Targeted High-Throughput DNA Sequencing for Gene Discovery in Retinitis Pigmentosa (original) (raw)

Abstract

The causes of retinitis pigmentosa (RP) are highly heterogeneous, with mutations in more than 60 genes known to cause syndromic and non-syndromic forms of disease. The prevalence of detectable mutations in known genes ranges from 25 to 85%, depending on mode of inheritance. For example, the likelihood of detecting a disease-causing mutation in known genes in patients with autosomal dominant RP (adRP) is 60% in Americans and less in other populations. Thus many RP genes are still unknown or mutations lie outside of commonly tested regions. Furthermore, current screening strategies can be costly and time-consuming.

We are developing targeted high-throughput DNA sequencing to address these problems. In this approach, a microarray with oligonucleotides targeted to hundreds of genes is used to capture sheared human DNA, and the sequence of the eluted DNA is determined by ultra-high-throughput sequencing using next-generation DNA sequencing technology. The first capture array we have designed contains 62 full-length retinal disease genes, including introns and promoter regions, and an additional 531 genes limited to exons and flanking sequences. The full-length genes include all genes known to cause at least 1% of RP or other inherited retinal diseases. All of the genes listed in the RetNet database are included on the capture array as well as many additional retinal-expressed genes. After validation studies, the first DNA’s tested will be from 89 unrelated adRP families in which the prevalent RP genes have been excluded. This approach should identify new RP genes and will substantially reduce the cost per patient.

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Authors and Affiliations

  1. Department of Ophthalmology and Visual Science, School of Public Health, Human Genetics Center; University of Texas Health Science Center, Houston, TX, USA
    Stephen P. Daiger
  2. The University of Texas Health Science Center Houston, Human Genetics Center, 1200 Herman Pressler, Houston, TX, 77030, USA
    Lori S. Sullivan & Sara J. Bowne
  3. Retina Foundation of the Southwest, Dallas, TX, USA
    David G. Birch
  4. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA
    John R. Heckenlively
  5. F.M. Kirby Center for Molecular Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
    Eric A. Pierce
  6. Genome Sequencing Center, Washington University, St. Louis, MO, USA
    George M. Weinstock

Authors

  1. Stephen P. Daiger
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  2. Lori S. Sullivan
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  3. Sara J. Bowne
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  4. David G. Birch
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  5. John R. Heckenlively
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  6. Eric A. Pierce
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  7. George M. Weinstock
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Corresponding author

Correspondence toStephen P. Daiger .

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Editors and Affiliations

  1. Health Science Center, University of Oklahoma, Stanton L. Young Blvd. 608, Oklahoma City, 73104, USA
    Robert E. Anderson
  2. Division of Ophthalmology, Cleveland Clinic Foundation, Euclid Ave. 9500, Cleveland, 44195, USA
    Joe G. Hollyfield
  3. School of Medicine, University of California, San Francisco, Kirkham St. 10, San Francisco, 94143, USA
    Matthew M. LaVail

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Daiger, S.P. et al. (2010). Targeted High-Throughput DNA Sequencing for Gene Discovery in Retinitis Pigmentosa. In: Anderson, R., Hollyfield, J., LaVail, M. (eds) Retinal Degenerative Diseases. Advances in Experimental Medicine and Biology, vol 664. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-1399-9\_37

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