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Wu L, Schaid DJ, Sicotte H, Wieben ED, Li H, Petersen GM. Case-only exome sequencing and complex disease susceptibility gene discovery: study design considerations. J Med Genet 2014; 52:10-6. [PMID: 25371537 DOI: 10.1136/jmedgenet-2014-102697] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Whole exome sequencing (WES) provides an unprecedented opportunity to identify the potential aetiological role of rare functional variants in human complex diseases. Large-scale collaborations have generated germline WES data on patients with a number of diseases, especially cancer, but less often on healthy controls under the same sequencing procedures. These data can be a valuable resource for identifying new disease susceptibility loci if study designs are appropriately applied. This review describes suggested strategies and technical considerations when focusing on case-only study designs that use WES data in complex disease scenarios. These include variant filtering based on frequency and functionality, gene prioritisation, interrogation of different data types and targeted sequencing validation. We propose that if case-only WES designs were applied in an appropriate manner, new susceptibility genes containing rare variants for human complex diseases can be detected.
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Affiliation(s)
- Lang Wu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA Center for Clinical and Translational Science, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Hugues Sicotte
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric D Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
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Hall G, Gbadegesin RA, Lavin P, Wu G, Liu Y, Oh EC, Wang L, Spurney RF, Eckel J, Lindsey T, Homstad A, Malone AF, Phelan PJ, Shaw A, Howell DN, Conlon PJ, Katsanis N, Winn MP. A novel missense mutation of Wilms' Tumor 1 causes autosomal dominant FSGS. J Am Soc Nephrol 2014; 26:831-43. [PMID: 25145932 DOI: 10.1681/asn.2013101053] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
FSGS is a clinical disorder characterized by focal scarring of the glomerular capillary tuft, podocyte injury, and nephrotic syndrome. Although idiopathic forms of FSGS predominate, recent insights into the molecular and genetic causes of FSGS have enhanced our understanding of disease pathogenesis. Here, we report a novel missense mutation of the transcriptional regulator Wilms' Tumor 1 (WT1) as the cause of nonsyndromic, autosomal dominant FSGS in two Northern European kindreds from the United States. We performed sequential genome-wide linkage analysis and whole-exome sequencing to evaluate participants from family DUK6524. Subsequently, whole-exome sequencing and direct sequencing were performed on proband DNA from family DUK6975. We identified multiple suggestive loci on chromosomes 6, 11, and 13 in family DUK6524 and identified a segregating missense mutation (R458Q) in WT1 isoform D as the cause of FSGS in this family. The identical mutation was found in family DUK6975. The R458Q mutation was not found in 1600 control chromosomes and was predicted as damaging by in silico simulation. We depleted wt1a in zebrafish embryos and observed glomerular injury and filtration defects, both of which were rescued with wild-type but not mutant human WT1D mRNA. Finally, we explored the subcellular mechanism of the mutation in vitro. WT1(R458Q) overexpression significantly downregulated nephrin and synaptopodin expression, promoted apoptosis in HEK293 cells and impaired focal contact formation in podocytes. Taken together, these data suggest that the WT1(R458Q) mutation alters the regulation of podocyte homeostasis and causes nonsyndromic FSGS.
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Affiliation(s)
- Gentzon Hall
- Division of Nephrology, Departments of Medicine, Duke Molecular Physiology Institute
| | | | - Peter Lavin
- Department of Transplant, Urology and Nephrology, Beaumont Hospital, Dublin, Ireland
| | | | - Yangfan Liu
- Cell Biology, Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina
| | - Edwin C Oh
- Cell Biology, Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina
| | | | | | - Jason Eckel
- Division of Nephrology, Departments of Medicine
| | | | | | - Andrew F Malone
- Division of Nephrology, Departments of Medicine, Duke Molecular Physiology Institute
| | - Paul J Phelan
- Division of Nephrology, Departments of Medicine, Duke Molecular Physiology Institute
| | - Andrey Shaw
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri; and
| | | | - Peter J Conlon
- Department of Transplant, Urology and Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Nicholas Katsanis
- Departments of Medicine, Cell Biology, Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina
| | - Michelle P Winn
- Division of Nephrology, Departments of Medicine, Duke Molecular Physiology Institute,
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