title: Mobile interspersed repeats are major structural variants in the human genome.
abstract: 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.
authors.affiliation: Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
authors.forename: Cheng Ran Lisa
authors.initials: CR
authors.lastname: Huang
authors.forename: Anna M
authors.initials: AM
authors.lastname: Schneider
authors.forename: Yunqi
authors.initials: Y
authors.lastname: Lu
authors.forename: Tejasvi
authors.initials: T
authors.lastname: Niranjan
authors.forename: Peilin
authors.initials: P
authors.lastname: Shen
authors.forename: Matoya A
authors.initials: MA
authors.lastname: Robinson
authors.forename: Jared P
authors.initials: JP
authors.lastname: Steranka
authors.forename: David
authors.initials: D
authors.lastname: Valle
authors.forename: Curt I
authors.initials: CI
authors.lastname: Civin
authors.forename: Tao
authors.initials: T
authors.lastname: Wang
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Wheelan
authors.forename: Hongkai
authors.initials: H
authors.lastname: Ji
authors.forename: Jef D
authors.initials: JD
authors.lastname: Boeke
authors.forename: Kathleen H
authors.initials: KH
authors.lastname: Burns
mesh_terms: D041321:Chromosomes, Human, X; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004251:DNA Transposable Elements; D040181:Genetic Diseases, X-Linked / Q000235:genetics; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis
chemical_list: D004251:DNA Transposable Elements; D004262:DNA Restriction Enzymes