High-Throughput LINE-1 Retrotransposon Discovery in Humans
Ontology highlight
ABSTRACT: 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.
PROVIDER: phs000273.v1.p1 | EGA |
REPOSITORIES: EGA
Publications
High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes.
Ewing Adam D AD Kazazian Haig H HH
Genome research 20100520 9
Using high-throughput sequencing, we devised a technique to determine the insertion sites of virtually all members of the human-specific L1 retrotransposon family in any human genome. Using diagnostic nucleotides, we were able to locate the approximately 800 L1Hs copies corresponding specifically to the pre-Ta, Ta-0, and Ta-1 L1Hs subfamilies, with over 90% of sequenced reads corresponding to human-specific elements. We find that any two individual genomes differ at an average of 285 sites with ...[more]
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