title: Alu insertion profiling: array-based methods to detect Alu insertions in the human genome.
abstract: The analysis of the genetic variability associated to Alu sequences was hampered by the absence of genome-wide methodologies able to efficiently detect new polymorphisms/mutations among these repetitive elements. Here we describe two Alu insertion profiling (AIP) methods based on the hybridization of Alu-flanking genomic fragments on tiling microarrays. Protocols are designed to preferentially detect active Alu subfamilies. We tested AIP methods by analyzing chromosomes 1 and 6 in two genomic samples. In genomic regions covered by array-features, with a sensitivity of 2% (AIP1) -4% (AIP2) and 5% (AIP1) -8% (AIP2) for the old J and S Alu lineages respectively, we obtained a sensitivity of 67% (AIP1) -90% (AIP2) for the young Ya subfamily. Among the loci showing sample-to-sample differences, 5 (AIP1) -8 (AIP2) were associated to known Alu polymorphisms. Moreover, we were able to confirm by PCR and DNA sequencing 4 new intragenic Alu elements, polymorphic in 10 additional individuals.
authors.affiliation: Advanced Technology Center for Aging Research, Scientific Technological Area, INRCA-IRCCS, Ancona, Italy.
authors.forename: Maurizio
authors.initials: M
authors.lastname: Cardelli
authors.forename: Francesca
authors.initials: F
authors.lastname: Marchegiani
authors.forename: Mauro
authors.initials: M
authors.lastname: Provinciali
mesh_terms: D020087:Alu Elements; D002878:Chromosomes, Human, Pair 1 / Q000235:genetics; D002896:Chromosomes, Human, Pair 6 / Q000235:genetics; D004251:DNA Transposable Elements; D020869:Gene Expression Profiling / Q000379:methods*; D056426:Genetic Loci; D015894:Genome, Human; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics; D016254:Mutagenesis, Insertional; D020411:Oligonucleotide Array Sequence Analysis; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D044767:Ubiquitin-Protein Ligases / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D008565:Membrane Proteins; C460140:NKAIN2 protein, human; D044767:Ubiquitin-Protein Ligases; C111567:parkin protein