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 language | English |
|---|---|
| Pages (from-to) | 340-346 |
| Number of pages | 7 |
| Journal | Genomics |
| Volume | 99 |
| Issue number | 6 |
| DOIs | |
| Publication status | Published - Jun 2012 |
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Keywords
- Alu
- Microarray
- Retroelements
- Tiling array
- Transposons
ASJC Scopus subject areas
- Genetics
Cite this
Alu insertion profiling : Array-based methods to detect Alu insertions in the human genome. / Cardelli, Maurizio; Marchegiani, Francesca; Provinciali, Mauro.
In: Genomics, Vol. 99, No. 6, 06.2012, p. 340-346.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Alu insertion profiling
T2 - Array-based methods to detect Alu insertions in the human genome
AU - Cardelli, Maurizio
AU - Marchegiani, Francesca
AU - Provinciali, Mauro
PY - 2012/6
Y1 - 2012/6
N2 - 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.
AB - 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.
KW - Alu
KW - Microarray
KW - Retroelements
KW - Tiling array
KW - Transposons
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UR - http://www.scopus.com/inward/citedby.url?scp=84861752695&partnerID=8YFLogxK
U2 - 10.1016/j.ygeno.2012.03.005
DO - 10.1016/j.ygeno.2012.03.005
M3 - Article
C2 - 22495107
AN - SCOPUS:84861752695
VL - 99
SP - 340
EP - 346
JO - Genomics
JF - Genomics
SN - 0888-7543
IS - 6
ER -