Building an Iranian Reference Panel by Imputing Low-coverage Genomic Data

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Poursoleymani, Rooholla | 2022

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Type of Document: M.Sc. Thesis
Language: Farsi
Document No: 55778 (19)
University: Sharif University of Technology
Department: Computer Engineering
Advisor(s): Foroughmand Araabi, Mohammad Hadi
Abstract:
One of the most available genomics data in Iran is non-invasive parental testing (NIPT) data obtained from the blood of pregnant mothers after the tenth week of pregnancy using the new generation sequencing technology. Sequencer output is a combination of maternal and fetal read data, most of which (about 90%) is from maternal DNA. These data have very low coverage of the genome, but their advantage is that they read the entire human genome. Low coverage data has led to the loss of large parts of the genome, but having a large number of samples helps to compensate for this problem. The purpose of this project is to use this data with the help of imputation methods to build a reference for the Iranian genomes. The imputation of missing genomics data is a category of methods that try to predict the lost data in the genome of each sample using statistical methods. These methods are divided into two categories based on the use or non-use of the reference panel. Unfortunately, the lack of complete genome data in Iran has led to the lack of an Iranian reference for retrieving lost data points
Keywords:
Genome Sequencing ; Missing Value Imputation Methods ; Next Generation of Sequencing (NGS) ; Whole Genome Alignment ; Non-Invasive Parental Testing ; Reference Panel