Advancing genetic testing for deafness with genomic technology
- A Eliot Shearer1,2,
- E Ann Black-Ziegelbein1,
- Michael S Hildebrand1,3,
- Robert W Eppsteiner1,
- Harini Ravi4,5,
- Swati Joshi4,5,
- Angelica C Guiffre4,5,
- Christina M Sloan1,2,
- Scott Happe4,5,
- Susanna D Howard1,
- Barbara Novak6,
- Adam P DeLuca6,7,
- Kyle R Taylor6,7,
- Todd E Scheetz6,7,8,
- Terry A Braun6,7,8,
- Thomas L Casavant6,7,9,
- William J Kimberling1,
- Emily M LeProust5,7,
- Richard J H Smith1,2,9
- 1Department of Otolaryngology—Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
- 2Department of Molecular Physiology & Biophysics, University of Iowa College of Medicine, Iowa City, Iowa, USA
- 3Department of Medicine, Epilepsy Research Centre, University of Melbourne, Melbourne, Australia
- 4Agilent Technologies, Cedar Creek, Texas, USA
- 5Agilent Technologies, Santa Clara, California, USA
- 6Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
- 7Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, USA
- 8Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA.
- 9Interdepartmental PhD Program in Genetics, University of Iowa, Iowa City, Iowa, USA
- Correspondence to Professor Richard J H Smith, 5270 CBRB, Department of Otolaryngology—Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA;
- Received 15 April 2013
- Revised 30 May 2013
- Accepted 3 June 2013
- Published Online First 26 June 2013
Background Non-syndromic hearing loss (NSHL) is the most common sensory impairment in humans. Until recently its extreme genetic heterogeneity precluded comprehensive genetic testing. Using a platform that couples targeted genomic enrichment (TGE) and massively parallel sequencing (MPS) to sequence all exons of all genes implicated in NSHL, we tested 100 persons with presumed genetic NSHL and in so doing established sequencing requirements for maximum sensitivity and defined MPS quality score metrics that obviate Sanger validation of variants.
Methods We examined DNA from 100 sequentially collected probands with presumed genetic NSHL without exclusions due to inheritance, previous genetic testing, or type of hearing loss. We performed TGE using post-capture multiplexing in variable pool sizes followed by Illumina sequencing. We developed a local Galaxy installation on a high performance computing cluster for bioinformatics analysis.
Results To obtain maximum variant sensitivity with this platform 3.2–6.3 million total mapped sequencing reads per sample were required. Quality score analysis showed that Sanger validation was not required for 95% of variants. Our overall diagnostic rate was 42%, but this varied by clinical features from 0% for persons with asymmetric hearing loss to 56% for persons with bilateral autosomal recessive NSHL.
Conclusions These findings will direct the use of TGE and MPS strategies for genetic diagnosis for NSHL. Our diagnostic rate highlights the need for further research on genetic deafness focused on novel gene identification and an improved understanding of the role of non-exonic mutations. The unsolved families we have identified provide a valuable resource to address these areas.