The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing
Open accessAbstract
The extreme genetic heterogeneity of nonsyndromic hearing loss (NSHL) makes genetic diagnosis expensive and time consuming using available methods. To assess the feasibility of target-enrichment and massively parallel sequencing technologies to interrogate all exons of all genes implicated in NSHL, we tested nine patients diagnosed with hearing loss. Solid-phase (NimbleGen) or solution-based (SureSelect) sequence capture, followed by 454 or Illumina sequencing, respectively, were compared. Sequencing reads were mapped using GSMAPPER, BFAST, and BOWTIE, and pathogenic variants were identified using a custom-variant calling and annotation pipeline (ASAP) that incorporates publicly available in silico pathogenicity prediction tools (SIFT, BLOSUM, Polyphen2, and Align-GVGD). Samples included one negative control, three positive controls (one biological replicate), and six unknowns (10 samples total), in which we genotyped 605 single nucleotide polymorphisms (SNPs) by Sanger sequencing to measure sensitivity and specificity for SureSelect-Illumina and NimbleGen-454 methods at saturating sequence coverage. Causative mutations were identified in the positive controls but not in the negative control. In five of six idiopathic hearing loss patients we identified the pathogenic mutation. Massively parallel sequencing technologies provide sensitivity, specificity, and reproducibility at levels sufficient to perform genetic diagnosis of hearing loss.
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Cites
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066
Targeted capture and massively parallel sequencing of 12 human exomes
Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E. E., et al. (2009) · Nature · doi:10.1038/nature08250 · Cited by 2,030
Exome sequencing identifies the cause of a mendelian disorder
Ng, S. B., Buckingham, K. J., Lee, C., Bigham, A. W., Tabor, H. K., Dent, K. M., Huff, C. D., Shannon, P. T., Jabs, E. W., Nickerson, D. A., et al. (2010) · Nature Genetics · doi:10.1038/ng.499 · Cited by 1,957
Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1523 · Cited by 1,433
Whole-Genome Sequencing in a Patient with Charcot–Marie–Tooth Neuropathy
Lupski, J. R., Reid, J. G., Gonzaga-Jauregui, C., Rio Deiros, D., Chen, D. C. Y., Nazareth, L., Bainbridge, M., Dinh, H., Jing, C., Wheeler, D. A., et al. (2010) · New England Journal of Medicine · doi:10.1056/nejmoa0908094 · Cited by 759
Cited by
Wagle, N., Berger, M. F., Davis, M. J., Blumenstiel, B., DeFelice, M., Pochanard, P., Ducar, M., Van Hummelen, P., MacConaill, L. E., Hahn, W. C., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0184 · Cited by 533
De Franco, E., Flanagan, S. E., Houghton, J. A., Allen, H. L., Mackay, D. J., Temple, I. K., Ellard, S., & Hattersley, A. T. (2015) · The Lancet · doi:10.1016/s0140-6736(15)60098-8 · Cited by 349
Targeted next generation sequencing as a diagnostic tool in epileptic disorders
Lemke, J. R., Riesch, E., Scheurenbrand, T., Schubach, M., Wilhelm, C., Steiner, I., Hansen, J., Courage, C., Gallati, S., Bürki, S., et al. (2012) · Epilepsia · doi:10.1111/j.1528-1167.2012.03516.x · Cited by 332
Massively Parallel Sequencing for Genetic Diagnosis of Hearing Loss: The New Standard of Care
Shearer, A. E., & Smith, R. J. H. (2015) · Otolaryngology–Head and Neck Surgery · doi:10.1177/0194599815591156 · Cited by 144
Self-citationTollefson, M. R., Gogal, R. A., Weaver, A. M., Schaefer, A. M., Marini, R. J., Azaiez, H., Kolbe, D. L., Wang, D., Weaver, A. E., Casavant, T. L., et al. (2023) · Human Genetics · doi:10.1007/s00439-023-02559-9 · Cited by 20
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Metadata
- Authors
- Shearer, A. E., DeLuca, A. P., Hildebrand, M. S., Taylor, K. R., Gurrola, J., Scherer, S., Scheetz, T. E., & Smith, R. J. H.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2010-11-15
- Volume
- 107
- Issue
- 49
- Pages
- 21104-21109
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W1968852642
- Cited by
- 340
- References
- 5
- FWCI
- 14.39
- Type
- journal article
- Language
- en
- Open access
- green
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- Shearer, A. E., DeLuca, A. P., Hildebrand, M. S., Taylor, K. R., Gurrola, J., Scherer, S., Scheetz, T. E., & Smith, R. J. H. (2010). Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1012989107
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