Publication: Analysis Of The 1000-Genome Project Sequencing Data Reveals An Unexpectedly High Level Of Human Genetic Polymorphisms Derived From Mobile Elements

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Title Analysis Of The 1000-Genome Project Sequencing Data Reveals An Unexpectedly High Level Of Human Genetic Polymorphisms Derived From Mobile Elements
Authors/Editors* P, Liang, X, Luo, F, Zhang
Where published* The 59th Annual Meeting of American Society of Human Genetics
How published* Proceedings
Year* 2009
Mobile elements constitute approximately half of the human genome, and they impact the evolution and function of the genomes via a variety of mechanisms. With members of certain classes of mobile elements remain active, they contribute to an important part of genetic polymorphisms among humans via recent and de novo DNA transposition, as well as homologous recombination, attributing partly to the phenotype differences in humans, such as disease susceptibility. So far, several thousands of retrotransposon insertion polymorphisms (RIPs) have been documented, with the majority of those identified from computational comparative genomic analyses based on limited human genomic sequences. But an accurate estimation of the actual level of such types of polymorphisms existing in humans remains infeasible due to technical difficulties. In an effort to address this question, we utilized the very recently available new and rich human genome sequence data generated by The 1000 Genome Project Consortium. In this preliminary analysis, we focused on the data for a few individual genomes, for which deep sequencing data has been available, and used the pair end sequence reads for identifying mobile element insertions that are present in the reference genome but not in the new genomes. By comparing such the data with those documented in the database of Retrotransposon Insertion Polymorphisms in humans (dbRIP), we observed an unexpectedly large number of novel polymorphisms from Alu and L1 insertions, with the majority belonging to older subfamilies that are thought to be less active. Surprisingly, we also identified a large number of candidate cases for the movement of DNA transposons, which are considered to be completely deadin the human genomes. In addition, we attempted to assess the rate of de novo DNA transposition in one reproductive generation by comparing between the children and their parents. While these computationally identified DNA transposition polymorphisms required to be validated, our preliminary data does suggest: 1) personal genome data generated using the 2nd generation of sequencing technologies is of great utility for identifying novel transposition-derived genetic variations; 2) the degree of such type of variations may be much higher than what we currently appreciate. This research is in part supported by grants from the Canada Research Chair program, CFI, Ontario MRI and Brock University to PL and is facilitated by the use of SHARCNET HPC.

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