ATLAS: A system to selectively identify human-specific L1 insertions

Retrotransposition of L1 LINEs (long interspersed elements) continues to sculpt the human genome. However, because recent insertions are dimorphic, they are not fully represented in sequence databases. Here, we have developed a system, termed "ATLAS" (amplification typing of L1 active subfamilies), that enables the selective amplification and display of DNA fragments containing the termini of human-specific L1s and their respective flanking sequences. We demonstrate that ATLAS is robust and that the resultant display patterns are highly reproducible, segregate in Centre d'Etude du Polymorphisme Humain pedigrees, and provide an individual-specific fingerprint. ATLAS also allows the identification of L1s that are absent from current genome databases, and we show that some of these L1s can retrotranspose at high frequencies in cultured human cells. Finally, we demonstrate that ATLAS also can identify single-nucleotide polymorphisms within a subset of older, primate-specific L1s. Thus, ATLAS provides a simple, high-throughput means to assess genetic variation associated with L1 retrotransposons.