DNA copy-number analysis of the 22q11 deletion-syndrome region using array-CGH with genomic and PCR-based targets

  • Authors:
    • Kiran Kumar Mantripragada
    • Isabel Tapia-Páez
    • Elisabeth Blennow
    • Peter Nilsson
    • Anna Wedell
    • Jan P. Dumanski
  • View Affiliations

  • Published online on: February 1, 2004     https://doi.org/10.3892/ijmm.13.2.273
  • Pages: 273-279
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Abstract

Deletions and duplications of genomic segments commonly cause developmental disorders. The resolution and efficiency in diagnosing such gene-dosage alterations can be drastically increased using microarray-based comparative genomic hybridization (array-CGH). However, array-CGH currently relies on spotting genomic clones as targets, which confers severe limitations to the approach including resolution of analysis and reliable gene-dosage assessment of regions with high content of redundant sequences. To improve the methodology for analysis, we compared the use of genomic clones, repeat-free pools of amplified genomic DNA and cDNAs (single and pooled) as targets on the array. For this purpose, we chose q11.2 locus on chromosome 22 as a testing ground. Microdeletions at 22q11 cause birth defects collectively described as the DiGeorge/velocardiofacial syndrome. The majority of patients present 3 Mb typical deletions. Here, we report the construction of a gene-dosage array, covering 6 Mb of 22q11 and including the typically deleted region. We hybridized DNA from six DiGeorge syndrome patients to the array, and show that as little as 11.5 kb non-redundant, repeat-free PCR-generated sequence can be used for reliable detection of hemizygous deletions. By extrapolation, this would allow analysis of the genome with an average resolution of 25 kb. In the case of cDNAs our results indicate that 3.5 kb sequence is necessary for accurate identification of haploid/diploid dosage alterations. Thus, for regions rich in redundant sequences and repeats, such as 22q11, a specifically tailored array-CGH approach is good for gene copy number profiling.

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February 2004
Volume 13 Issue 2

Print ISSN: 1107-3756
Online ISSN:1791-244X

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Spandidos Publications style
Mantripragada KK, Tapia-Páez I, Blennow E, Nilsson P, Wedell A and Dumanski JP: DNA copy-number analysis of the 22q11 deletion-syndrome region using array-CGH with genomic and PCR-based targets. Int J Mol Med 13: 273-279, 2004
APA
Mantripragada, K.K., Tapia-Páez, I., Blennow, E., Nilsson, P., Wedell, A., & Dumanski, J.P. (2004). DNA copy-number analysis of the 22q11 deletion-syndrome region using array-CGH with genomic and PCR-based targets. International Journal of Molecular Medicine, 13, 273-279. https://doi.org/10.3892/ijmm.13.2.273
MLA
Mantripragada, K. K., Tapia-Páez, I., Blennow, E., Nilsson, P., Wedell, A., Dumanski, J. P."DNA copy-number analysis of the 22q11 deletion-syndrome region using array-CGH with genomic and PCR-based targets". International Journal of Molecular Medicine 13.2 (2004): 273-279.
Chicago
Mantripragada, K. K., Tapia-Páez, I., Blennow, E., Nilsson, P., Wedell, A., Dumanski, J. P."DNA copy-number analysis of the 22q11 deletion-syndrome region using array-CGH with genomic and PCR-based targets". International Journal of Molecular Medicine 13, no. 2 (2004): 273-279. https://doi.org/10.3892/ijmm.13.2.273