1
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Blue EE, Yu CE, Thornton TA, Chapman NH, Kernfeld E, Jiang N, Shively KM, Buckingham KJ, Marvin CT, Bamshad MJ, Bird TD, Wijsman EM. Variants regulating ZBTB4 are associated with age-at-onset of Alzheimer's disease. GENES, BRAIN, AND BEHAVIOR 2018; 17:e12429. [PMID: 29045054 PMCID: PMC5902667 DOI: 10.1111/gbb.12429] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 01/01/2023]
Abstract
The identification of novel genetic modifiers of age-at-onset (AAO) of Alzheimer's disease (AD) could advance our understanding of AD and provide novel therapeutic targets. A previous genome scan for modifiers of AAO among families affected by early-onset AD caused by the PSEN2 N141I variant identified 2 loci with significant evidence for linkage: 1q23.3 and 17p13.2. Here, we describe the fine-mapping of these 2 linkage regions, and test for replication in 6 independent datasets. By fine-mapping these linkage signals in a single large family, we reduced the linkage regions to 11% their original size and nominated 54 candidate variants. Among the 11 variants associated with AAO of AD in a larger sample of Germans from Russia, the strongest evidence implicated promoter variants influencing NCSTN on 1q23.3 and ZBTB4 on 17p13.2. The association between ZBTB4 and AAO of AD was replicated by multiple variants in independent, trans-ethnic datasets. Our results show association between AAO of AD and both ZBTB4 and NCSTN. ZBTB4 is a transcriptional repressor that regulates the cell cycle, including the apoptotic response to amyloid beta, while NCSTN is part of the gamma secretase complex, known to influence amyloid beta production. These genes therefore suggest important roles for amyloid beta and cell cycle pathways in AAO of AD.
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Affiliation(s)
- Elizabeth E. Blue
- Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Chang-En Yu
- Division of Gerontology, University of Washington, Seattle, WA 98195, USA
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Nicola H. Chapman
- Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Eric Kernfeld
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Nan Jiang
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Kathryn M. Shively
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Kati J. Buckingham
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Colby T. Marvin
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Michael J. Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Thomas D. Bird
- Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
- Department of Neurology, University of Washington, Seattle, WA 98195, USA
| | - Ellen M. Wijsman
- Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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2
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Yousaf R, Ahmed ZM, Giese AP, Morell RJ, Lagziel A, Dabdoub A, Wilcox ER, Riazuddin S, Friedman TB, Riazuddin S. Modifier variant of METTL13 suppresses human GAB1-associated profound deafness. J Clin Invest 2018; 128:1509-1522. [PMID: 29408807 DOI: 10.1172/jci97350] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/30/2018] [Indexed: 12/29/2022] Open
Abstract
A modifier variant can abrogate the risk of a monogenic disorder. DFNM1 is a locus on chromosome 1 encoding a dominant suppressor of human DFNB26 recessive, profound deafness. Here, we report that DFNB26 is associated with a substitution (p.Gly116Glu) in the pleckstrin homology domain of GRB2-associated binding protein 1 (GAB1), an essential scaffold in the MET proto-oncogene, receptor tyrosine kinase/HGF (MET/HGF) pathway. A dominant substitution (p.Arg544Gln) of METTL13, encoding a predicted methyltransferase, is the DFNM1 suppressor of GAB1-associated deafness. In zebrafish, human METTL13 mRNA harboring the modifier allele rescued the GAB1-associated morphant phenotype. In mice, GAB1 and METTL13 colocalized in auditory sensory neurons, and METTL13 coimmunoprecipitated with GAB1 and SPRY2, indicating at least a tripartite complex. Expression of MET-signaling genes in human lymphoblastoid cells of individuals homozygous for p.Gly116Glu GAB1 revealed dysregulation of HGF, MET, SHP2, and SPRY2, all of which have reported variants associated with deafness. However, SPRY2 was not dysregulated in normal-hearing humans homozygous for both the GAB1 DFNB26 deafness variant and the dominant METTL13 deafness suppressor, indicating a plausible mechanism of suppression. Identification of METTL13-based modification of MET signaling offers a potential therapeutic strategy for a wide range of associated hearing disorders. Furthermore, MET signaling is essential for diverse functions in many tissues including the inner ear. Therefore, identification of the modifier of MET signaling is likely to have broad clinical implications.
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Affiliation(s)
- Rizwan Yousaf
- Laboratory of Molecular Genetics, Department of Otorhinolaryngology - Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA
| | - Zubair M Ahmed
- Laboratory of Molecular Genetics, Department of Otorhinolaryngology - Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA
| | - Arnaud Pj Giese
- Laboratory of Molecular Genetics, Department of Otorhinolaryngology - Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA
| | - Robert J Morell
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | - Ayala Lagziel
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | - Alain Dabdoub
- Laboratory of Cochlear Development, NIDCD, NIH, Bethesda, Maryland, USA
| | - Edward R Wilcox
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | - Sheikh Riazuddin
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan.,Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | - Saima Riazuddin
- Laboratory of Molecular Genetics, Department of Otorhinolaryngology - Head and Neck Surgery, University of Maryland, Baltimore, Maryland, USA.,Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan.,Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
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3
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Ortiz-Virumbrales M, Moreno CL, Kruglikov I, Marazuela P, Sproul A, Jacob S, Zimmer M, Paull D, Zhang B, Schadt EE, Ehrlich ME, Tanzi RE, Arancio O, Noggle S, Gandy S. CRISPR/Cas9-Correctable mutation-related molecular and physiological phenotypes in iPSC-derived Alzheimer's PSEN2 N141I neurons. Acta Neuropathol Commun 2017; 5:77. [PMID: 29078805 PMCID: PMC5660456 DOI: 10.1186/s40478-017-0475-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 09/16/2017] [Indexed: 12/18/2022] Open
Abstract
Basal forebrain cholinergic neurons (BFCNs) are believed to be one of the first cell types to be affected in all forms of AD, and their dysfunction is clinically correlated with impaired short-term memory formation and retrieval. We present an optimized in vitro protocol to generate human BFCNs from iPSCs, using cell lines from presenilin 2 (PSEN2) mutation carriers and controls. As expected, cell lines harboring the PSEN2N141I mutation displayed an increase in the Aβ42/40 in iPSC-derived BFCNs. Neurons derived from PSEN2N141I lines generated fewer maximum number of spikes in response to a square depolarizing current injection. The height of the first action potential at rheobase current injection was also significantly decreased in PSEN2N141I BFCNs. CRISPR/Cas9 correction of the PSEN2 point mutation abolished the electrophysiological deficit, restoring both the maximal number of spikes and spike height to the levels recorded in controls. Increased Aβ42/40 was also normalized following CRISPR/Cas-mediated correction of the PSEN2N141I mutation. The genome editing data confirms the robust consistency of mutation-related changes in Aβ42/40 ratio while also showing a PSEN2-mutation-related alteration in electrophysiology.
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4
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Cacace R, Sleegers K, Van Broeckhoven C. Molecular genetics of early-onset Alzheimer's disease revisited. Alzheimers Dement 2016; 12:733-48. [DOI: 10.1016/j.jalz.2016.01.012] [Citation(s) in RCA: 304] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/20/2016] [Accepted: 01/28/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Rita Cacace
- Neurodegenerative Brain Diseases group; Department of Molecular Genetics; VIB; Antwerp Belgium
- Laboratory of Neurogenetics; Institute Born-Bunge, University of Antwerp; Antwerp Belgium
| | - Kristel Sleegers
- Neurodegenerative Brain Diseases group; Department of Molecular Genetics; VIB; Antwerp Belgium
- Laboratory of Neurogenetics; Institute Born-Bunge, University of Antwerp; Antwerp Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases group; Department of Molecular Genetics; VIB; Antwerp Belgium
- Laboratory of Neurogenetics; Institute Born-Bunge, University of Antwerp; Antwerp Belgium
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5
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Lalli MA, Bettcher BM, Arcila ML, Garcia G, Guzman C, Madrigal L, Ramirez L, Acosta-Uribe J, Baena A, Wojta KJ, Coppola G, Fitch R, de Both MD, Huentelman MJ, Reiman EM, Brunkow ME, Glusman G, Roach JC, Kao AW, Lopera F, Kosik KS. Whole-genome sequencing suggests a chemokine gene cluster that modifies age at onset in familial Alzheimer's disease. Mol Psychiatry 2015; 20:1294-300. [PMID: 26324103 PMCID: PMC4759097 DOI: 10.1038/mp.2015.131] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/10/2015] [Accepted: 07/23/2015] [Indexed: 12/22/2022]
Abstract
We have sequenced the complete genomes of 72 individuals affected with early-onset familial Alzheimer's disease caused by an autosomal dominant, highly penetrant mutation in the presenilin-1 (PSEN1) gene, and performed genome-wide association testing to identify variants that modify age at onset (AAO) of Alzheimer's disease. Our analysis identified a haplotype of single-nucleotide polymorphisms (SNPs) on chromosome 17 within a chemokine gene cluster associated with delayed onset of mild-cognitive impairment and dementia. Individuals carrying this haplotype had a mean AAO of mild-cognitive impairment at 51.0 ± 5.2 years compared with 41.1 ± 7.4 years for those without these SNPs. This haplotype thus appears to modify Alzheimer's AAO, conferring a large (~10 years) protective effect. The associated locus harbors several chemokines including eotaxin-1 encoded by CCL11, and the haplotype includes a missense polymorphism in this gene. Validating this association, we found plasma eotaxin-1 levels were correlated with disease AAO in an independent cohort from the University of California San Francisco Memory and Aging Center. In this second cohort, the associated haplotype disrupted the typical age-associated increase of eotaxin-1 levels, suggesting a complex regulatory role for this haplotype in the general population. Altogether, these results suggest eotaxin-1 as a novel modifier of Alzheimer's disease AAO and open potential avenues for therapy.
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Affiliation(s)
- M A Lalli
- Neuroscience Research Institute, Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA, USA
| | - B M Bettcher
- Memory and Aging Center, Department of Neurology, University of California at San Francisco, San Francisco, CA, USA
| | - M L Arcila
- Neuroscience Research Institute, Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA, USA
| | - G Garcia
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - C Guzman
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - L Madrigal
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - L Ramirez
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - J Acosta-Uribe
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - A Baena
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - K J Wojta
- Departments of Psychiatry and Neurology, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles, CA, USA
| | - G Coppola
- Departments of Psychiatry and Neurology, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles, CA, USA
| | - R Fitch
- Memory and Aging Center, Department of Neurology, University of California at San Francisco, San Francisco, CA, USA
| | - M D de Both
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - M J Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - E M Reiman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
- Banner Alzheimer's Institute, Department of Psychiatry, University of Arizona, Tucson, AZ, USA
| | - M E Brunkow
- Institute for Systems Biology, Seattle, WA, USA
| | - G Glusman
- Institute for Systems Biology, Seattle, WA, USA
| | - J C Roach
- Institute for Systems Biology, Seattle, WA, USA
| | - A W Kao
- Memory and Aging Center, Department of Neurology, University of California at San Francisco, San Francisco, CA, USA
| | - F Lopera
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - K S Kosik
- Neuroscience Research Institute, Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA, USA
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6
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Lee JH, Cheng R, Vardarajan B, Lantigua R, Reyes-Dumeyer D, Ortmann W, Graham RR, Bhangale T, Behrens TW, Medrano M, Jiménez-Velázquez IZ, Mayeux R. Genetic Modifiers of Age at Onset in Carriers of the G206A Mutation in PSEN1 With Familial Alzheimer Disease Among Caribbean Hispanics. JAMA Neurol 2015; 72:1043-51. [PMID: 26214276 PMCID: PMC5010776 DOI: 10.1001/jamaneurol.2015.1424] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE The present study identified potential genetic modifiers that may delay or accelerate age at onset of familial Alzheimer disease (AD) by examining age at onset in PSEN1 mutation carrier families, and further investigation of these modifiers may provide insight into the pathobiology of AD and potential therapeutic measures. OBJECTIVE To identify genetic variants that modify age at onset of AD. DESIGN, SETTING, AND PARTICIPANTS Using a subset of Caribbean Hispanic families that carry the PSEN1 p.G206A mutation, we performed a 2-stage genome study. The mutation carrier families from an ongoing genetic study served as a discovery set, and the cohort of those with LOAD served as a confirmation set. To identify candidate loci, we performed linkage analysis using 5 p.G206A carrier families (n = 56), and we also performed whole-exome association analysis using 31 p.G206A carriers from 26 families. To confirm the genetic modifiers identified from the p.G206A carrier families, we analyzed the GWAS data for 2888 elderly individuals with LOAD. All study participants were Caribbean Hispanics. MAIN OUTCOMES AND MEASURES Age at onset of AD. RESULTS Linkage analysis of AD identified the strongest linkage support at 4q35 (LOD [logarithm of odds] score, 3.69), and the GWAS of age at onset identified variants on 1p13.1, 2q13, 4q25, and 17p11. In the confirmation stage, genewise analysis identified SNX25, PDLIM3, and 3 SH3 domain genes (SORBS2, SH3RF3, and NPHP1) to be significantly associated with LOAD. Subsequent allelic association analysis confirmed SNX25, PDLIM3, and SORBS2 as genetic modifiers of age at onset of EOAD and LOAD and provided modest support for SH3RF3 and NPHP1. CONCLUSIONS AND RELEVANCE Our 2-stage analysis revealed that SNX25, PDLIM3, and SORBS2 may serve as genetic modifiers of age at onset in both EOAD and LOAD.
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Affiliation(s)
- Joseph H. Lee
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York2Gertrude H. Sergievsky Center, Columbia University, New York, New York3Department of Epidemiology, School of Public Health, Columbia Univer
| | - Rong Cheng
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York2Gertrude H. Sergievsky Center, Columbia University, New York, New York
| | - Badri Vardarajan
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York2Gertrude H. Sergievsky Center, Columbia University, New York, New York
| | - Rafael Lantigua
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York4Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Dolly Reyes-Dumeyer
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York
| | | | | | | | - Timothy W. Behrens
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Martin Medrano
- School of Medicine, Pontificia Universidad Catolica Madre y Maestra, Santiago, Dominican Republic
| | | | - Richard Mayeux
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York2Gertrude H. Sergievsky Center, Columbia University, New York, New York3Department of Epidemiology, School of Public Health, Columbia Univer
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7
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The genetic landscape of Alzheimer disease: clinical implications and perspectives. Genet Med 2015; 18:421-30. [PMID: 26312828 PMCID: PMC4857183 DOI: 10.1038/gim.2015.117] [Citation(s) in RCA: 557] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/07/2015] [Indexed: 11/12/2022] Open
Abstract
The search for the genetic factors contributing to Alzheimer disease (AD) has evolved tremendously throughout the years. It started from the discovery of fully penetrant mutations in Amyloid precursor protein, Presenilin 1, and Presenilin 2 as a cause of autosomal dominant AD, the identification of the ɛ4 allele of Apolipoprotein E as a strong genetic risk factor for both early-onset and late-onset AD, and evolved to the more recent detection of at least 21 additional genetic risk loci for the genetically complex form of AD emerging from genome-wide association studies and massive parallel resequencing efforts. These advances in AD genetics are positioned in light of the current endeavor directing toward translational research and personalized treatment of AD. We discuss the current state of the art of AD genetics and address the implications and relevance of AD genetics in clinical diagnosis and risk prediction, distinguishing between monogenic and multifactorial AD. Furthermore, the potential and current limitations of molecular reclassification of AD to streamline clinical trials in drug development and biomarker studies are addressed. Genet Med18 5, 421–430.
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8
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Lalli MA, Garcia G, Madrigal L, Arcos-Burgos M, Arcila ML, Kosik KS, Lopera F. Exploratory data from complete genomes of familial alzheimer disease age-at-onset outliers. Hum Mutat 2012; 33:1630-4. [PMID: 22829467 DOI: 10.1002/humu.22167] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 07/07/2012] [Indexed: 11/08/2022]
Abstract
Identifying genes that modify the age at onset (AAO) of Alzheimer disease and targeting them pharmacologically represent a potential treatment strategy. In this exploratory study, we sequenced the complete genomes of six individuals with familial Alzheimer disease due to the autosomal dominant mutation p.Glu280Ala in PSEN1 (MIM# 104311; NM_000021.3:c.839A>C). The disease and its AAO are highly heritable, motivating our search for genetic variants that modulate AAO. The median AAO of dementia in carriers of the mutant allele is 49 years. Extreme phenotypic outliers for AAO in this genetically isolated population with limited environmental variance are likely to harbor onset modifying genetic variants. A narrow distribution of AAO in this kindred suggests large effect sizes of genetic determinants of AAO in these outliers. Identity by descent (IBD) analysis and a combination of bioinformatics filters have suggested several candidate variants for AAO modifiers. Future work and replication studies on these variants may provide mechanistic insights into the etiopathology of Alzheimer disease.
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Affiliation(s)
- Matthew A Lalli
- Neuroscience Research Institute, University of California at Santa Barbara, CA, USA
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9
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Marchani EE, Wijsman EM. Estimation and visualization of identity-by-descent within pedigrees simplifies interpretation of complex trait analysis. Hum Hered 2011; 72:289-97. [PMID: 22189471 PMCID: PMC3267995 DOI: 10.1159/000334083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Linkage analysis identifies markers that appear to be co-inherited with a trait within pedigrees. The inheritance of a chromosomal segment may be probabilistically reconstructed, with missing data complicating inference. Inheritance patterns are further obscured in the analysis of complex traits, where variants in one or more genes may contribute to phenotypic variation within a pedigree. In this case, determining which relatives share a trait variant is not simple. We describe how to represent these patterns of inheritance for marker loci. We summarize how to sample patterns of inheritance consistent with genotypic and pedigree data using gl_auto, available in MORGAN v3.0. We describe identification of classes of equivalent inheritance patterns with the program IBDgraph. We finally provide an example of how these programs may be used to simplify interpretation of linkage analysis of complex traits in general pedigrees. We borrow information across loci in a parametric linkage analysis of a large pedigree. We explore the contribution of each equivalence class to a linkage signal, illustrate estimated patterns of identity-by-descent sharing, and identify a haplotype tagging the chromosomal segment driving the linkage signal. Haplotype carriers are more likely to share the linked trait variant, and can be prioritized for subsequent DNA sequencing.
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Affiliation(s)
- Elizabeth E. Marchani
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Wash., USA
| | - Ellen M. Wijsman
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Wash., USA
- Department of Biostatistics, University of Washington, Seattle, Wash., USA
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Choi Y, Marchani EE, Bird TD, Steinbart EJ, Blacker D, Wijsman EM. Genome scan of age-at-onset in the NIMH Alzheimer disease sample uncovers multiple loci, along with evidence of both genetic and sample heterogeneity. Am J Med Genet B Neuropsychiatr Genet 2011; 156B:785-98. [PMID: 21812099 PMCID: PMC3168696 DOI: 10.1002/ajmg.b.31220] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 07/06/2011] [Indexed: 01/01/2023]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder of late life with a complex genetic basis. Although several genes are known to play a role in rare early onset AD, only the APOE gene is known to have a high contribution to risk of the common late-onset form of the disease (LOAD, onset >60 years). APOE genotypes vary in their AD risk as well as age-at-onset distributions, and it is likely that other loci will similarly affect AD age-at-onset. Here we present the first analysis of age-at-onset in the NIMH LOAD sample that allows for both a multilocus trait model and genetic heterogeneity among the contributing sites, while at the same time accommodating age censoring, effects of known genetic covariates, and full pedigree and marker information. The results provide evidence for genomic regions not previously implicated in this data set, including regions on chromosomes 7q, 15, and 19p. They also affirm evidence for loci on chromosomes 1q, 6p, 9q, 11, and, of course, the APOE locus on 19q, all of which have been reported previously in the same sample. The analyses failed to find evidence for linkage to chromosome 10 with inclusion of unaffected subjects and extended pedigrees. Several regions implicated in these analyses in the NIMH sample have been previously reported in genome scans of other AD samples. These results, therefore, provide independent confirmation of AD loci in family-based samples on chromosomes 1q, 7q, 19p, and suggest that further efforts towards identifying the underlying causal loci are warranted.
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Affiliation(s)
- Yoonha Choi
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Elizabeth E. Marchani
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Thomas D. Bird
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA,Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle Division, Seattle, WA,Department of Neurology, University of Washington, Seattle, WA
| | - Ellen J. Steinbart
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle Division, Seattle, WA,Department of Neurology, University of Washington, Seattle, WA
| | - Deborah Blacker
- Department of Psychiatry, Massachusetts General Hospital/Harvard Medical School; Dept of Epidemiology, Harvard School of Public Health; Boston, MA
| | - Ellen M. Wijsman
- Department of Biostatistics, University of Washington, Seattle, WA,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA,Department of Genome Sciences, University of Washington, Seattle, WA,correspondence to Ellen M. Wijsman, Department of Medicine, Division of Medical Genetics, Box 357720, University of Washington, Seattle, WA 98195-7720. (206) 543-8987.
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11
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Wijsman EM, Pankratz ND, Choi Y, Rothstein JH, Faber KM, Cheng R, Lee JH, Bird TD, Bennett DA, Diaz-Arrastia R, Goate AM, Farlow M, Ghetti B, Sweet RA, Foroud TM, Mayeux R. Genome-wide association of familial late-onset Alzheimer's disease replicates BIN1 and CLU and nominates CUGBP2 in interaction with APOE. PLoS Genet 2011; 7:e1001308. [PMID: 21379329 PMCID: PMC3040659 DOI: 10.1371/journal.pgen.1001308] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 01/12/2011] [Indexed: 12/13/2022] Open
Abstract
Late-onset Alzheimer's disease (LOAD) is the most common form of dementia in the elderly. The National Institute of Aging-Late Onset Alzheimer's Disease Family Study and the National Cell Repository for Alzheimer's Disease conducted a joint genome-wide association study (GWAS) of multiplex LOAD families (3,839 affected and unaffected individuals from 992 families plus additional unrelated neurologically evaluated normal subjects) using the 610 IlluminaQuad panel. This cohort represents the largest family-based GWAS of LOAD to date, with analyses limited here to the European-American subjects. SNPs near APOE gave highly significant results (e.g., rs2075650, p = 3.2×10(-81)), but no other genome-wide significant evidence for association was obtained in the full sample. Analyses that stratified on APOE genotypes identified SNPs on chromosome 10p14 in CUGBP2 with genome-wide significant evidence for association within APOE ε4 homozygotes (e.g., rs201119, p = 1.5×10(-8)). Association in this gene was replicated in an independent sample consisting of three cohorts. There was evidence of association for recently-reported LOAD risk loci, including BIN1 (rs7561528, p = 0.009 with, and p = 0.03 without, APOE adjustment) and CLU (rs11136000, p = 0.023 with, and p = 0.008 without, APOE adjustment), with weaker support for CR1. However, our results provide strong evidence that association with PICALM (rs3851179, p = 0.69 with, and p = 0.039 without, APOE adjustment) and EXOC3L2 is affected by correlation with APOE, and thus may represent spurious association. Our results indicate that genetic structure coupled with ascertainment bias resulting from the strong APOE association affect genome-wide results and interpretation of some recently reported associations. We show that a locus such as APOE, with large effects and strong association with disease, can lead to samples that require appropriate adjustment for this locus to avoid both false positive and false negative evidence of association. We suggest that similar adjustments may also be needed for many other large multi-site studies.
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Affiliation(s)
- Ellen M. Wijsman
- Division of Medical Genetics, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Nathan D. Pankratz
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Yoonha Choi
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Joseph H. Rothstein
- Division of Medical Genetics, University of Washington, Seattle, Washington, United States of America
| | - Kelley M. Faber
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Rong Cheng
- The Gertrude H. Sergievsky Center, The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Joseph H. Lee
- The Gertrude H. Sergievsky Center, The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Thomas D. Bird
- Division of Medical Genetics, University of Washington, Seattle, Washington, United States of America
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle Division, Seattle, Washington, United States of America
- Department of Neurology, University of Washington, Seattle, Washington, United States of America
| | - David A. Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Ramon Diaz-Arrastia
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Alison M. Goate
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Martin Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Bernardino Ghetti
- Department of Pathology, Division of Neuropathology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Robert A. Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Tatiana M. Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Richard Mayeux
- The Gertrude H. Sergievsky Center, The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
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Rubenstein K, Matsushita M, Berninger VW, Raskind WH, Wijsman EM. Genome scan for spelling deficits: effects of verbal IQ on models of transmission and trait gene localization. Behav Genet 2011; 41:31-42. [PMID: 20852926 PMCID: PMC3030654 DOI: 10.1007/s10519-010-9390-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 08/26/2010] [Indexed: 02/03/2023]
Abstract
Dyslexia is a complex learning disability with evidence for a genetic basis. Strategies that may be useful for dissecting its genetic basis include the study of component phenotypes, which may simplify the underlying genetic complexity, and use of an analytic approach that accounts for the multilocus nature of the trait to guide the investigation and increase power to detect individual loci. Here we present results of a genetic analysis of spelling disability as a component phenotype. Spelling disability is informative in analysis of extended pedigrees because it persists into adulthood. We show that a small number of hypothesized loci are sufficient to explain the inheritance of the trait in our sample, and that each of these loci maps to one of four genomic regions. Individual trait models and locations are a function of whether a verbal IQ adjustment is included, suggesting mediation through both IQ-related and unrelated pathways.
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Affiliation(s)
- Kevin Rubenstein
- Department of Biostatistics, University of Washington, Box 357232, Seattle, WA, USA
| | - Mark Matsushita
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 357720, Seattle, WA 98195-7720, USA
| | - Virginia W. Berninger
- Department of Educational Psychology, University of Washington, Box 353600, Seattle, WA, USA
| | - Wendy H. Raskind
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 357720, Seattle, WA 98195-7720, USA, Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Ellen M. Wijsman
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 357720, Seattle, WA 98195-7720, USA, 4333 Brooklyn Ave, NE, Box 989460, Seattle, WA 98195-9460, USA. Department of Biostatistics, University of Washington, Seattle, WA, USA
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13
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Jayadev S, Leverenz JB, Steinbart E, Stahl J, Klunk W, Yu CE, Bird TD. Alzheimer's disease phenotypes and genotypes associated with mutations in presenilin 2. Brain 2010; 133:1143-54. [PMID: 20375137 PMCID: PMC2850581 DOI: 10.1093/brain/awq033] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 01/11/2009] [Accepted: 01/15/2009] [Indexed: 11/13/2022] Open
Abstract
Mutations in presenilin 2 are rare causes of early onset familial Alzheimer's disease. Eighteen presenilin 2 mutations have been reported, although not all have been confirmed pathogenic. Much remains to be learned about the range of phenotypes associated with these mutations. We have analysed our unique collection of 146 affected cases in 11 Volga German families, 101 who are likely to have the same N141I mutation in presenilin 2 (54 genotyped confirmed). We have also assessed the detailed neuropathologic findings in 18 autopsies from these families and reviewed the world's literature on other presenilin 2 mutations; presenting a novel mutation that is predicted to lead to a premature truncation codon. Seven presenilin 2 mutations reported in the literature have strong evidence for pathogenicity whereas others may be benign polymorphisms. One hundred and one affected persons, with sufficient historical information from the Volga German pedigrees (N141I mutation), had a mean onset age of 53.7 years+/-7.8 (range 39-75) and mean age at death of 64.2 years+/-9.8 (range 43-88). These figures overlap with and generally fall between the results from the subjects in our centre who have late onset familial Alzheimer's disease or mutations in presenilin 1. Seizures were noted in 20 (30%) of 64 subjects with detailed medical records. Two mutation carriers lived beyond age 80 without developing dementia, representing uncommon examples of decreased penetrance. Two persons had severe amyloid angiopathy and haemorrhagic stroke. Eighteen cases had detailed histopathology available and analysed at our institution. Braak stage was five or six, amyloid angiopathy and neuritic plaques were common and more than 75% had Lewy bodies in the amygdala. TAR DNA-binding protein-43 inclusions were uncommon. In addition, a 58-year-old female with a 2 year course of cognitive decline and no family history of dementia has abnormal fludeoxyglucose-positron emission tomography imaging and a novel 2 base pair deletion in presenilin 2 at nucleotide 342/343, predicted to produce a frame-shift and premature termination. We conclude that mutations in presenilin 2 are rare with only seven being well documented in the literature. The best studied N141I mutation produces an Alzheimer's disease phenotype with a wide range of onset ages overlapping both early and late onset Alzheimer's disease, often associated with seizures, high penetrance and typical Alzheimer's disease neuropathology. A novel premature termination mutation supports loss of function or haploinsufficiency as pathogenic mechanisms in presenilin 2 associated Alzheimer's disease.
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Affiliation(s)
- Suman Jayadev
- 1 Department of Neurology, University of Washington, Seattle, WA, USA
| | - James B. Leverenz
- 1 Department of Neurology, University of Washington, Seattle, WA, USA
- 2 Mental Illness Research Education and Clinical Centre, Veterans Administration Puget Sound Health Care System, Seattle, WA, USA
- 3 Parkinson Disease Research Education and Clinical Centre, Veterans Administration Puget Sound Health Care System, Seattle, WA, USA
| | - Ellen Steinbart
- 1 Department of Neurology, University of Washington, Seattle, WA, USA
- 4 Geriatric Research Education and Clinical Centre, Seattle, WA, USA
| | - Justin Stahl
- 5 Virginia Mason Clinic, Veterans Administration Puget Sound Health Care System, Seattle, WA, USA
| | - William Klunk
- 6 Departments of Psychiatry and Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Cheng-En Yu
- 4 Geriatric Research Education and Clinical Centre, Seattle, WA, USA
| | - Thomas D. Bird
- 1 Department of Neurology, University of Washington, Seattle, WA, USA
- 4 Geriatric Research Education and Clinical Centre, Seattle, WA, USA
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