Homo sapiens Raw sequence reads

Eukaryotic genomes are shaped by mobile genetic elements. In modern humans, active copies of Long INterspersed Element-1 (LINE-1, L1) are continually generating new insertion variants of this sequence and other retrotransposons. To characterize structural variants caused by L1, we developed a targeted means for Transposon Insertion Profiling by sequencing (TIP-seq) and used it to map L1 in 108 individuals of 15 population groups. We found 1918 L1 insertions; 1208 are not included in the human reference genome assembly. We demonstrate that L1 variants are useful markers of human ancestries and share evolutionary history with single nucleotide polymorphisms (SNPs). Linkage disequilibrium with SNPs can be used to identify L1 insertions on haplotypes associated with human phenotypes. Insertion site sequences reflect known aspects of retrotransposition. Moreover, broader epigenetic features at L1 sites suggest preferences inherent to insertion or the likelihood that a L1 will be maintained in populations. As the most comprehensive list of polymorphic L1 to date, this work provides a resource for studying genetic variation in humans.