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Development of a genotyping microarray for Usher syndrome

Frans PM Cremers, William J Kimberling, Maigi Külm, Arjan P de Brouwer, Erwin van Wijk, Heleen te Brinke, Cor WRJ Cremers, Lies H Hoefsloot, Sandro Banfi, Francesca Simonelli, et al.
(2007) JOURNAL OF MEDICAL GENETICS. 44(2). p.153-160
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Abstract
Background: Usher syndrome, a combination of retinitis pigmentosa (RP) and sensorineural hearing loss with or without vestibular dysfunction, displays a high degree of clinical and genetic heterogeneity. Three clinical subtypes can be distinguished, based on the age of onset and severity of the hearing impairment, and the presence or absence of vestibular abnormalities. Thus far, eight genes have been implicated in the syndrome, together comprising 347 protein-coding exons. Methods: To improve DNA diagnostics for patients with Usher syndrome, we developed a genotyping microarray based on the arrayed primer extension (APEX) method. Allele-specific oligonucleotides corresponding to all 298 Usher syndrome-associated sequence variants known to date, 76 of which are novel, were arrayed. Results: Approximately half of these variants were validated using original patient DNAs, which yielded an accuracy of > 98%. The efficiency of the Usher genotyping microarray was tested using DNAs from 370 unrelated European and American patients with Usher syndrome. Sequence variants were identified in 64/140 (46%) patients with Usher syndrome type I, 45/189 (24%) patients with Usher syndrome type II, 6/21 (29%) patients with Usher syndrome type III and 6/20 (30%) patients with atypical Usher syndrome. The chip also identified two novel sequence variants, c.400C > T (p.R134X) in PCDH15 and c.1606T > C (p.C536S) in USH2A. Conclusion: The Usher genotyping microarray is a versatile and affordable screening tool for Usher syndrome. Its efficiency will improve with the addition of novel sequence variants with minimal extra costs, making it a very useful first-pass screening tool.
Keywords
ARRAYED PRIMER EXTENSION, SYNDROME-TYPE-II, LEBER CONGENITAL AMAUROSIS, MYOSIN VIIA GENE, RECESSIVE RETINITIS-PIGMENTOSA, EAR SENSORY CELLS, SYNDROME TYPE 1F, MUTATION DETECTION, HEARING-LOSS, USH2A GENE

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MLA
Cremers, Frans PM, et al. “Development of a Genotyping Microarray for Usher Syndrome.” JOURNAL OF MEDICAL GENETICS, vol. 44, no. 2, 2007, pp. 153–60, doi:10.1136/jmg.2006.044784.
APA
Cremers, F. P., Kimberling, W. J., Külm, M., de Brouwer, A. P., van Wijk, E., te Brinke, H., … Kremer, H. (2007). Development of a genotyping microarray for Usher syndrome. JOURNAL OF MEDICAL GENETICS, 44(2), 153–160. https://doi.org/10.1136/jmg.2006.044784
Chicago author-date
Cremers, Frans PM, William J Kimberling, Maigi Külm, Arjan P de Brouwer, Erwin van Wijk, Heleen te Brinke, Cor WRJ Cremers, et al. 2007. “Development of a Genotyping Microarray for Usher Syndrome.” JOURNAL OF MEDICAL GENETICS 44 (2): 153–60. https://doi.org/10.1136/jmg.2006.044784.
Chicago author-date (all authors)
Cremers, Frans PM, William J Kimberling, Maigi Külm, Arjan P de Brouwer, Erwin van Wijk, Heleen te Brinke, Cor WRJ Cremers, Lies H Hoefsloot, Sandro Banfi, Francesca Simonelli, Johannes C Fleischhauer, Wolfgang Berger, Phil M Kelley, Elene Haralambous, Maria Bitner-Glindzicz, Andrew R Webster, Zubin Saihan, Elfride De Baere, Bart Leroy, Giuliana Silvestri, Gareth J McKay, Robert K Koenekoop, Jose M Millan, Thomas Rosenberg, Tarja Joensuu, Eeva-Marja Sankila, Dominique Weil, Mike D Weston, Bernd Wissinger, and Hannie Kremer. 2007. “Development of a Genotyping Microarray for Usher Syndrome.” JOURNAL OF MEDICAL GENETICS 44 (2): 153–160. doi:10.1136/jmg.2006.044784.
Vancouver
1.
Cremers FP, Kimberling WJ, Külm M, de Brouwer AP, van Wijk E, te Brinke H, et al. Development of a genotyping microarray for Usher syndrome. JOURNAL OF MEDICAL GENETICS. 2007;44(2):153–60.
IEEE
[1]
F. P. Cremers et al., “Development of a genotyping microarray for Usher syndrome,” JOURNAL OF MEDICAL GENETICS, vol. 44, no. 2, pp. 153–160, 2007.
@article{369918,
  abstract     = {{Background: Usher syndrome, a combination of retinitis pigmentosa (RP) and sensorineural hearing loss with or without vestibular dysfunction, displays a high degree of clinical and genetic heterogeneity. Three clinical subtypes can be distinguished, based on the age of onset and severity of the hearing impairment, and the presence or absence of vestibular abnormalities. Thus far, eight genes have been implicated in the syndrome, together comprising 347 protein-coding exons. 
Methods: To improve DNA diagnostics for patients with Usher syndrome, we developed a genotyping microarray based on the arrayed primer extension (APEX) method. Allele-specific oligonucleotides corresponding to all 298 Usher syndrome-associated sequence variants known to date, 76 of which are novel, were arrayed. 
Results: Approximately half of these variants were validated using original patient DNAs, which yielded an accuracy of > 98%. The efficiency of the Usher genotyping microarray was tested using DNAs from 370 unrelated European and American patients with Usher syndrome. Sequence variants were identified in 64/140 (46%) patients with Usher syndrome type I, 45/189 (24%) patients with Usher syndrome type II, 6/21 (29%) patients with Usher syndrome type III and 6/20 (30%) patients with atypical Usher syndrome. The chip also identified two novel sequence variants, c.400C > T (p.R134X) in PCDH15 and c.1606T > C (p.C536S) in USH2A. 
Conclusion: The Usher genotyping microarray is a versatile and affordable screening tool for Usher syndrome. Its efficiency will improve with the addition of novel sequence variants with minimal extra costs, making it a very useful first-pass screening tool.}},
  author       = {{Cremers, Frans PM and Kimberling, William J and Külm, Maigi and de Brouwer, Arjan P and van Wijk, Erwin and te Brinke, Heleen and Cremers, Cor WRJ and Hoefsloot, Lies H and Banfi, Sandro and Simonelli, Francesca and Fleischhauer, Johannes C and Berger, Wolfgang and Kelley, Phil M and Haralambous, Elene and Bitner-Glindzicz, Maria and Webster, Andrew R and Saihan, Zubin and De Baere, Elfride and Leroy, Bart and Silvestri, Giuliana and McKay, Gareth J and Koenekoop, Robert K and Millan, Jose M and Rosenberg, Thomas and Joensuu, Tarja and Sankila, Eeva-Marja and Weil, Dominique and Weston, Mike D and Wissinger, Bernd and Kremer, Hannie}},
  issn         = {{0022-2593}},
  journal      = {{JOURNAL OF MEDICAL GENETICS}},
  keywords     = {{ARRAYED PRIMER EXTENSION,SYNDROME-TYPE-II,LEBER CONGENITAL AMAUROSIS,MYOSIN VIIA GENE,RECESSIVE RETINITIS-PIGMENTOSA,EAR SENSORY CELLS,SYNDROME TYPE 1F,MUTATION DETECTION,HEARING-LOSS,USH2A GENE}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{153--160}},
  title        = {{Development of a genotyping microarray for Usher syndrome}},
  url          = {{http://dx.doi.org/10.1136/jmg.2006.044784}},
  volume       = {{44}},
  year         = {{2007}},
}
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