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Targeted High-Throughput DNA Sequencing for Gene Discovery in Retinitis Pigmentosa

  • Stephen P. Daiger
  • Lori S. Sullivan
  • Sara J. Bowne
  • David G. Birch
  • John R. Heckenlively
  • Eric A. Pierce
  • George M. Weinstock
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 664)

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.

Keywords

Retinitis Pigmentosa Retinal Degeneration Retinal Disease Autosomal Dominant Retinitis Pigmentosa Retinal Gene 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Stephen P. Daiger
    • 1
  • Lori S. Sullivan
    • 2
  • Sara J. Bowne
    • 2
  • David G. Birch
    • 3
  • John R. Heckenlively
    • 4
  • Eric A. Pierce
    • 5
  • George M. Weinstock
    • 6
  1. 1.Department of Ophthalmology and Visual ScienceSchool of Public Health, Human Genetics Center; University of Texas Health Science CenterHoustonUSA
  2. 2.The University of Texas Health Science Center Houston, Human Genetics CenterHoustonUSA
  3. 3.Retina Foundation of the SouthwestDallasUSA
  4. 4.Kellogg Eye Center, University of MichiganAnn ArborUSA
  5. 5.F.M. Kirby Center for Molecular OphthalmologyUniversity of Pennsylvania School of MedicinePhiladelphiaUSA
  6. 6.Genome Sequencing Center, Washington UniversitySt. LouisUSA

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