Characterization of Genomic Regions for Improved Reference Genomes Using OM & Sequencing Tech
Wednesday, June 26, 2024
3:00 PM-5:00 PM
BIOMED PhD Thesis Defense
Title:
Characterization of Genomic Regions for Improved Reference Genomes Using Optical Mapping (OM) and Sequencing Technologies
Speaker:
Jessica Wong, PhD Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University
Advisor:
Ming Xiao, PhD
Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University
Details:
The completion of the hg38 human reference genome in 2003 marked a significant milestone in genomics research, serving as a critical resource for understanding the genetic basis of health and diseases, and guiding the development of various genotyping and computational tools. Despite its importance, the reference genome has several limitations. It lacks global genetic diversity as it is based on a small sample of U.S. donors, it fails to include many common sequencing variations, and it does not accurately reflect haplotype configurations from different populations. Moreover, large portions of the genome, including pericentromeric and subtelomeric regions, remain uncharacterized due to their highly polymorphic and repetitive nature, which poses significant challenges for current sequencing technologies. These limitations hinder the accurate alignment of reads and downstream analyses, resulting in the exclusion of complex regions from genomic studies and an incomplete understanding of structural variations, which are critical in genetic diversity and disease.
To address these gaps, the integration of long-read sequencing technologies and optical mapping has been proposed. These technologies offer higher accuracy and the ability to resolve complex regions and SVs that short-read sequencing cannot. The integration of these methods were used to create comprehensive, haplotype-resolved reference genomes in different populations. TThis thesis sought to develop and validate pipelines that integrate these advanced technologies to study regions across diverse populations, ultimately leading to better identification of variants and improving genotype-to-phenotype correlations.
Contact Information
Natalia Broz
njb33@drexel.edu