title: Combining Amplification Typing of L1 Active Subfamilies (ATLAS) with High-Throughput Sequencing.
abstract: With the advent of new generations of high-throughput sequencing technologies, the catalog of human genome variants created by retrotransposon activity is expanding rapidly. However, despite these advances in describing L1 diversity and the fact that L1 must retrotranspose in the germline or prior to germline partitioning to be evolutionarily successful, direct assessment of de novo L1 retrotransposition in the germline or early embryogenesis has not been achieved for endogenous L1 elements. A direct study of de novo L1 retrotransposition into susceptible loci within sperm DNA (Freeman et al., Hum Mutat 32(8):978-988, 2011) suggested that the rate of L1 retrotransposition in the germline is much lower than previously estimated (<1 in 400 individuals versus 1 in 9 individuals (Kazazian, Nat Genet 22(2):130, 1999). Based on these revised estimates of the L1 retrotransposition rate, we modified the ATLAS L1 display technique (Badge et al., Am J Hum Genet 72(4):823-838, 2003) to investigate de novo L1 retrotransposition in human genomes. In this chapter, we describe how we combined a high-coverage ATLAS variant with high-throughput sequencing, achieving 11-25× sequence depth per single amplicon, to study L1 retrotransposition in whole genome amplified (WGA) DNAs.
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. rr11@sanger.ac.uk.
authors.forename: Raheleh
authors.initials: R
authors.lastname: Rahbari
authors.affiliation: Department of Genetics, University of Leicester, Leicester, UK.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Badge
mesh_terms: D019295:Computational Biology / Q000379:methods; D015894:Genome, Human; D015698:Genomic Library; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D058889:Molecular Typing / Q000379:methods; D016133:Polymerase Chain Reaction / Q000379:methods
keywords: L1; LINE-1; Non-LTR retrotransposon; Polymorphism; Retroelement; Retrotransposition