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 in | Brain (London, England : 1878) Vol. 138; no. 12; pp. 3673 - 3684 |
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Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
Oxford University Press
01.12.2015
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Subjects | |
Online Access | Get full text |
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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. |
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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 |
Author_xml | – sequence: 1 givenname: Valentina surname: Escott-Price fullname: Escott-Price, Valentina – sequence: 2 givenname: Rebecca surname: Sims fullname: Sims, Rebecca – sequence: 3 givenname: Christian surname: Bannister fullname: Bannister, Christian – sequence: 4 givenname: Denise surname: Harold fullname: Harold, Denise – sequence: 5 givenname: Maria surname: Vronskaya fullname: Vronskaya, Maria – sequence: 6 givenname: Elisa surname: Majounie fullname: Majounie, Elisa – sequence: 7 givenname: Nandini surname: Badarinarayan fullname: Badarinarayan, Nandini – sequence: 8 givenname: Kevin surname: Morgan fullname: Morgan, Kevin – sequence: 9 givenname: Peter surname: Passmore fullname: Passmore, Peter – sequence: 10 givenname: Clive surname: Holmes fullname: Holmes, Clive – sequence: 11 givenname: John surname: Powell fullname: Powell, John – sequence: 12 givenname: Carol surname: Brayne fullname: Brayne, Carol – sequence: 13 givenname: Michael surname: Gill fullname: Gill, Michael – sequence: 14 givenname: Simon surname: Mead fullname: Mead, Simon – sequence: 15 givenname: Alison surname: Goate fullname: Goate, Alison – sequence: 16 givenname: Carlos surname: Cruchaga fullname: Cruchaga, Carlos – sequence: 17 givenname: Jean-Charles surname: Lambert fullname: Lambert, Jean-Charles – sequence: 18 givenname: Cornelia surname: van Duijn fullname: van Duijn, Cornelia – sequence: 19 givenname: Wolfgang surname: Maier fullname: Maier, Wolfgang – sequence: 20 givenname: Alfredo surname: Ramirez fullname: Ramirez, Alfredo – sequence: 21 givenname: Peter surname: Holmans fullname: Holmans, Peter – sequence: 22 givenname: Lesley surname: Jones fullname: Jones, Lesley – sequence: 23 givenname: John surname: Hardy fullname: Hardy, John – sequence: 24 givenname: Sudha surname: Seshadri fullname: Seshadri, Sudha – sequence: 25 givenname: Gerard D. surname: Schellenberg fullname: Schellenberg, Gerard D. – sequence: 26 givenname: Philippe surname: Amouyel fullname: Amouyel, Philippe – sequence: 27 givenname: Julie surname: Williams fullname: Williams, Julie |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26490334$$D View this record in MEDLINE/PubMed |
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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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Keywords | Alzheimer’s disease polygenic score predictive model |
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Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 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 |
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