title: Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity.
abstract: We have utilized computational biology to screen GenBank for the presence of recently integrated Ya5 and Yb8 Alu family members. Our analysis identified 2640 Ya5 Alu family members and 1852 Yb8 Alu family members from the draft sequence of the human genome. We selected a set of 475 of these elements for detailed analyses. Analysis of the DNA sequences from the individual Alu elements revealed a low level of random mutations within both subfamilies consistent with the recent origin of these elements within the human genome. Polymerase chain reaction assays were used to determine the phylogenetic distribution and human genomic variation associated with each Alu repeat. Over 99 % of the Ya5 and Yb8 Alu family members were restricted to the human genome and absent from orthologous positions within the genomes of several non-human primates, confirming the recent origin of these Alu subfamilies in the human genome. Approximately 1 % of the analyzed Ya5 and Yb8 Alu family members had integrated into previously undefined repeated regions of the human genome. Analysis of mosaic Yb8 elements suggests gene conversion played an important role in generating sequence diversity among these elements. Of the 475 evaluated elements, a total of 106 of the Ya5 and Yb8 Alu family members were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. The newly identified Alu insertion polymorphisms will be useful tools for the study of human genomic diversity.
authors.affiliation: Departments of Pathology, Genetics Biochemistry and Molecular Biology Stanley S. Scott Cancer Center Neuroscience Center of Excellence, Louisiana State University Health Sciences Center, 1901 Perdido Street, New Orleans 70112, USA.
authors.forename: M L
authors.initials: ML
authors.lastname: Carroll
authors.forename: A M
authors.initials: AM
authors.lastname: Roy-Engel
authors.forename: S V
authors.initials: SV
authors.lastname: Nguyen
authors.forename: A H
authors.initials: AH
authors.lastname: Salem
authors.forename: E
authors.initials: E
authors.lastname: Vogel
authors.forename: B
authors.initials: B
authors.lastname: Vincent
authors.forename: J
authors.initials: J
authors.lastname: Myers
authors.forename: Z
authors.initials: Z
authors.lastname: Ahmad
authors.forename: L
authors.initials: L
authors.lastname: Nguyen
authors.forename: M
authors.initials: M
authors.lastname: Sammarco
authors.forename: W S
authors.initials: WS
authors.lastname: Watkins
authors.forename: J
authors.initials: J
authors.lastname: Henke
authors.forename: W
authors.initials: W
authors.lastname: Makalowski
authors.forename: L B
authors.initials: LB
authors.lastname: Jorde
authors.forename: P L
authors.initials: PL
authors.lastname: Deininger
authors.forename: M A
authors.initials: MA
authors.lastname: Batzer
mesh_terms: D020087:Alu Elements / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D019295:Computational Biology; D018899:CpG Islands / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D019992:Databases as Topic; D019143:Evolution, Molecular; D005785:Gene Conversion / Q000235:genetics; D018628:Gene Dosage; D014644:Genetic Variation / Q000235:genetics; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D016254:Mutagenesis, Insertional / Q000235:genetics; D009154:Mutation / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic / Q000235:genetics; D011323:Primates / Q000235:genetics; D044469:Racial Groups / Q000235:genetics
chemical_list: D017931:DNA Primers