High-Throughput Retrotransposon Discovery in Humans

The aim of this study is to discover LINE-1 (L1) insertion sites present in humans that are absent from the reference
genome sequence. We use the distinguishing nucleotide characteristics of human-specific L1 elements to resequence
the L1 3' flanking regions thus locating the L1 insertion sites whether or not they are present in the reference
genome assembly. In doing so, we have uncovered a higher than expected number of non-reference L1 insertions, an
average of 152 insertions per individual. In addition, we find that any two individuals differ at an average
of 285 sites with respect to presence or absence of L1 insertions in those sites, and use this to estimate the
rate of retrotransposition in humans at 1 event per 140 live births (95% c.i. 1/95 to 1/270). We show that
individual 'L1 profiles' recapitulate genetic ancestry as expected, and find that dimorphic insertions
are more frequent in introns relative to fixed insertions.]]>
Protocol for retrotransposon insertion site discovery via Illumina sequencingAfter the study was initiated in 2007, the technique was optimized through several iterations until 2009. The first manuscript
describing the work was prepared in 2010.]]>