TY - JOUR
T1 - An advanced enrichment method for rare somatic retroelement insertions sequencing
AU - Komkov, Alexander Y.
AU - Minervina, Anastasia A.
AU - Nugmanov, Gaiaz A.
AU - Saliutina, Mariia V.
AU - Khodosevich, Konstantin V.
AU - Lebedev, Yuri B.
AU - Mamedov, Ilgar Z.
PY - 2018
Y1 - 2018
N2 - 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.
AB - 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.
KW - Genomic normalization
KW - Kamchatka Crab duplex-specific nuclease
KW - Somatic retroelement insertions
U2 - 10.1186/s13100-018-0136-1
DO - 10.1186/s13100-018-0136-1
M3 - Journal article
C2 - 30450130
AN - SCOPUS:85055772968
SN - 1759-8753
VL - 9
SP - 1
EP - 11
JO - Mobile DNA
JF - Mobile DNA
IS - 1
M1 - 31
ER -