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Title: Variation of Homo genus specific NUMTs: Insight into the human evolution
Author: Zacarías Pons, Lluís
Director: Merino Arranz, David
Tutor: Jordana Comin, Xavier
Keywords: population genetics
Issue Date: 4-Jun-2019
Publisher: Universitat Oberta de Catalunya (UOC)
Abstract: Insertions of mitochondrial DNA (mtDNA) sequences into nuclear genome (NUMTs) have been largely identified in Homo genus, some of them occurring after the divergence from other primates. The low number of required insertions required to obtain a good level of population differentiation, altogether with the absence of homoplasy in NUMTs (given its mitochondrial origin) suggest that these insertions may be considered a useful marker to trace Homo populations through history . Therefore, NUMTs may offer a new perspective of human phylogeny and ancient events, such as the relation and inbreeding among different prehistorical populations. This study aims to study current populations using aligned genomes from 2,535 subjects of the Phase 3 of the 1000 Genomes Project and ancestral Neanderthal and Denisovan samples through 69 different homo-specific NUMTs. However, the homology with mtDNA (which may be mis-aligned to the nuclear genome) poses a serious problem to the NUMT presence polymorphism status determination. In addition, since these sequences are mostly located in non-coding regions, they are only available on Whole Genome Sequencing (WGS) samples thus resulting in a really low coverage. To handle these limitations and perform a large-scale analysis, we developed an approach based on overlapping insertion regions detection, paired-end distances and local alignments to the GRCh37 human reference sequence containing and lacking the studied NUMT. This pipeline allowed to obtain a catalog of variation of Homo-specific NUMTs and to refine some given NUMTs position coordinates. Finally, NUMT insertions were concluded to perform a good population analysis.
Language: English
Appears in Collections:Bachelor thesis, research projects, etc.

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