Alu insertion profiling: Array-based methods to detect Alu insertions in the human genome

Research output: Contribution to journalArticle

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.

Original languageEnglish
Pages (from-to)340-346
Number of pages7
JournalGenomics
Volume99
Issue number6
DOIs
Publication statusPublished - Jun 2012

Fingerprint

Human Genome
Alu Elements
Chromosomes, Human, Pair 6
Chromosomes, Human, Pair 1
DNA Sequence Analysis
Genome
Polymerase Chain Reaction
Mutation

Keywords

  • Alu
  • Microarray
  • Retroelements
  • Tiling array
  • Transposons

ASJC Scopus subject areas

  • Genetics

Cite this

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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.",
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