López Gerena, Juan Omar

Publication Search Results

Now showing 1 - 1 of 1

High precision detection of LINE-1s in human genomes
(2022-05-20) López Gerena, Juan Omar; Seguel, Jaime; College of Engineering; Vélez Rivera, Bienvenido; Schütz Schmuck, Marko; Torres García, Wandaliz; Department of Computer Science and Engineering; Isaza Brando, Clara E.
Long interspersed elements 1 (LINE-1s or L1s) are autonomous retrotransposons that make up about 17% of the human genome. Strong correlations between abnormal L1 expression and several human diseases have been reported, which has motivated an interest in accurate quantification of the number of L1 copies present in any given biological specimen. A main obstacle towards this aim is that L1s are relatively long DNA segments with regions of high variability often with truncated or added fragments. These particularities render traditional alignment strategies, such as seed-and-extend, inefficient, as the number of segments that are similar to L1s explodes exponentially. Here, a new strategy is introduced to increase quantification efficiency, resulting in a more accurate identification of L1s. This dissertation discusses this method and experimentally validates its superiority for L1 detection over alternative methods, and also considers some additional potential applications.