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Machine learning workflows to estimate class probabilities for precision cancer diagnostics on DNA methylation microarray data

Abstract

DNA methylation data-based precision cancer diagnostics is emerging as the state of the art for molecular tumor classification. Standards for choosing statistical methods with regard to well-calibrated probability estimates for these typically highly multiclass classification tasks are still lacking. To support this choice, we evaluated well-established machine learning (ML) classifiers including random forests (RFs), elastic net (ELNET), support vector machines (SVMs) and boosted trees in combination with post-processing algorithms and developed ML workflows that allow for unbiased class probability (CP) estimation. Calibrators included ridge-penalized multinomial logistic regression (MR) and Platt scaling by fitting logistic regression (LR) and Firth’s penalized LR. We compared these workflows on a recently published brain tumor 450k DNA methylation cohort of 2,801 samples with 91 diagnostic categories using a 5 × 5-fold nested cross-validation scheme and demonstrated their generalizability on external data from The Cancer Genome Atlas. ELNET was the top stand-alone classifier with the best calibration profiles. The best overall two-stage workflow was MR-calibrated SVM with linear kernels closely followed by ridge-calibrated tuned RF. For calibration, MR was the most effective regardless of the primary classifier. The protocols developed as a result of these comparisons provide valuable guidance on choosing ML workflows and their tuning to generate well-calibrated CP estimates for precision diagnostics using DNA methylation data. Computation times vary depending on the ML algorithm from <15 min to 5 d using multi-core desktop PCs. Detailed scripts in the open-source R language are freely available on GitHub, targeting users with intermediate experience in bioinformatics and statistics and using R with Bioconductor extensions.

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Fig. 1: Pipeline of methylation microarray data-based machine learning workflow development and comparison for well-calibrated personalized cancer diagnostics.
Fig. 2: External validation on various tumor types from TCGA.

Data and code availability

The described collection of R scripts and the associated data files provided in GitHub repositories (https://github.com/mwsill/mnp_training and https://github.com/mematt/ml4calibrated450k) are free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2. All analyses were performed within either local (https://www.R-project.org/) or Docker containerized (https://www.docker.com) versions (rocker; https://www.rocker-project.org or https://github.com/rocker-org.) of the R: A language and environment for statistical programming v3.3.3–3.5.2 using the R Studio IDE, a free and open-source integrated development environment for R (v1.0.136 or v1.1.463; https://www.rstudio.com/products/RStudio/). Unprocessed IDAT files containing complete methylation values for the reference set and validation set as published in ref. 1 are available for download from the NCBI GEO under accession number GSE109381 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109381). The variance-filtered outer- (fold IDs: 1.0, 2.0, …, 5.0) and innerfold (fold IDs: 1.1, 1.2, …, 1.5; 2.1, 2.2, …, 2.5; …; 5.1, 5.2, …, 5.5) training-test set pairs (altogether n = 30; i.e., 1.0–5.5; Fig. 1, part 2, outer and inner CV loops) of .RData files can be generated through scripts on Github (https://github.com/mematt/ml4calibrated450k/blob/master/data/subfunction_load_subset_filter_match_betasKk.R) or are directly downloadable (~5.3 GB) from our Dropbox (http://bit.ly/2vBg8yc). For details on how to prepare the 450k DNA methylation tumor samples from TCGA, please see the GitHub repository (https://github.com/mwsill/mnp_training/blob/master/tsne.R), and to download the source data, visit the NCI GDC Legacy Archive (https://gdc-portal.nci.nih.gov/legacy-archive). The combined TCGA cohort with vRF+MR predictions is available as a .xlsx file (Supplementary Data 1).

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Acknowledgements

The authors gratefully acknowledge funding from the DKFZ-Heidelberg Center for Personalized Oncology (DKFZ-HIPO) through HIPO-036 and from the German Childhood Cancer Foundation (‘Neuropath 2.0 - Increasing diagnostic accuracy in paediatric neurooncology’ (DKS 2015.01)). M.E.M. gratefully acknowledges funding from the German Federal Ministry for Economic Affairs and Energy within the scope of Zentrales Innovationsprogramm Mittelstand (ZF 4514602TS8). The results shown in the external validation section and Fig. 2 are entirely based on data generated by TCGA Research Network: https://www.cancer.gov/tcga.

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M.E.M. and M.S. conceptualized and developed machine learning workflows, performed the comparative analyses and wrote the manuscript. M.S. and V.H. performed data preparation. D.C., D.T.W.J., S.M.P. and A.v.D. composed the reference cohort and defined methylation classes. A.B. and M.Z. supervised the statistical aspects and data analysis. M.S. supervised the work and wrote the manuscript. All authors critically reviewed the manuscript and approved the final version.

Corresponding author

Correspondence to Martin Sill.

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Competing interests

A patent for a ‘DNA-methylation based method for classifying tumor species of the brain’ has been applied for by the Deutsches Krebsforschungszentrum Stiftung des öffentlichen Rechts and Ruprecht-Karls-Universität Heidelberg (EP 3067432 A1) with V.H., D.C., D.T.W.J., S.M.P., A.v.D. and M.S. as inventors. The other authors have no competing interests to declare.

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Peer review information Nature Protocols thanks Casey Greene, Ludmila Danilova and Levi Waldron for their contribution to the peer review of this work.

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Key reference using this protocol

Capper, D. et al. Nature 555, 469–474 (2018): https://doi.org/10.1038/nature26000

Publications focused on one particular method

Capper, D. et al. Acta Neuropathol. 136, 181–210 (2018): https://doi.org/10.1007/s00401-018-1879-y

Sharma, T. et al. Acta Neuropathol. 138, 309–326 (2019): https://doi.org/10.1007/s00401-019-02020-0

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Maros, M.E., Capper, D., Jones, D.T.W. et al. Machine learning workflows to estimate class probabilities for precision cancer diagnostics on DNA methylation microarray data. Nat Protoc 15, 479–512 (2020). https://doi.org/10.1038/s41596-019-0251-6

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