Detection of clinically relevant exonic copy-number changes by array CGH

Philip M. Boone, Carlos A. Bacino, Chad A. Shaw, Patricia A. Eng, Patricia M. Hixson, Amber N. Pursley, Sung Hae L. Kang, Yaping Yang, Joanna Wiszniewska, Beata A. Nowakowska, Daniela Del Gaudio, Zhilian Xia, Gayle Simpson-Patel, La Donna L. Immken, James B. Gibson, Anne C.H. Tsai, Jennifer A. Bowers, Tyler E. Reimschisel, Christian P. Schaaf, Lorraine PotockiFernando Scaglia, Tomasz Gambin, Maciej Sykulski, Magdalena Bartnik, Katarzyna Derwinska, Barbara Wisniowiecka-Kowalnik, Seema R. Lalani, Frank J. Probst, Weimin Bi, Arthur L. Beaudet, Ankita Patel, James R. Lupski, Sau Wai Cheung, Pawel Stankiewicz

Research output: Contribution to journalArticle

179 Scopus citations

Abstract

Array comparative genomic hybridization (aCGH) is a powerful tool for the molecular elucidation and diagnosis of disorders resulting from genomic copy-number variation (CNV). However, intragenic deletions or duplications-those including genomic intervals of a size smaller than a gene-have remained beyond the detection limit of most clinical aCGH analyses. Increasing array probe number improves genomic resolution, although higher cost may limit implementation, and enhanced detection of benign CNV can confound clinical interpretation. We designed an array with exonic coverage of selected disease and candidate genes and used it clinically to identify losses or gains throughout the genome involving at least one exon and as small as several hundred base pairs in size. In some patients, the detected copy-number change occurs within a gene known to be causative of the observed clinical phenotype, demonstrating the ability of this array to detect clinically relevant CNVs with subkilobase resolution. In summary, we demonstrate the utility of a custom-designed, exon-targeted oligonucleotide array to detect intragenic copy-number changes in patients with various clinical phenotypes.

Original languageEnglish (US)
Pages (from-to)1326-1342
Number of pages17
JournalHuman mutation
Volume31
Issue number12
DOIs
StatePublished - Dec 1 2010

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Keywords

  • CGH
  • CNV
  • Comparative genomic hybridization
  • Copy-number variation
  • Exon mutations
  • Intragenic rearrangements

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Boone, P. M., Bacino, C. A., Shaw, C. A., Eng, P. A., Hixson, P. M., Pursley, A. N., Kang, S. H. L., Yang, Y., Wiszniewska, J., Nowakowska, B. A., Del Gaudio, D., Xia, Z., Simpson-Patel, G., Immken, L. D. L., Gibson, J. B., Tsai, A. C. H., Bowers, J. A., Reimschisel, T. E., Schaaf, C. P., ... Stankiewicz, P. (2010). Detection of clinically relevant exonic copy-number changes by array CGH. Human mutation, 31(12), 1326-1342. https://doi.org/10.1002/humu.21360