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Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

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Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. / 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.; Robinson, Matthew R.; Gratten, Jacob; Visscher, Peter M.; Hannon, Eilis; Mill, Jonathan; Brown, Matthew A.; Laing, Nigel G.; Mather, Karen A.; Sachdev, Perminder S.; Ngo, Shyuan T.; Steyn, Frederik J.; Wallace, Leanne; Henders, Anjali K.; Needham, Merrilee; Veldink, Jan H.; Mathers, Susan; Nicholson, Garth; Rowe, Dominic B.; Henderson, Robert D.; McCombe, Pamela A.; Pamphlett, Roger; Yang, Jian; Blair, Ian P.; McRae, Allan F.; Wray, Naomi R.

In: NPJ Genomic medicine, Vol. 5, No. 1, 10, 01.12.2020.

Research output: Contribution to journalArticle

Harvard

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, vol. 5, no. 1, 10. https://doi.org/10.1038/s41525-020-0118-3

APA

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, 5(1), [10]. https://doi.org/10.1038/s41525-020-0118-3

Vancouver

Nabais MF, Lin T, Benyamin B, Williams KL, Garton FC, Vinkhuyzen AAE et al. Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. NPJ Genomic medicine. 2020 Dec 1;5(1). 10. https://doi.org/10.1038/s41525-020-0118-3

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. ; Robinson, Matthew R. ; Gratten, Jacob ; Visscher, Peter M. ; Hannon, Eilis ; Mill, Jonathan ; Brown, Matthew A. ; Laing, Nigel G. ; Mather, Karen A. ; Sachdev, Perminder S. ; Ngo, Shyuan T. ; Steyn, Frederik J. ; Wallace, Leanne ; Henders, Anjali K. ; Needham, Merrilee ; Veldink, Jan H. ; Mathers, Susan ; Nicholson, Garth ; Rowe, Dominic B. ; Henderson, Robert D. ; McCombe, Pamela A. ; Pamphlett, Roger ; Yang, Jian ; Blair, Ian P. ; McRae, Allan F. ; Wray, Naomi R. / Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. In: NPJ Genomic medicine. 2020 ; Vol. 5, No. 1.

Bibtex Download

@article{9054fd7229dc40bd9de8c1955d084339,
title = "Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis",
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.",
author = "Nabais, {Marta F.} and Tian Lin and Beben Benyamin and Williams, {Kelly L.} and Garton, {Fleur C.} and Vinkhuyzen, {Anna A.E.} and Futao Zhang and Vallerga, {Costanza L.} and Restuadi Restuadi and Anna Freydenzon and Zwamborn, {Ramona A.J.} and Hop, {Paul J.} and Robinson, {Matthew R.} and Jacob Gratten and Visscher, {Peter M.} and Eilis Hannon and Jonathan Mill and Brown, {Matthew A.} and Laing, {Nigel G.} and Mather, {Karen A.} and Sachdev, {Perminder S.} and Ngo, {Shyuan T.} and Steyn, {Frederik J.} and Leanne Wallace and Henders, {Anjali K.} and Merrilee Needham and Veldink, {Jan H.} and Susan Mathers and Garth Nicholson and Rowe, {Dominic B.} and Henderson, {Robert D.} and McCombe, {Pamela A.} and Roger Pamphlett and Jian Yang and Blair, {Ian P.} and McRae, {Allan F.} and Wray, {Naomi R.}",
year = "2020",
month = "12",
day = "1",
doi = "10.1038/s41525-020-0118-3",
language = "English",
volume = "5",
journal = "NPJ Genomic medicine",
issn = "2056-7944",
publisher = "Nature Publishing Group",
number = "1",

}

RIS (suitable for import to EndNote) Download

TY - JOUR

T1 - Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

AU - Nabais, Marta F.

AU - Lin, Tian

AU - Benyamin, Beben

AU - Williams, Kelly L.

AU - Garton, Fleur C.

AU - Vinkhuyzen, Anna A.E.

AU - Zhang, Futao

AU - Vallerga, Costanza L.

AU - Restuadi, Restuadi

AU - Freydenzon, Anna

AU - Zwamborn, Ramona A.J.

AU - Hop, Paul J.

AU - Robinson, Matthew R.

AU - Gratten, Jacob

AU - Visscher, Peter M.

AU - Hannon, Eilis

AU - Mill, Jonathan

AU - Brown, Matthew A.

AU - Laing, Nigel G.

AU - Mather, Karen A.

AU - Sachdev, Perminder S.

AU - Ngo, Shyuan T.

AU - Steyn, Frederik J.

AU - Wallace, Leanne

AU - Henders, Anjali K.

AU - Needham, Merrilee

AU - Veldink, Jan H.

AU - Mathers, Susan

AU - Nicholson, Garth

AU - Rowe, Dominic B.

AU - Henderson, Robert D.

AU - McCombe, Pamela A.

AU - Pamphlett, Roger

AU - Yang, Jian

AU - Blair, Ian P.

AU - McRae, Allan F.

AU - Wray, Naomi R.

PY - 2020/12/1

Y1 - 2020/12/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85080109617&partnerID=8YFLogxK

U2 - 10.1038/s41525-020-0118-3

DO - 10.1038/s41525-020-0118-3

M3 - Article

AN - SCOPUS:85080109617

VL - 5

JO - NPJ Genomic medicine

JF - NPJ Genomic medicine

SN - 2056-7944

IS - 1

M1 - 10

ER -

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