An advanced enrichment method for rare somatic retroelement insertions sequencing
| Autor: | Yuri B. Lebedev, A Komkov, Anastasia A. Minervina, Ilgar Z. Mamedov, G Nugmanov, Konstantin Khodosevich, Mariia V. Saliutina |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
lcsh:QH426-470 Somatic cell Methodology Tumor cells Computational biology Biology Germline Human genetics Re identification DNA sequencing Kamchatka Crab duplex-specific nuclease 03 medical and health sciences lcsh:Genetics 030104 developmental biology 0302 clinical medicine Somatic retroelement insertions Genomic normalization Molecular Biology Developmental biology 030217 neurology & neurosurgery |
| Zdroj: | Komkov, A Y, Minervina, A A, Nugmanov, G A, Saliutina, M V, Khodosevich, K V, Lebedev, Y B & Mamedov, I Z 2018, ' An advanced enrichment method for rare somatic retroelement insertions sequencing ', Mobile DNA, vol. 9, no. 1, 31, pp. 1-11 . https://doi.org/10.1186/s13100-018-0136-1 Mobile DNA Mobile DNA, Vol 9, Iss 1, Pp 1-11 (2018) |
| ISSN: | 1759-8753 |
| Popis: | 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. Electronic supplementary material The online version of this article (10.1186/s13100-018-0136-1) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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