Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis
Nabais MF, Lin T, Benyamin B, Williams KL, Garton FC, Vinkhuyzen AAE, Zhang F, Vallerga CL, Restuadi R, Freydenzon A, Zwamborn RAJ, Hop PJ, Robinson MR, Gratten J, Visscher PM, Hannon E, Mill J, Brown MA, Laing NG, Mather KA, Sachdev PS, Ngo ST, Steyn FJ, Wallace L, Henders AK, Needham M, Veldink JH, Mathers S, Nicholson G, Rowe DB, Henderson RD, McCombe PA, Pamphlett R, Yang J, Blair IP, McRae AF, Wray NR. 2020. Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. npj Genomic Medicine. 5, 10.
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Journal Article
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Author
Nabais, Marta F.;
Lin, Tian;
Benyamin, Beben;
Williams, Kelly L.;
Garton, Fleur C.;
Vinkhuyzen, Anna A. E.;
Zhang, Futao;
Vallerga, Costanza L.;
Restuadi, Restuadi;
Freydenzon, Anna;
Zwamborn, Ramona A. J.;
Hop, Paul J.
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All
Abstract
We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor.
Publishing Year
Date Published
2020-02-27
Journal Title
npj Genomic Medicine
Publisher
Springer Nature
Volume
5
Article Number
10
ISSN
IST-REx-ID
Cite this
Nabais MF, Lin T, Benyamin B, et al. Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. npj Genomic Medicine. 2020;5. doi:10.1038/s41525-020-0118-3
Nabais, M. F., Lin, T., Benyamin, B., Williams, K. L., Garton, F. C., Vinkhuyzen, A. A. E., … Wray, N. R. (2020). Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. Npj Genomic Medicine. Springer Nature. https://doi.org/10.1038/s41525-020-0118-3
Nabais, Marta F., Tian Lin, Beben Benyamin, Kelly L. Williams, Fleur C. Garton, Anna A. E. Vinkhuyzen, Futao Zhang, et al. “Significant Out-of-Sample Classification from Methylation Profile Scoring for Amyotrophic Lateral Sclerosis.” Npj Genomic Medicine. Springer Nature, 2020. https://doi.org/10.1038/s41525-020-0118-3.
M. F. Nabais et al., “Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis,” npj Genomic Medicine, vol. 5. Springer Nature, 2020.
Nabais MF, Lin T, Benyamin B, Williams KL, Garton FC, Vinkhuyzen AAE, Zhang F, Vallerga CL, Restuadi R, Freydenzon A, Zwamborn RAJ, Hop PJ, Robinson MR, Gratten J, Visscher PM, Hannon E, Mill J, Brown MA, Laing NG, Mather KA, Sachdev PS, Ngo ST, Steyn FJ, Wallace L, Henders AK, Needham M, Veldink JH, Mathers S, Nicholson G, Rowe DB, Henderson RD, McCombe PA, Pamphlett R, Yang J, Blair IP, McRae AF, Wray NR. 2020. Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. npj Genomic Medicine. 5, 10.
Nabais, Marta F., et al. “Significant Out-of-Sample Classification from Methylation Profile Scoring for Amyotrophic Lateral Sclerosis.” Npj Genomic Medicine, vol. 5, 10, Springer Nature, 2020, doi:10.1038/s41525-020-0118-3.
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