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Pan-cancer image-based detection of clinically actionable genetic alterations

An Author Correction to this article was published on 03 November 2020

This article has been updated

Abstract

Molecular alterations in cancer can cause phenotypic changes in tumor cells and their microenvironment. Routine histopathology tissue slides, which are ubiquitously available, can reflect such morphological changes. Here, we show that deep learning can consistently infer a wide range of genetic mutations, molecular tumor subtypes, gene expression signatures and standard pathology biomarkers directly from routine histology. We developed, optimized, validated and publicly released a one-stop-shop workflow and applied it to tissue slides of more than 5,000 patients across multiple solid tumors. Our findings show that a single deep learning algorithm can be trained to predict a wide range of molecular alterations from routine, paraffin-embedded histology slides stained with hematoxylin and eosin. These predictions generalize to other populations and are spatially resolved. Our method can be implemented on mobile hardware, potentially enabling point-of-care diagnostics for personalized cancer treatment. More generally, this approach could elucidate and quantify genotype–phenotype links in cancer.

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Fig. 1: Deep learning workflow for the prediction of molecular features from histology images.
Fig. 2: Inference of genetic mutations from histological images.
Fig. 3: Inference of putative oncogenic drivers from histological images.
Fig. 4: Inference of molecular subtypes, gene expression signatures and standard biomarkers directly from histology.
Fig. 5: Explainability of deep learning-based analysis of histological images.
Fig. 6: Highest-scoring image tiles for molecular features in gastric cancer.

Data availability

All data, including histological images and information about the age and sex of the participants from the TCGA database are available at https://portal.gdc.cancer.gov/. Genetic data for patients in the TCGA cohorts are available at https://portal.gdc.cancer.gov/ and https://cbioportal.org. Raw data for the DACHS cohort are stored and administered by the DACHS consortium (more information is available from http://dachs.dkfz.org/dachs/). The corresponding authors of this study are not involved in data sharing decisions of the DACHS consortium. All other data supporting the findings of this study are available from the corresponding author upon reasonable request. Source data are provided with this paper.

Code availability

All source codes are available under an open-source license at https://github.com/jnkather/DeepHistology/releases/tag/v0.2.

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Acknowledgements

These results are in part based on data generated by the TCGA Research Network (http://cancergenome.nih.gov/). J.N.K. received funding from RWTH University Aachen (START 2018–691906). V.S. was funded by Breast Cancer Now. P. Boor received DFG grants SFB/TRR57, SFB/TRR219, BO3755/3-1 and BO3755/6-1, as well as support from the German Ministry of Education and Research (BMBF) (STOP-FSGS-01GM1901A) and the German Ministry for Economic Affairs and Energy (BMWi) (EMPAIA project). A.T.P. was funded by the NIH and NIDCR (K08-DE026500), an Institutional Research Grant (IRG-16-222-56) from the American Cancer Society, a Cancer Research Foundation Research Grant, and a University of Chicago Medicine Comprehensive Cancer Center Support Grant (P30-CA14599). T.L. was funded by Horizon 2020 (through the European Research Council (ERC) Consolidator Grant PhaseControl (771083)), a Mildred-Scheel Endowed Professorship from the German Cancer Aid (Deutsche Krebshilfe), the German Research Foundation (DFG) (SFB CRC1382/P01, SFB-TRR57/P06 and LU 1360/3-1), the Ernst Jung Foundation Hamburg and the Interdisciplinary Center for Clinical Research (IZKF) at RWTH Aachen.

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Affiliations

Authors

Contributions

J.N.K., A.T.P. and T.L. designed the study. L.R.H., H.I.G., N.A.C., J.J.S., P.A.v.D.B., L.F.S.K., P. Boor and A.P. oversaw the tumor annotation. C.L., A.E., J.K., H.S.M., J.M.N., R.D.B. and K.A.J.S. manually annotated all of the tumors. J.N.K., J.K., J.M.N. and P. Bankhead designed and implemented the algorithm. J.N.K., C.L., A.S., S.K., R.D.B. and N.O.-B. curated the list of molecular alterations. H.B., M.H., A.T.P., A.M.H. and V.S. provided external validation samples and gave statistical advice. C.T., D.J., A.T.P., P. Boor, V.S. and T.L. provided infrastructure and supervised the study. All authors contributed to the data analysis and writing of the manuscript.

Corresponding authors

Correspondence to Jakob Nikolas Kather or Alexander T. Pearson or Tom Luedde.

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Competing interests

J.N.K. has an informal, unpaid advisory role at Pathomix (Heidelberg, Germany) that does not relate to this research. J.N.K. declares no other relationships or competing interests. All other authors declare no competing interests.

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Extended data

Extended Data Fig. 1 Distribution of predictability scores for feature classes in all cancer types.

ao, Target features were assigned to one of four categories as shown in Supplementary Table 1: Genetic variants, oncogenic drivers, high-level signatures and standard-of-care features. For each of these classes, predictability by deep learning was assessed and the distribution of false-detection-rate (FDR)-corrected p-values is shown, with low p-values capped at 10-5. High-level signatures were highly predictable in most tumor types. p, Color legend for all panels.

Source data

Extended Data Fig. 2 Additional statistics for lung adenocarcinoma, colorectal cancer and breast cancer.

ac, Detailed prediction statistics for lung adenocarcinoma (LUAD). Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. e-h, Detailed view of the features with highest AUROC values. il, Detailed prediction statistics for colorectal cancer (COAD, READ): Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. mp, Correspondingly, a detailed view of the features with highest AUROC values. qt, Detailed prediction statistics for breast cancer (BRCA): Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. u-x, Correspondingly, a detailed view of the features with highest AUROC values. Low p-values capped at 10-5. Blank panels do not contain any data points, but were added keep a consistent format for all plots. Error bars show patient-level AUROC with bootstrapped confidence intervals, the marker denotes the mean, * denotes two-sided t-test FDR-corrected p-value< 0.05. ”n“ refers to the number of patients.

Source data

Extended Data Fig. 3 Additional statistics for gastric cancer and melanoma.

ac, Detailed prediction statistics for gastric cancer (STAD). Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. eh, Detailed view of the features with highest AUROC values. il, Detailed prediction statistics for melanoma primary tumor samples (SKCM): Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. mp, Correspondingly, a detailed view of the features with highest AUROC values. qt, Detailed prediction statistics for melanoma metastatic samples (SKCM): Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. ux, Correspondingly, a detailed view of the features with highest AUROC values. Low p-values capped at 10-5. Blank panels do not contain any data points, but were added keep a consistent format for all plots. Error bars show patient-level AUROC with bootstrapped confidence intervals, the marker denotes the mean, * denotes two-sided t-test FDR-corrected p-value< 0.05. ”n“ refers to the number of patients.

Source data

Extended Data Fig. 4 Additional statistics for prostate, pancreatic and squamous lung cancer.

ac, Detailed prediction statistics for prostate cancer (PRAD). Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. eh, Detailed view of the features with highest AUROC values. il, Detailed prediction statistics for pancreatic cancer samples (PAAD): Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. mp, Correspondingly, a detailed view of the features with highest AUROC values. q–t, Detailed prediction statistics for squamous lung cancer (LUSC): Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. ux, Correspondingly, a detailed view of the features with highest AUROC values. Low p-values capped at 10-5. Blank panels do not contain any data points, but were added keep a consistent format for all plots. Error bars show patient-level AUROC with bootstrapped confidence intervals, the marker denotes the mean, * denotes two-sided t-test FDR-corrected p-value< 0.05. ”n“ refers to the number of patients.

Source data

Extended Data Fig. 5 Additional statistics for hepatocellular, renal papillary and renal clear cell carcinoma.

a–c, Detailed prediction statistics for hepatocellular carcinoma (LIHC). Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. eh, Detailed view of the features with highest AUROC values. il, Detailed prediction statistics for renal papillary carcinoma (KIRP): Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. mp, Correspondingly, a detailed view of the features with highest AUROC values. qt, Detailed prediction statistics for renal cell clear cell carcinoma (KIRC): Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. ux, Correspondingly, a detailed view of the features with highest AUROC values. Low p-values capped at 10-5. Blank panels do not contain any data points, but were added keep a consistent format for all plots. Error bars show patient-level AUROC with bootstrapped confidence intervals, the marker denotes the mean, * denotes two-sided t-test FDR-corrected p-value< 0.05. ”n“ refers to the number of patients.

Source data

Extended Data Fig. 6 Additional statistics for renal chromophobe cancer, head and neck cancer and cervical cancer.

ac, Detailed prediction statistics for renal chromophobe cancer (KICH). Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. eh, Detailed view of the features with highest AUROC values. il, Detailed prediction statistics for head and neck cancer (HNSC): Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. mp, Correspondingly, a detailed view of the features with highest AUROC values. qt, Detailed prediction statistics for cervical cancer (CESC): Area under the receiver operating curve (AUROC) with corresponding p-values, for each feature. ux, Correspondingly, a detailed view of the features with highest AUROC values. Low p-values capped at 10-5. Blank panels do not contain any data points, but were added keep a consistent format for all plots. Error bars show patient-level AUROC with bootstrapped confidence intervals, the marker denotes the mean, * denotes two-sided t-test FDR-corrected p-value< 0.05. ”n“ refers to the number of patients.

Source data

Extended Data Fig. 7 Results of additional technical optimization experiments: Normalization.

a, Comparison of cross-validated absolute differences in AUROC to the baseline model (no normalization), genetic variants. b, Comparison of AUROC differences for genetic driver mutations. c, Comparison of AUROC differences for expression signatures and subtypes.

Source data

Extended Data Fig. 8 Results of additional technical optimization experiments: Weakly supervised.

a, Comparison of cross-validated absolute differences in AUROC to the baseline model (no normalization), genetic variants. b, Comparison of AUROC differences for genetic driver mutations. c, Comparison of AUROC differences for expression signatures and subtypes.

Source data

Extended Data Fig. 9 Results of additional technical optimization experiments: Frozen tissue.

a, Comparison of cross-validated absolute differences in AUROC to the baseline model (no normalization), genetic variants. b, Comparison of AUROC differences for genetic driver mutations. c, Comparison of AUROC differences for expression signatures and subtypes.

Source data

Extended Data Fig. 10 Additional details on the statistical procedures.

a, For patient-level three-fold cross-validation, the patient cohort was split into three random partitions. Each partition had approximately the same proportion of patients within each class. Three classifiers were trained and their patient-level predictions on the respective test set were concatenated. Thus, a prediction was gained for each patient in the cohort, but no patient was ever part of a training set and a test set of the same classifier at the same time. b, The percentage of predicted tiles for each class was used for a receiver operating characteristic (ROC) analysis with 10x bootstrapped pointwise confidence bounds. c, In addition to the ROC analysis, the prediction scores (percent predicted tiles) for patients in each class was compared to prediction scores for patients in all other classes. The resulting false-detection-rate (FDR)-corrected p-value in a two-sided t-test for this comparison was reported for each feature of interest. Icons are from Twitter Twemoji (CC-BY 4.0 license). d, Distribution of tumor content across slides in all tumor types: Central mark = median, bottom and top edge of the box = 25th and 75th percentile, line extends to the most extreme data points, circles = outliers. Outliers larger than 2000 mm2 are not plotted. Median tumor content on slide is 139 mm2 of tumor tissue per slide for colorectal cancer (CRC). Number of tissue slides (plotted here) are available in Supplementary Table 2. e, Design of additional technical optimization experiments: The baseline approach in this study was to perform image analysis of tiles based on manual tumor annota-tions in every single tissue slide, without performing any color normalization. The baseline approach was compared to three alternative approaches as sketched here.

Source data

Supplementary information

Source data

Source Data Fig. 1

Individual hyperparameter optimization experiments (from c) and prevalence of mutations (from d).

Source Data Fig. 2

Pan-cancer data for any mutation (variants).

Source Data Fig. 3

Pan-cancer data for drivers.

Source Data Fig. 4

Data for any mutation (variants), drivers, signatures and standard features in colorectal cancer, breast cancer, lung adenocarcinoma and gastric cancer (ad), pan-cancer data for signatures (eh) and pan-cancer data for standard of care (i and j).

Source Data Extended Data Fig. 1

Data for any mutation (variants), drivers, signatures and standard features in any cancer type (pan-cancer).

Source Data Extended Data Fig. 2

Data for any mutation (variants), drivers, signatures and standard features in lung adenocarcinoma, colorectal cancer and breast cancer.

Source Data Extended Data Fig. 3

Data for any mutation (variants), drivers, signatures and standard features in gastric cancer, primary melanoma (SKCM-01) and melanoma metastases (SKCM-06).

Source Data Extended Data Fig. 4

Data for any mutation (variants), drivers, signatures and standard features in prostate, pancreatic and lung squamous carcinoma.

Source Data Extended Data Fig. 5

Data for any mutation (variants), drivers, signatures and standard features in hepatocellular, renal papillary and renal clear cell carcinoma.

Source Data Extended Data Fig. 6

Data for any mutation (variants), drivers, signatures and standard features in renal chromophobe, head and neck and cervical cancer.

Source Data Extended Data Fig. 7

Alternative methods (normalization).

Source Data Extended Data Fig. 8

Alternative methods (weakly supervised).

Source Data Extended Data Fig. 9

Alternative methods (frozen samples).

Source Data Extended Data Fig. 10

Number of image tiles per WSI, pan-cancer (from d).

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Kather, J.N., Heij, L.R., Grabsch, H.I. et al. Pan-cancer image-based detection of clinically actionable genetic alterations. Nat Cancer 1, 789–799 (2020). https://doi.org/10.1038/s43018-020-0087-6

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