Detection of cryptic pathogenic copy number variations and constitutional loss of heterozygosity using high resolution SNP microarray analysis in 117 patients referred for cytogenetic analysis and impact on clinical practice

Bruno, D. L., Ganesamoorthy, D., Schoumans, J., Bankier, A., Coman, D., Delatycki, M., Gardner, R. J. M., Hunter, M., James, P. A., Kannu, P., McGillivray, G., Pachter, N., Peters, H., Rieubland, C., Savarirayan, R., Scheffer, I. E., Sheffield, L., Tan, T., White, S. M., Yeung, A., Bowman, Z., Ngo, C., Choy, K. W., Cacheux, V., Wong, L., Amor, D. J. and Slater, H. R. (2009) Detection of cryptic pathogenic copy number variations and constitutional loss of heterozygosity using high resolution SNP microarray analysis in 117 patients referred for cytogenetic analysis and impact on clinical practice. Journal of Medical Genetics, 46 2: 123-131. doi:10.1136/jmg.2008.062604


Author Bruno, D. L.
Ganesamoorthy, D.
Schoumans, J.
Bankier, A.
Coman, D.
Delatycki, M.
Gardner, R. J. M.
Hunter, M.
James, P. A.
Kannu, P.
McGillivray, G.
Pachter, N.
Peters, H.
Rieubland, C.
Savarirayan, R.
Scheffer, I. E.
Sheffield, L.
Tan, T.
White, S. M.
Yeung, A.
Bowman, Z.
Ngo, C.
Choy, K. W.
Cacheux, V.
Wong, L.
Amor, D. J.
Slater, H. R.
Title Detection of cryptic pathogenic copy number variations and constitutional loss of heterozygosity using high resolution SNP microarray analysis in 117 patients referred for cytogenetic analysis and impact on clinical practice
Journal name Journal of Medical Genetics   Check publisher's open access policy
ISSN 0022-2593
1468-6244
Publication date 2009-02
Sub-type Article (original research)
DOI 10.1136/jmg.2008.062604
Open Access Status
Volume 46
Issue 2
Start page 123
End page 131
Total pages 9
Place of publication London United Kingdom
Publisher B M J Group
Language eng
Formatted abstract
Background:
Microarray genome analysis is realising its promise for improving detection of genetic abnormalities in individuals with mental retardation and congenital abnormality. Copy number variations (CNVs) are now readily detectable using a variety of platforms and a major challenge is the distinction of pathogenic from ubiquitous, benign polymorphic CNVs. The aim of this study was to investigate replacement of time consuming, locus specific testing for specific microdeletion and microduplication syndromes with microarray analysis, which theoretically should detect all known syndromes with CNV aetiologies as well as new ones.

Methods:
Genome wide copy number analysis was performed on 117 patients using Affymetrix 250K microarrays.

Results:
434 CNVs (195 losses and 239 gains) were found, including 18 pathogenic CNVs and 9 identified as “potentially pathogenic”. Almost all pathogenic CNVs were larger than 500 kb, significantly larger than the median size of all CNVs detected. Segmental regions of loss of heterozygosity larger than 5 Mb were found in 5 patients.

Conclusions:
Genome microarray analysis has improved diagnostic success in this group of patients. Several examples of recently discovered “new syndromes” were found suggesting they are more common than previously suspected and collectively are likely to be a major cause of mental retardation. The findings have several implications for clinical practice. The study revealed the potential to make genetic diagnoses that were not evident in the clinical presentation, with implications for pretest counselling and the consent process. The importance of contributing novel CNVs to high quality databases for genotype–phenotype analysis and review of guidelines for selection of individuals for microarray analysis is emphasised.
Keyword Comparative genomic hybridization
Idiopathic mental-retardation
Array-Cgh
Microdeletion syndrome
Structural variation
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
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