Swaminathan, S;
Huentelman, MJ;
Corneveaux, JJ;
Myers, AJ;
Faber, KM;
Foroud, T;
Mayeux, R;
... Grp, NIA-LOADNCRADFS; + view all
(2012)
Analysis of Copy Number Variation in Alzheimer's Disease in a Cohort of Clinically Characterized and Neuropathologically Verified Individuals.
PLOS ONE
, 7
(12)
, Article e50640. 10.1371/journal.pone.0050640.
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Abstract
Copy number variations (CNVs) are genomic regions that have added (duplications) or deleted (deletions) genetic material. They may overlap genes affecting their function and have been shown to be associated with disease. We previously investigated the role of CNVs in late-onset Alzheimer's disease (AD) and mild cognitive impairment using Alzheimer’s Disease Neuroimaging Initiative (ADNI) and National Institute of Aging-Late Onset AD/National Cell Repository for AD (NIA-LOAD/NCRAD) Family Study participants, and identified a number of genes overlapped by CNV calls. To confirm the findings and identify other potential candidate regions, we analyzed array data from a unique cohort of 1617 Caucasian participants (1022 AD cases and 595 controls) who were clinically characterized and whose diagnosis was neuropathologically verified. All DNA samples were extracted from brain tissue. CNV calls were generated and subjected to quality control (QC). 728 cases and 438 controls who passed all QC measures were included in case/control association analyses including candidate gene and genome-wide approaches. Rates of deletions and duplications did not significantly differ between cases and controls. Case-control association identified a number of previously reported regions (CHRFAM7A, RELN and DOPEY2) as well as a new gene (HLA-DRA). Meta-analysis of CHRFAM7A indicated a significant association of the gene with AD and/or MCI risk (P = 0.006, odds ratio = 3.986 (95% confidence interval 1.490–10.667)). A novel APP gene duplication was observed in one case sample. Further investigation of the identified genes in independent and larger samples is warranted.
| Type: | Article |
|---|---|
| Title: | Analysis of Copy Number Variation in Alzheimer's Disease in a Cohort of Clinically Characterized and Neuropathologically Verified Individuals |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1371/journal.pone.0050640 |
| Publisher version: | http://dx.doi.org/10.1371/journal.pone.0050640 |
| Language: | English |
| Additional information: | © 2012 Swaminathan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Genotyping of the TGen cohort was supported by Kronos Science; the National Institute of Neurological Disorders and Stroke (NINDS) (R01NS059873); the National Institute on Aging (NIA) (R01AG034504, R01AG031581, P30AG19610, Z01AG000950-06, P30AG10161, R01AG15819); the Banner Alzheimer's Foundation; the Johnnie B. Byrd Sr. Alzheimer's Disease Institute; the Medical Research Council; the Intramural Research Program of the National Institutes of Health (NIH); and the State of Arizona. Many data and biomaterials for the TGen cohort were collected from several NIA and National Alzheimer’s Coordinating Center (NACC) (U01AG016976) funded sites. These include: John Hopkins Alzheimer's Disease Research Center (NIA AG05146); University of California, Los Angeles (NIA P50AG16570); The Kathleen Price Bryan Brain Bank, Duke University Medical Center (NIA AG05128, NINDS NS39764, National Institute of Mental Health MH60451 also funded by Glaxo Smith Kline); Massachusetts Alzheimer’s Disease Research Center (P50AG005134); University of Michigan (NIH P50-AG08671); University of Kentucky (NIH AG05144); Washington University, St Louis Alzheimer’s Disease Research Center (NIH P50AG05681); University of Washington, Seattle (NIH P50AG05136); Boston University Alzheimer’s Disease Research Center (NIH P30-AG13846); Sun Health Research Institute Brain Donation Program of Sun City, Arizona (NIA P30AG19610; Arizona Alzheimer’s Disease Core Center, Arizona Department of Health Services, contract 211002, Arizona Alzheimer’s Research Center; Arizona Biomedical Research Commission, contracts 4001, 0011, 05–901 and 1001 to the Arizona Parkinson's Disease Consortium; Michael J. Fox Foundation for Parkinson’s Research); Rush University Medical Center, Rush Alzheimer's Disease Center (NIH AG10161). Additional tissues include samples from the following sites: Newcastle Brain Tissue Resource (funding via the Medical Research Council (MRC), local National Health Service (NHS) trusts and Newcastle University); MRC London Brain Bank for Neurodegenerative Diseases (funding via the Medical Research Council); South West Dementia Brain Bank (funding via numerous sources including the Higher Education Funding Council for England (HEFCE), Alzheimer’s Research Trust (ART), BRACE as well as North Bristol NHS Trust Research and Innovation Department and the National Institute for Health Research (NIHR) Dementias and Neurodegenerative Diseases Research Network (DeNDRoN); The Netherlands Brain Bank (funding via numerous sources including Stichting MS Research, Brain Net Europe, Hersenstichting Nederland Breinbrekend Werk, International Parkinson Fonds, Internationale Stiching Alzheimer Onderzoek). Data collection and sharing for the Alzheimer's Disease Neuroimaging Initiative (ADNI) project was funded by the ADNI (NIH U01AG024904; RC2AG036535). ADNI is funded by the NIA, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: Abbott; Alzheimer’s Association; Alzheimer’s Drug Discovery Foundation; Amorfix Life Sciences Ltd.; AstraZeneca; Bayer HealthCare; BioClinica, Inc.; Biogen Idec Inc.; Bristol-Myers Squibb Company; Eisai Inc.; Elan Pharmaceuticals Inc.; Eli Lilly and Company; F. Hoffman-La Roche Ltd and its affiliated company Genentech, Inc.; GE Healthcare; Innogenetics, N.V.; Janssen Alzheimer Immunotherapy Research & Development, LLC.; Johnson & Johnson Pharmaceutical Research & Development LLC.; Medpace, Inc.; Merck & Co., Inc; Meso Scale Diagnostics, LLC.; Novartis Pharmaceuticals Corporation; Pfizer Inc.; Servier; Synarc Inc.; and Takeda Pharmaceutical Company. The Canadian Institutes of Health Research is providing funds to support ADNI clinical sites in Canada. Private sector contributions are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimer's Disease Cooperative Society at the University of California, San Diego. ADNI data are disseminated by the Laboratory of Neuro Imaging at the University of California, Los Angeles. This research was also supported by NIH grants P30AG010129, K01AG030514, the Dana Foundation, U01AG032984 Alzheimer's Disease Genetics Consortium grant, NIA R01AG19771, P30AG010133, the Indiana Economic Development Corporation (IEDC #87884), and the Foundation for the NIH for data analysis. Funding support for the National Institute of Aging-Late Onset AD/National Cell Repository for AD (NIA-LOAD/NCRAD) Family Study was provided through NIA grants U24AG026395 (NIA-LOAD Family Study), U24AG021886 (National Cell Repository for Alzheimer's Disease) and other NIA grants. Genotyping services were provided by the Center for Inherited Disease Research funded through a federal contract (HHSN268200782096C) from the NIH to the John Hopkins University. Samples from the NCRAD, which receives government support under a cooperative agreement (U24AG021886) awarded by the NIA were used in the ADNI and NIA-LOAD/NCRAD Family studies. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Genotyping of the TGen cohort was supported by Kronos Science. This study was partly funded by Glaxo Smith Kline. Data collection and sharing for the Alzheimer's Disease Neuroimaging Initiative (ADNI) project was funded by the ADNI (NIH U01AG024904; RC2AG036535). ADNI is funded by the NIA, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: Abbott; Alzheimer’s Association; Alzheimer’s Drug Discovery Foundation; Amorfix Life Sciences Ltd.; AstraZeneca; Bayer HealthCare; BioClinica, Inc.; Biogen Idec Inc.; Bristol-Myers Squibb Company; Eisai Inc.; Elan Pharmaceuticals Inc.; Eli Lilly and Company; F. Hoffman-La Roche Ltd and its affiliated company Genentech, Inc.; GE Healthcare; Innogenetics, N.V.; Janssen Alzheimer Immunotherapy Research & Development, LLC.; Johnson & Johnson Pharmaceutical Research & Development LLC.; Medpace, Inc.; Merck & Co., Inc; Meso Scale Diagnostics, LLC.; Novartis Pharmaceuticals Corporation; Pfizer Inc.; Servier; Synarc Inc.; and Takeda Pharmaceutical Company. There are no patents, products in development or marketed products to declare. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Neurodegenerative Diseases |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/1381484 |
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