Common polygenic variation enhances risk prediction for Alzheimer’s disease

The identification of subjects at high risk for Alzheimer's disease is important for prognosis and early intervention. We investigated the polygenic architecture of Alzheimer's disease and the accuracy of Alzheimer's disease prediction models, including and excluding the polygenic com...

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Published inBrain (London, England : 1878) Vol. 138; no. 12; pp. 3673 - 3684
Main Authors Escott-Price, Valentina, Sims, Rebecca, Bannister, Christian, Harold, Denise, Vronskaya, Maria, Majounie, Elisa, Badarinarayan, Nandini, Morgan, Kevin, Passmore, Peter, Holmes, Clive, Powell, John, Brayne, Carol, Gill, Michael, Mead, Simon, Goate, Alison, Cruchaga, Carlos, Lambert, Jean-Charles, van Duijn, Cornelia, Maier, Wolfgang, Ramirez, Alfredo, Holmans, Peter, Jones, Lesley, Hardy, John, Seshadri, Sudha, Schellenberg, Gerard D., Amouyel, Philippe, Williams, Julie
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.12.2015
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Abstract The identification of subjects at high risk for Alzheimer's disease is important for prognosis and early intervention. We investigated the polygenic architecture of Alzheimer's disease and the accuracy of Alzheimer's disease prediction models, including and excluding the polygenic component in the model. This study used genotype data from the powerful dataset comprising 17 008 cases and 37 154 controls obtained from the International Genomics of Alzheimer's Project (IGAP). Polygenic score analysis tested whether the alleles identified to associate with disease in one sample set were significantly enriched in the cases relative to the controls in an independent sample. The disease prediction accuracy was investigated in a subset of the IGAP data, a sample of 3049 cases and 1554 controls (for whom APOE genotype data were available) by means of sensitivity, specificity, area under the receiver operating characteristic curve (AUC) and positive and negative predictive values. We observed significant evidence for a polygenic component enriched in Alzheimer's disease (P = 4.9 × 10(-26)). This enrichment remained significant after APOE and other genome-wide associated regions were excluded (P = 3.4 × 10(-19)). The best prediction accuracy AUC = 78.2% (95% confidence interval 77-80%) was achieved by a logistic regression model with APOE, the polygenic score, sex and age as predictors. In conclusion, Alzheimer's disease has a significant polygenic component, which has predictive utility for Alzheimer's disease risk and could be a valuable research tool complementing experimental designs, including preventative clinical trials, stem cell selection and high/low risk clinical studies. In modelling a range of sample disease prevalences, we found that polygenic scores almost doubles case prediction from chance with increased prediction at polygenic extremes.
AbstractList The identification of subjects at high risk for Alzheimer's disease is important for prognosis and early intervention. We investigated the polygenic architecture of Alzheimer's disease and the accuracy of Alzheimer's disease prediction models, including and excluding the polygenic component in the model. This study used genotype data from the powerful dataset comprising 17 008 cases and 37 154 controls obtained from the International Genomics of Alzheimer's Project (IGAP). Polygenic score analysis tested whether the alleles identified to associate with disease in one sample set were significantly enriched in the cases relative to the controls in an independent sample. The disease prediction accuracy was investigated in a subset of the IGAP data, a sample of 3049 cases and 1554 controls (for whom APOE genotype data were available) by means of sensitivity, specificity, area under the receiver operating characteristic curve (AUC) and positive and negative predictive values. We observed significant evidence for a polygenic component enriched in Alzheimer's disease (P = 4.9 × 10(-26)). This enrichment remained significant after APOE and other genome-wide associated regions were excluded (P = 3.4 × 10(-19)). The best prediction accuracy AUC = 78.2% (95% confidence interval 77-80%) was achieved by a logistic regression model with APOE, the polygenic score, sex and age as predictors. In conclusion, Alzheimer's disease has a significant polygenic component, which has predictive utility for Alzheimer's disease risk and could be a valuable research tool complementing experimental designs, including preventative clinical trials, stem cell selection and high/low risk clinical studies. In modelling a range of sample disease prevalences, we found that polygenic scores almost doubles case prediction from chance with increased prediction at polygenic extremes.
The identification of subjects at high risk for Alzheimer's disease is important for prognosis and early intervention. We investigated the polygenic architecture of Alzheimer's disease and the accuracy of Alzheimer's disease prediction models, including and excluding the polygenic component in the model. This study used genotype data from the powerful dataset comprising 17 008 cases and 37 154 controls obtained from the International Genomics of Alzheimer's Project (IGAP). Polygenic score analysis tested whether the alleles identified to associate with disease in one sample set were significantly enriched in the cases relative to the controls in an independent sample. The disease prediction accuracy was investigated in a subset of the IGAP data, a sample of 3049 cases and 1554 controls (for whom APOE genotype data were available) by means of sensitivity, specificity, area under the receiver operating characteristic curve (AUC) and positive and negative predictive values. We observed significant evidence for a polygenic component enriched in Alzheimer's disease (P = 4.9 × 10(-26)). This enrichment remained significant after APOE and other genome-wide associated regions were excluded (P = 3.4 × 10(-19)). The best prediction accuracy AUC = 78.2% (95% confidence interval 77-80%) was achieved by a logistic regression model with APOE, the polygenic score, sex and age as predictors. In conclusion, Alzheimer's disease has a significant polygenic component, which has predictive utility for Alzheimer's disease risk and could be a valuable research tool complementing experimental designs, including preventative clinical trials, stem cell selection and high/low risk clinical studies. In modelling a range of sample disease prevalences, we found that polygenic scores almost doubles case prediction from chance with increased prediction at polygenic extremes.The identification of subjects at high risk for Alzheimer's disease is important for prognosis and early intervention. We investigated the polygenic architecture of Alzheimer's disease and the accuracy of Alzheimer's disease prediction models, including and excluding the polygenic component in the model. This study used genotype data from the powerful dataset comprising 17 008 cases and 37 154 controls obtained from the International Genomics of Alzheimer's Project (IGAP). Polygenic score analysis tested whether the alleles identified to associate with disease in one sample set were significantly enriched in the cases relative to the controls in an independent sample. The disease prediction accuracy was investigated in a subset of the IGAP data, a sample of 3049 cases and 1554 controls (for whom APOE genotype data were available) by means of sensitivity, specificity, area under the receiver operating characteristic curve (AUC) and positive and negative predictive values. We observed significant evidence for a polygenic component enriched in Alzheimer's disease (P = 4.9 × 10(-26)). This enrichment remained significant after APOE and other genome-wide associated regions were excluded (P = 3.4 × 10(-19)). The best prediction accuracy AUC = 78.2% (95% confidence interval 77-80%) was achieved by a logistic regression model with APOE, the polygenic score, sex and age as predictors. In conclusion, Alzheimer's disease has a significant polygenic component, which has predictive utility for Alzheimer's disease risk and could be a valuable research tool complementing experimental designs, including preventative clinical trials, stem cell selection and high/low risk clinical studies. In modelling a range of sample disease prevalences, we found that polygenic scores almost doubles case prediction from chance with increased prediction at polygenic extremes.
Heritability estimates for Alzheimer’s disease in genome-wide association studies increase substantially when weak effect loci are also considered. Escott-Price et al. investigate the polygenic architecture of Alzheimer’s disease and the accuracy of prediction models, and show that including the polygenic component of risk significantly improves accuracy of case prediction. Heritability estimates for Alzheimer’s disease in genome-wide association studies increase substantially when weak effect loci are also considered. Escott-Price et al. investigate the polygenic architecture of Alzheimer’s disease and the accuracy of prediction models, and show that including the polygenic component of risk significantly improves accuracy of case prediction. The identification of subjects at high risk for Alzheimer’s disease is important for prognosis and early intervention. We investigated the polygenic architecture of Alzheimer’s disease and the accuracy of Alzheimer’s disease prediction models, including and excluding the polygenic component in the model. This study used genotype data from the powerful dataset comprising 17 008 cases and 37 154 controls obtained from the International Genomics of Alzheimer’s Project (IGAP). Polygenic score analysis tested whether the alleles identified to associate with disease in one sample set were significantly enriched in the cases relative to the controls in an independent sample. The disease prediction accuracy was investigated in a subset of the IGAP data, a sample of 3049 cases and 1554 controls (for whom APOE genotype data were available) by means of sensitivity, specificity, area under the receiver operating characteristic curve (AUC) and positive and negative predictive values. We observed significant evidence for a polygenic component enriched in Alzheimer’s disease ( P = 4.9 × 10 −26 ). This enrichment remained significant after APOE and other genome-wide associated regions were excluded ( P = 3.4 × 10 −19 ). The best prediction accuracy AUC = 78.2% (95% confidence interval 77–80%) was achieved by a logistic regression model with APOE , the polygenic score, sex and age as predictors. In conclusion, Alzheimer’s disease has a significant polygenic component, which has predictive utility for Alzheimer’s disease risk and could be a valuable research tool complementing experimental designs, including preventative clinical trials, stem cell selection and high/low risk clinical studies. In modelling a range of sample disease prevalences, we found that polygenic scores almost doubles case prediction from chance with increased prediction at polygenic extremes.
Author Schellenberg, Gerard D.
Badarinarayan, Nandini
Goate, Alison
Morgan, Kevin
Vronskaya, Maria
Maier, Wolfgang
Hardy, John
Sims, Rebecca
Holmans, Peter
Cruchaga, Carlos
Brayne, Carol
Majounie, Elisa
Amouyel, Philippe
Passmore, Peter
Jones, Lesley
Powell, John
Bannister, Christian
Seshadri, Sudha
van Duijn, Cornelia
Mead, Simon
Gill, Michael
Ramirez, Alfredo
Escott-Price, Valentina
Harold, Denise
Williams, Julie
Holmes, Clive
Lambert, Jean-Charles
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/26490334$$D View this record in MEDLINE/PubMed
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Collinge, John
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Proitsi, Petroula
Heun, Reiner
Russo, Giancarlo
Fox, Nick
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ODonovan, Michael
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Mann, David
Jessen, Frank
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Lovestone, Simon
Wiltfang, Jens
Deloukas, Panagiotis
Hamshere, Marian
Mühleisen, Thomas W
Morris, John C
McQuillin, Andrew
Al-Chalabi, Ammar
Singleton, Andrew B
Gerrish, Amy
Becker, Tim
Moebus, Susanne
Smith, A David
Frölich, Lutz
Livingston, Gill
Shaw, Christopher E
Nöthen, Markus M
Pahwa, Jaspreet Singh
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Lacour, André
Thomas, Charlene
Gwilliam, Rhian
Morgan, Angharad
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Bass, Nicholas J
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Johnston, Janet
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Hampel, Harald
Kauwe, John S K
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Carrasquillo, Minerva M
Lupton, Michelle K
Chapman, Jade
Dichgans, Martin
Guerreiro, Rita
Love, Seth
Mayo, Kevin
Williams, Amy
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Copyright The Author (2015). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
The Author (2015). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com 2015
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Issue 12
Keywords Alzheimer’s disease
polygenic score
predictive model
Language English
License The Author (2015). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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content type line 23
Data used in the preparation of this article were obtained from the Genetic and Environmental Risk for Alzheimer’s disease (GERAD) (which now incorporates the Defining Genetic, Polygenic and Environmental Risk for Alzheimer’s Disease using multiple powerful cohorts, focused Epigenetics and Stem cell metabolomics, PERADES consortium) and the International Genomics of Alzheimer’s Disease (IGAP) Consortia. For details of these consortia, see Appendix I and the Supplementary material.
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Snippet The identification of subjects at high risk for Alzheimer's disease is important for prognosis and early intervention. We investigated the polygenic...
Heritability estimates for Alzheimer’s disease in genome-wide association studies increase substantially when weak effect loci are also considered....
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SubjectTerms Alleles
Alzheimer Disease - genetics
Apolipoproteins E - genetics
Case-Control Studies
Genetic Predisposition to Disease - genetics
Genetic Testing
Genetic Variation - genetics
Genome-Wide Association Study
Genotype
Humans
Logistic Models
Multifactorial Inheritance - genetics
Original
Risk
ROC Curve
Title Common polygenic variation enhances risk prediction for Alzheimer’s disease
URI https://www.ncbi.nlm.nih.gov/pubmed/26490334
https://www.proquest.com/docview/1736413885
https://pubmed.ncbi.nlm.nih.gov/PMC5006219
Volume 138
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