Analysis of Somatic LINE-1 Insertions in Neurons

Part of the Neuromethods book series (NM, volume 131)


The method described here is designed to detect and localize somatic genome variation caused by the human retrotransposon LINE-1 (L1) in the genome of neuronal cells. This method combines single-cell manipulation and whole genome amplification technology with a hybridization-based, high-throughput sequencing method called Retrotransposon Capture sequencing (RC-seq) for the precise analysis of the L1 insertion content of single cell genomes. The method is divided into four major sections: extraction of neuronal nuclei and single nuclei isolation; whole genome amplification; RC-seq; and experimental validation of putative insertions.

Key words

Retrotransposition Somatic mosaicism Single-cell Whole genome sequencing (WGS) LINE-1 Mobile genetic element Neurogenesis 



G.J.F. acknowledges the support of a CSL Centenary Fellowship. F.J.S-L. was supported by a postdoctoral fellowship from the Alfonso Martín Escudero Foundation (Spain) and the Peoples Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No PIOF-GA-2013-623324.

We also acknowledge the significant contribution of Dr. Adam D. Ewing in TEBreak settings adjustment for RC-seq sequencing data analysis, and J. Samuel Jesuadian and Marie-Jeanne H. C. Kempen in technical assistance.


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© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Mater Research Institute—University of QueenslandWoolloongabbaAustralia
  2. 2.Pfizer-Andalusian Government-University of Granada Centre for Genomics and Oncologic Research (Genyo)GranadaSpain
  3. 3.Queensland Brain InstituteUniversity of QueenslandBrisbaneAustralia

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