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Ji J, Shen L, Bootwalla M, Quindipan C, Tatarinova T, Maglinte DT, Buckley J, Raca G, Saitta SC, Biegel JA, Gai X. A semiautomated whole-exome sequencing workflow leads to increased diagnostic yield and identification of novel candidate variants. Cold Spring Harb Mol Case Stud 2019; 5:a003756. [PMID: 30755392 DOI: 10.1101/mcs.a003756] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/06/2019] [Indexed: 01/10/2023] Open
Abstract
Advancing the clinical utility of whole-exome sequencing (WES) for patients with suspected genetic disorders is largely driven by bioinformatics approaches that streamline data processing and analysis. Herein, we describe our experience with implementing a semiautomated and phenotype-driven WES diagnostic workflow, incorporating both the DRAGEN pipeline and the Exomiser variant prioritization tool, at an academic children's hospital with an ethnically diverse pediatric patient population. We achieved a 41% molecular diagnostic rate for 66 duo-, quad-, or trio-WES cases, and 28% for 40 singleton-WES cases. Preliminary results were returned to ordering physicians within 1 wk for 12 of 38 (32%) probands with positive findings, which were instrumental in guiding the appropriate clinical management for a variety of patients, especially in critical care settings. The semiautomated and streamlined WES workflow also enabled us to identify novel variants in candidate disease genes in patients with developmental delay and autism and immune disorders and cancer, including ANK2, BPTF, BCL11A, FOXN1, PLAA, ATRX, DNAJC21, and RAD50. Together, we demonstrated the implementation of a streamlined WES workflow that was successfully applied for both clinical and research purposes.
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Velez G, Bassuk AG, Schaefer KA, Brooks B, Gakhar L, Mahajan M, Kahn P, Tsang SH, Ferguson PJ, Mahajan VB. A novel de novo CAPN5 mutation in a patient with inflammatory vitreoretinopathy, hearing loss, and developmental delay. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002519. [PMID: 29472286 PMCID: PMC5983175 DOI: 10.1101/mcs.a002519] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/16/2018] [Indexed: 12/05/2022] Open
Abstract
Mutations that activate the protease calpain-5 (CAPN5) cause a nonsyndromic adult-onset autoinflammatory eye disease characterized by uveitis, altered synaptic signaling, retinal degeneration, neovascularization, and intraocular fibrosis. We describe a pediatric patient with severe inflammatory vitreoretinopathy accompanied by hearing loss and developmental delay associated with a novel, de novo CAPN5 missense mutation (c.865C>T, p.Arg289Trp) that shows greater hyperactivation of the calpain protease, indicating a genotype–phenotype correlation that links mutation severity to proteolytic activity and the possibility of earlier onset syndromic disease with auditory and neurological abnormalities.
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Affiliation(s)
- Gabriel Velez
- Omics Laboratory, Stanford University, Palo Alto, California 94304, USA.,Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California 94304, USA.,Medical Scientist Training Program, University of Iowa, Iowa City, Iowa 52242, USA
| | - Alexander G Bassuk
- Department of Pediatrics, University of Iowa, Iowa City, Iowa 52242, USA
| | - Kellie A Schaefer
- Omics Laboratory, Stanford University, Palo Alto, California 94304, USA.,Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California 94304, USA
| | - Brian Brooks
- Pediatric, Developmental, and Genetic Eye Disease Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lokesh Gakhar
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, USA.,Protein Crystallography Facility, University of Iowa, Iowa City, Iowa 52242, USA
| | - MaryAnn Mahajan
- Omics Laboratory, Stanford University, Palo Alto, California 94304, USA.,Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California 94304, USA
| | - Philip Kahn
- Department of Pediatrics, Division of Pediatric Rheumatology, New York University, New York, New York 10016, USA
| | - Stephen H Tsang
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine and Bernard & Shirlee Brown Glaucoma Laboratory, Edward S. Harkness Eye Institute, Columbia University, New York, New York 10016, USA.,Department of Pathology & Cell Biology, College of Physicians & Surgeons, Columbia University, New York, New York 10032, USA
| | - Polly J Ferguson
- Department of Pediatrics, University of Iowa, Iowa City, Iowa 52242, USA
| | - Vinit B Mahajan
- Omics Laboratory, Stanford University, Palo Alto, California 94304, USA.,Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California 94304, USA.,Palo Alto Veterans Administration, Palo Alto, California 94538, USA
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