An advanced enrichment method for rare somatic retroelement insertions sequencing

• Published in: Mobile DNA
• Main Authors: Alexander Y. Komkov, Anastasia A. Minervina, Gaiaz A. Nugmanov, Mariia V. Saliutina, Konstantin V. Khodosevich, Yuri B. Lebedev, Ilgar Z. Mamedov
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2018
• Subjects: Somatic retroelement insertions; Genomic normalization; Kamchatka Crab duplex-specific nuclease; Genetics; QH426-470; Kamchatka; Kamchatka crab
• Online Access: https://doi.org/10.1186/s13100-018-0136-1; https://doaj.org/article/cf35768c383146e68c0de6bd418e038c

Abstract Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells.