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2004
LSU-HHMI Summer Undergraduate Research Program |
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 Cheney
Huang and Nadica Stoilova, Mark Batzer, Biological Sciences
Display-based Ascertainment of Recent L1 Elements in the
Human Genome
The L1-Ta subfamily of Long INterspersed Elements (LINEs) consists
exclusively of human-specific L1 elements. Some of these elements
are currently active, that is, capable of retrotransposition
and producing polymorphisms and genetic defects. The Ta subfamily
accounts for almost all L1 replication in humans. Because the
public database of the human genome is based primarily (~75%)
on one individual, any determination of L1 insertion loci using
the public database would likely be biased in favor of inserts
that are found at high frequencies in all human populations
and inserts that are present in that individual’s population
of origin. As such, the loci characterized exclusively using
the public database (computationally) have limited utility.
Therefore, we have implemented a “wet bench” approach
to complement the computational ascertainment of L1 loci. By
isolating L1-Ta elements by PCR display, we eliminated the bias
inherent in methods relying on the published database. In this
work, we applied our PCR-display methodology to the genomes
of three individuals each from six human populations: Egyptian,
African-American, German, Chinese, Japanese, and Southeast Asian
(excluding Chinese and Japanese). In the limited time available,
we sequenced 168 unique loci from which we obtained 58 contigs.
When compared to the Human Genome Database using BLAT, nine
were found to be absent, thus polymorphic, newly discovered
LINE elements. In the future, PCR primers will be designed for
the potentially new-found LINE’s and the loci will be
tested for their specificity in certain populations. Once completed
these loci can be used as population markers for use in forensics
studies, the study of human evolution and human population dynamics.
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