Use of support vector machines for disease risk prediction in genome-wide association studies: concerns and opportunities

Florian Mittag; Finja Büchel; Mohamad Saad; Andreas Jahn; Claudia Schulte; Zoltan Bochdanovits; Javier Simón-Sánchez; Mike A. Nalls; Margaux Keller; Dena G. Hernandez; J. Raphael Gibbs; Suzanne Lesage; Alexis Brice; Peter Heutink; Maria Martinez; Nicholas W Wood; John Hardy; Andrew B. Singleton; Andreas Zell; Thomas Gasser; Manu Sharma; Karen Morrison

doi:10.1002/humu.22161

Use of support vector machines for disease risk prediction in genome-wide association studies: concerns and opportunities

Florian Mittag, Finja Büchel, Mohamad Saad, Andreas Jahn, Claudia Schulte, Zoltan Bochdanovits, Javier Simón-Sánchez, Mike A. Nalls, Margaux Keller, Dena G. Hernandez, J. Raphael Gibbs, Suzanne Lesage, Alexis Brice, Peter Heutink, Maria Martinez, Nicholas W Wood, John Hardy, Andrew B. Singleton, Andreas Zell, Thomas GasserManu Sharma, Karen Morrison

Research output: Contribution to journal › Article › peer-review

41 Citations (Scopus)

Abstract

The success of genome-wide association studies (GWAS) in deciphering the genetic architecture of complex diseases has fueled the expectations whether the individual risk can also be quantified based on the genetic architecture. So far, disease risk prediction based on top-validated single-nucleotide polymorphisms (SNPs) showed little predictive value. Here, we applied a support vector machine (SVM) to Parkinson disease (PD) and type 1 diabetes (T1D), to show that apart from magnitude of effect size of risk variants, heritability of the disease also plays an important role in disease risk prediction. Furthermore, we performed a simulation study to show the role of uncommon (frequency 1–5%) as well as rare variants (frequency

Original language	English
Pages (from-to)	1708-1718
Number of pages	11
Journal	Human Mutation
Volume	33
Issue number	12
DOIs	https://doi.org/10.1002/humu.22161
Publication status	Published - 01 Dec 2012

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10.1002/humu.22161

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Mittag, F., Büchel, F., Saad, M., Jahn, A., Schulte, C., Bochdanovits, Z., Simón-Sánchez, J., Nalls, M. A., Keller, M., Hernandez, D. G., Gibbs, J. R., Lesage, S., Brice, A., Heutink, P., Martinez, M., Wood, N. W., Hardy, J., Singleton, A. B., Zell, A., ... Morrison, K. (2012). Use of support vector machines for disease risk prediction in genome-wide association studies: concerns and opportunities. Human Mutation, 33(12), 1708-1718. https://doi.org/10.1002/humu.22161

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abstract = "The success of genome-wide association studies (GWAS) in deciphering the genetic architecture of complex diseases has fueled the expectations whether the individual risk can also be quantified based on the genetic architecture. So far, disease risk prediction based on top-validated single-nucleotide polymorphisms (SNPs) showed little predictive value. Here, we applied a support vector machine (SVM) to Parkinson disease (PD) and type 1 diabetes (T1D), to show that apart from magnitude of effect size of risk variants, heritability of the disease also plays an important role in disease risk prediction. Furthermore, we performed a simulation study to show the role of uncommon (frequency 1–5%) as well as rare variants (frequency ",

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Mittag, F, Büchel, F, Saad, M, Jahn, A, Schulte, C, Bochdanovits, Z, Simón-Sánchez, J, Nalls, MA, Keller, M, Hernandez, DG, Gibbs, JR, Lesage, S, Brice, A, Heutink, P, Martinez, M, Wood, NW, Hardy, J, Singleton, AB, Zell, A, Gasser, T, Sharma, M & Morrison, K 2012, 'Use of support vector machines for disease risk prediction in genome-wide association studies: concerns and opportunities', Human Mutation, vol. 33, no. 12, pp. 1708-1718. https://doi.org/10.1002/humu.22161

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T1 - Use of support vector machines for disease risk prediction in genome-wide association studies: concerns and opportunities

AU - Mittag, Florian

AU - Büchel, Finja

AU - Saad, Mohamad

AU - Jahn, Andreas

AU - Schulte, Claudia

AU - Bochdanovits, Zoltan

AU - Simón-Sánchez, Javier

AU - Nalls, Mike A.

AU - Keller, Margaux

AU - Hernandez, Dena G.

AU - Gibbs, J. Raphael

AU - Lesage, Suzanne

AU - Brice, Alexis

AU - Heutink, Peter

AU - Martinez, Maria

AU - Wood, Nicholas W

AU - Hardy, John

AU - Singleton, Andrew B.

AU - Zell, Andreas

AU - Gasser, Thomas

AU - Sharma, Manu

AU - Morrison, Karen

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DO - 10.1002/humu.22161

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EP - 1718

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JF - Human Mutation

IS - 12

ER -

Use of support vector machines for disease risk prediction in genome-wide association studies: concerns and opportunities

Abstract

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