Cell
Volume 141, Issue 7, 25 June 2010, Pages 1171-1182
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Article
Mobile Interspersed Repeats Are Major Structural Variants in the Human Genome

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Summary

Characterizing structural variants in the human genome is of great importance, but a genome wide analysis to detect interspersed repeats has not been done. Thus, the degree to which mobile DNAs contribute to genetic diversity, heritable disease, and oncogenesis remains speculative. We perform transposon insertion profiling by microarray (TIP-chip) to map human L1(Ta) retrotransposons (LINE-1 s) genome-wide. This identified numerous novel human L1(Ta) insertional polymorphisms with highly variant allelic frequencies. We also explored TIP-chip's usefulness to identify candidate alleles associated with different phenotypes in clinical cohorts. Our data suggest that the occurrence of new insertions is twice as high as previously estimated, and that these repeats are under-recognized as sources of human genomic and phenotypic diversity. We have just begun to probe the universe of human L1(Ta) polymorphisms, and as TIP-chip is applied to other insertions such as Alu SINEs, it will expand the catalog of genomic variants even further.

Highlights

► Retrotransposons are important components of structural variation in human genomes ► TIP-chip maps human retroelements sometimes missed by whole-genome sequencing ► L1 retrotransposons are twice as active as previously estimated ► TIP-chip identifies candidate human disease alleles ignored by exon sequencing

DNA
EVO_ECOL

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Present address: Center for Stem Cell Biology and Regenerative Medicine, Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA