Advanced search
1 file | 484.21 KB Add to list

Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform

Author
Organization
Project
Bioinformatics: from nucleotids to networks (N2N)
Abstract
Background: Hereditary hearing loss (HL) can originate from mutations in one of many genes involved in the complex process of hearing. Identification of the genetic defects in patients is currently labor intensive and expensive. While screening with Sanger sequencing for GJB2 mutations is common, this is not the case for the other known deafness genes (> 60). Next generation sequencing technology (NGS) has the potential to be much more cost efficient. Published methods mainly use hybridization based target enrichment procedures that are time saving and efficient, but lead to loss in sensitivity. In this study we used a semi-automated PCR amplification and NGS in order to combine high sensitivity, speed and cost efficiency. Results: In this proof of concept study, we screened 15 autosomal recessive deafness genes in 5 patients with congenital genetic deafness. 646 specific primer pairs for all exons and most of the UTR of the 15 selected genes were designed using primerXL. Using patient specific identifiers, all amplicons were pooled and analyzed using the Roche 454 NGS technology. Three of these patients are members of families in which a region of interest has previously been characterized by linkage studies. In these, we were able to identify two new mutations in CDH23 and OTOF. For another patient, the etiology of deafness was unclear, and no causal mutation was found. In a fifth patient, included as a positive control, we could confirm a known mutation in TMC1. Conclusions: We have developed an assay that holds great promise as a tool for screening patients with familial autosomal recessive nonsyndromal hearing loss (ARNSHL). For the first time, an efficient, reliable and cost effective genetic test, based on PCR enrichment, for newborns with undiagnosed deafness is available.
Keywords
Genetic diagnostics, IMPAIRMENT, PCR based enrichment, Deafness, Next generation sequencing, MUTATIONS

Downloads

  • 1755-8794-5-17.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 484.21 KB

Citation

Please use this url to cite or link to this publication:

MLA
De Keulenaer, Sarah, JAN HELLEMANS, Steve Lefever, et al. “Molecular Diagnostics for Congenital Hearing Loss Including 15 Deafness Genes Using a Next Generation Sequencing Platform.” BMC MEDICAL GENOMICS 5 (2012): n. pag. Print.
APA
De Keulenaer, Sarah, HELLEMANS, J., Lefever, S., Renard, J.-P., De Schrijver, J., Van de Voorde, H., Tabatabaiefar, M. A., et al. (2012). Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform. BMC MEDICAL GENOMICS, 5.
Chicago author-date
De Keulenaer, Sarah, JAN HELLEMANS, Steve Lefever, Jean-Pierre Renard, Joachim De Schrijver, Hendrik Van de Voorde, Mohammad Amin Tabatabaiefar, et al. 2012. “Molecular Diagnostics for Congenital Hearing Loss Including 15 Deafness Genes Using a Next Generation Sequencing Platform.” Bmc Medical Genomics 5.
Chicago author-date (all authors)
De Keulenaer, Sarah, JAN HELLEMANS, Steve Lefever, Jean-Pierre Renard, Joachim De Schrijver, Hendrik Van de Voorde, Mohammad Amin Tabatabaiefar, Filip Van Nieuwerburgh, Daisy Flamez, Filip Pattyn, Bieke Scharlaken, Dieter Deforce, Sofie Bekaert, Wim Van Criekinge, Jo Vandesompele, Guy Van Camp, and Paul Coucke. 2012. “Molecular Diagnostics for Congenital Hearing Loss Including 15 Deafness Genes Using a Next Generation Sequencing Platform.” Bmc Medical Genomics 5.
Vancouver
1.
De Keulenaer S, HELLEMANS J, Lefever S, Renard J-P, De Schrijver J, Van de Voorde H, et al. Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform. BMC MEDICAL GENOMICS. 2012;5.
IEEE
[1]
S. De Keulenaer et al., “Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform,” BMC MEDICAL GENOMICS, vol. 5, 2012.
@article{3070495,
  abstract     = {Background: Hereditary hearing loss (HL) can originate from mutations in one of many genes involved in the complex process of hearing. Identification of the genetic defects in patients is currently labor intensive and expensive. While screening with Sanger sequencing for GJB2 mutations is common, this is not the case for the other known deafness genes (> 60). Next generation sequencing technology (NGS) has the potential to be much more cost efficient. Published methods mainly use hybridization based target enrichment procedures that are time saving and efficient, but lead to loss in sensitivity. In this study we used a semi-automated PCR amplification and NGS in order to combine high sensitivity, speed and cost efficiency. 
Results: In this proof of concept study, we screened 15 autosomal recessive deafness genes in 5 patients with congenital genetic deafness. 646 specific primer pairs for all exons and most of the UTR of the 15 selected genes were designed using primerXL. Using patient specific identifiers, all amplicons were pooled and analyzed using the Roche 454 NGS technology. Three of these patients are members of families in which a region of interest has previously been characterized by linkage studies. In these, we were able to identify two new mutations in CDH23 and OTOF. For another patient, the etiology of deafness was unclear, and no causal mutation was found. In a fifth patient, included as a positive control, we could confirm a known mutation in TMC1. 
Conclusions: We have developed an assay that holds great promise as a tool for screening patients with familial autosomal recessive nonsyndromal hearing loss (ARNSHL). For the first time, an efficient, reliable and cost effective genetic test, based on PCR enrichment, for newborns with undiagnosed deafness is available.},
  articleno    = {17},
  author       = {De Keulenaer, Sarah and HELLEMANS, JAN and Lefever, Steve and Renard, Jean-Pierre and De Schrijver, Joachim and Van de Voorde, Hendrik and Tabatabaiefar, Mohammad Amin and Van Nieuwerburgh, Filip and Flamez, Daisy and Pattyn, Filip and Scharlaken, Bieke and Deforce, Dieter and Bekaert, Sofie and Van Criekinge, Wim and Vandesompele, Jo and Van Camp, Guy and Coucke, Paul},
  issn         = {1755-8794},
  journal      = {BMC MEDICAL GENOMICS},
  keywords     = {Genetic diagnostics,IMPAIRMENT,PCR based enrichment,Deafness,Next generation sequencing,MUTATIONS},
  language     = {eng},
  pages        = {8},
  title        = {Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform},
  url          = {http://dx.doi.org/10.1186/1755-8794-5-17},
  volume       = {5},
  year         = {2012},
}

Altmetric
View in Altmetric
Web of Science
Times cited: