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Kohli MA, Cukier HN, Hamilton-Nelson KL, Rolati S, Kunkle BW, Whitehead PL, Züchner SL, Farrer LA, Martin ER, Beecham GW, Haines JL, Vance JM, Cuccaro ML, Gilbert JR, Schellenberg GD, Carney RM, Pericak-Vance MA. Segregation of a rare TTC3 variant in an extended family with late-onset Alzheimer disease. NEUROLOGY-GENETICS 2016; 2:e41. [PMID: 27066578 PMCID: PMC4817909 DOI: 10.1212/nxg.0000000000000041] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/20/2015] [Indexed: 01/08/2023]
Abstract
OBJECTIVE The genetic risk architecture of Alzheimer disease (AD) is complex with single pathogenic mutations leading to early-onset AD, while both rare and common genetic susceptibility variants contribute to the more widespread late-onset AD (LOAD); we sought to discover novel genes contributing to LOAD risk. METHODS Whole-exome sequencing and genome-wide genotyping were performed on 11 affected individuals in an extended family with an apparent autosomal dominant pattern of LOAD. Variants of interest were then evaluated in a large cohort of LOAD cases and aged controls. RESULTS We detected a single rare, nonsynonymous variant shared in all 11 LOAD individuals, a missense change in the tetratricopeptide repeat domain 3 (TTC3) gene. The missense variant, rs377155188 (p.S1038C), is predicted to be damaging. Affecteds-only multipoint linkage analysis demonstrated that this region of TTC3 has a LOD score of 2.66 in this family. CONCLUSION The TTC3 p.S1038C substitution may represent a segregating, rare LOAD risk variant. Previous studies have shown that TTC3 expression is consistently reduced in LOAD patients and negatively correlated with AD neuropathology and that TTC3 is a regulator of Akt signaling, a key pathway disrupted in LOAD. This study demonstrates how utilizing whole-exome sequencing in a large, multigenerational family with a high incidence of LOAD could reveal a novel candidate gene.
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Affiliation(s)
- Martin A Kohli
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Holly N Cukier
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Sophie Rolati
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Stephan L Züchner
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Lindsay A Farrer
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Jonathan L Haines
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - John R Gilbert
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Gerard D Schellenberg
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Regina M Carney
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics (M.A.K., H.N.C., K.L.H.-N., S.R., B.W.K., P.L.W., S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., S.L.Z., J.M.V., M.A.P.-V.), and Dr. John T. Macdonald Foundation Department of Human Genetics (S.L.Z., E.R.M., G.W.B., J.M.V., M.L.C., J.R.G., M.A.P.-V.), University of Miami, Miller School of Medicine, Miami, FL; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, Boston, MA; Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Department of Pathology and Laboratory Medicine (G.D.S.), University of Pennsylvania School of Medicine, Philadelphia, PA
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