developed based on data from non-Iranian populations. This mismatch can lead to incorrect results in genetic analyses. In this study, we have developed a novel method for constructing a reference panel of haplotypes for the Iranian population using exome sequencing data. This method, especially in scenarios with a low number of SNPs, has performed better than existing methods, accurately phasing haplotypes with lower error rates. The results of this study, supported by data from the 1000 Genomes Project, show that our proposed method has, on average, resulted in an %11 improvement in the mean error rate metric in regions with both low and high SNP counts. Additionally, in more complex regions with higher SNP counts, combining this method with the Beagle algorithm has led to a significant reduction in error rates, with an improvement of %5.5
  9. Keywords:
  10. Haplotype ; Whole Exome Sequencing ; Population Genetics ; Single Nucleotide Polymorphism (SNP) ; Haplotype Phasing

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