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Bronstein R, Capowski EE, Mehrotra S, Jansen AD, Navarro-Gomez D, Maher M, Place E, Sangermano R, Bujakowska KM, Gamm DM, Pierce EA. A combined RNA-seq and whole genome sequencing approach for identification of non-coding pathogenic variants in single families. Hum Mol Genet 2020; 29:967-979. [PMID: 32011687 PMCID: PMC7158377 DOI: 10.1093/hmg/ddaa016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/23/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
Inherited retinal degenerations (IRDs) are at the focus of current genetic therapeutic advancements. For a genetic treatment such as gene therapy to be successful, an accurate genetic diagnostic is required. Genetic diagnostics relies on the assessment of the probability that a given DNA variant is pathogenic. Non-coding variants present a unique challenge for such assessments as compared to coding variants. For one, non-coding variants are present at much higher number in the genome than coding variants. In addition, our understanding of the rules that govern the non-coding regions of the genome is less complete than our understanding of the coding regions. Methods that allow for both the identification of candidate non-coding pathogenic variants and their functional validation may help overcome these caveats allowing for a greater number of patients to benefit from advancements in genetic therapeutics. We present here an unbiased approach combining whole genome sequencing (WGS) with patient-induced pluripotent stem cell (iPSC)-derived retinal organoids (ROs) transcriptome analysis. With this approach, we identified and functionally validated a novel pathogenic non-coding variant in a small family with a previously unresolved genetic diagnosis.
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Affiliation(s)
- Revital Bronstein
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Elizabeth E Capowski
- Waisman Center Stem Cell Research Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sudeep Mehrotra
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Alex D Jansen
- Waisman Center Stem Cell Research Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Daniel Navarro-Gomez
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Mathew Maher
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Emily Place
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Riccardo Sangermano
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Kinga M Bujakowska
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - David M Gamm
- Department of Ophthalmology and Visual Sciences, Waisman Center Stem Cell Research Program, McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Eric A Pierce
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
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