Supplementary Materials for

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1 Supplementary Materials for Magnetic resonance image features identify glioblastoma phenotypic subtypes with distinct molecular pathway activities Haruka Itakura, Achal S. Achrol, Lex A. Mitchell, Joshua J. Loya, Tiffany Liu, Erick M. Westbroek, Abdullah H. Feroze, Scott Rodriguez, Sebastian Echegaray, Tej D. Azad, Kristen W. Yeom, Sandy Napel, Daniel L. Rubin, Steven D. Chang, Griffith R. Harsh IV, Olivier Gevaert* The PDF file includes: *Corresponding author. Published 2 September 2015, Sci. Transl. Med. 7, 303ra139 (2015) DOI: /scitranslmed.aaa7582 Methods Fig. S1. Relative contributions of the top 24 imaging features in characterizing each of the clusters. Table S1. Clinical characteristics of the Stanford cohort before and after selection of the development cohort. Table S2. Clinical characteristics of the TCGA cohort before and after selection of the validation cohort. Table S3. All 2D and multislice 2D quantitative MR image features used for analysis. Table S4. Two-dimensional and multislice 2D quantitative MR image features significantly associated with each cluster. Table S5. Cluster assignment by subjects in the development cohort with and without midline-crossing lesions. Table S6. Regulatory signaling pathways significantly associated with each cluster. References (45 47)

2 SUPPLEMENTARY METHODS Two-dimensional feature representations To represent 2D features, we computed quantitative image features from the largest slice of the tumor volume. To represent multislice 2D features, we aggregated 2D features from all slices within the three-dimensional tumor volume. The quantitative imaging feature extraction pipeline thus generated separate 2D and multislice 2D features for each patient. For each subject in each cohort, this generated a feature vector of 193 2D, and 195 multislice 2D quantitative image features, resulting in a total of 388 features (table S3). Validation of clusters To validate the reproducibility of the clusters derived from consensus clustering in the development cohort, we used the IGP analysis to demonstrate the existence of these clusters in the validation cohort. IGP, which measures the proportion of samples in the group whose nearest neighbor is also classified to the same group, validated the reproducibility and robustness of the generated clusters by quantifying how well centroids from the development cohort predicted test set co-memberships (24). Statistical significance in IGP denotes low probabilities that the clusters originated from a null distribution, in which centroids are placed randomly in the data and, consequently, result in low quality clusters. The p-value of a cluster is the fraction of the null distribution IGPs that approximate the value of 1 (perfect IGP) more than the actual IGP of the cluster. The null hypothesis that a cluster is not a high-quality cluster is rejected if the actual IGP of the group is high enough (i.e. approximates 1). A significant p-value indicates that a high-quality cluster corresponding to the original cluster was found in an independent

3 dataset (validation cohort). Hence, the development cohort cluster is deemed reproducible and validated. Next we trained a PAM model on the development cohort, fitting a nearest shrunken centroid classifier on the centroids generated from the development cohort clusters. By fitting these centroids in the validation cohort, we assigned individual patients to imaging subtypes defined by the development cohort. Mapping canonical pathways to imaging subtypes We used the matched molecular data in the TCGA validation cohort to assign canonical signaling pathways to the discovered imaging subtypes. TCGA provided CNV and gene expression data for 560 and 495 subjects, respectively. These data were integrated with curated pathways from the NCI Pathway Interaction Database using the PARADIGM algorithm to infer signaling pathway activities (up-regulation or down-regulation) to generate a molecular signaling pathway consisting of 131 features. Next we used the SAM algorithm to identify specific regulatory pathways that were significantly associated with each of the identified imaging subtypes for each of the 144 subjects. We placed the FDR threshold at <5%. Evaluating imaging subtypes for traditional risk factors We examined the subtypes for statistically significant differences in historically associated risk factors. Such factors included both clinical (age, KPS) (4, 45, 46) and molecular factors, including previously described gene expression cluster molecular subgroups (8), as well as CIMP status (10), IDH1 mutation (6, 7), MGMT hypermethylation (47), and EGFR amplification (9). Tumor volume data were available only for the development cohort. We

4 compared across-cluster values for all available data, using the Kruskal-Wallis one-way analysis of variance by ranks test for continuous variables and Fisher s exact test for categorical variables.

5 SUPPLEMENTARY FIGURES 2D-MS-LAII2R3.iqr 2D-MS-LAII2R3.madmedian 2D-MS-LAII2R3.madmean 2D-MS-LAII2R3.var 2D-MS-LAII2R3.min 2D-MS-LAII2R5.iqr 2D-MS-RDS.robustmin 2D-MS-RDS.trimmedmean25perc 2D-MS-RDS.mean 2D-MS-RDS.min 2D-MS-EdgeSharpnessWindow.robustmin 2D-MS-EdgeSharpnessWindow.mode 2D-MS-EdgeSharpnessWindow.min 2D-MS-compactness2dmean 2D-LAII2R5.range 2D-LAII2R5.madmean 2D-LAII2R8.range 2D-RDS.robustmin 2D-EdgeSharpnessScale.range 2D-EdgeSharpnessScale.iqr 2D-EdgeSharpnessScale.madmedian 2D-EdgeSharpnessScale.madmean 2D-EdgeSharpnessWindow.min 2D-Compactness2dmean Cluster 1 Cluster 2 Cluster Figure S1. Relative contributions of the top 24 imaging features in characterizing each of the clusters. The graphic displays the multivariate combination of the top 24 differentially expressed 2D and multislice 2D (2D-MS) imaging features across the three clusters (table S4). Displacement of colored bars to the right of the central vertical line demonstrates over-expression, whereas displacement to the left indicates under-expression of the given imaging feature. The length of the bar signifies magnitude.

6 SUPPLEMENTARY TABLES Table S1. Clinical characteristics of the Stanford cohort before and after selection of the development cohort. Stanford Cohort Stanford Development Cohort Characteristics (n = 364) (n = 121) Age, mean (SD) 62.2 (14.1) 64.6 (14.1) Sex, n male (%) 209 (57) 69 (57) KPS, n (%) >70% 192 (53) 65 (54) 50-70% 141 (39) 44 (37) <50% 28 (8) 11 (9) Mean ± SD 71.7 ± ± 17

7 Table S2. Clinical characteristics of the TCGA cohort before and after selection of the validation cohort. Of the validation cohort, 114 patients had clinical data. TCGA Cohort TCGA Validation Cohort Characteristic (n = 575) (n = 144) Age, mean ± SD 57.9 ± ± 15 Sex, n male (%) 352 (61) 73 (64) KPS, n (%) >70% 317 (55) 78 (68) 50-70% 89 (15) 19 (17) <50% 18 (3) 1 (1) Missing Mean ± SD 77.2 ± ± 12.3

8 Table S3. All 2D and multislice 2D quantitative MR image features used for analysis. Quantitative image features were extracted using a pipeline previously applied in non small cell lung cancer (19) and glioblastoma (15) to characterize intensity, shape, edge sharpness, and texture of lesions from images. Number Image feature 1 2D-spherecity 2 2D-volume 3 2D-surfaceArea 4 2D-roughness2dmean 5 2D-compactness2dmean 6 2D-LowIntensityProportion 7 2D-HistogramRaw-min 8 2D-HistogramRaw-mean 9 2D-HistogramRaw-median 10 2D-HistogramRaw-max 11 2D-HistogramRaw-var 12 2D-HistogramRaw-skewness 13 2D-HistogramRaw-kurtosis 14 2D-HistogramRaw-madmean 15 2D-HistogramRaw-madmedian 16 2D-HistogramRaw-iqr 17 2D-HistogramRaw-mode 18 2D-HistogramRaw-range 19 2D-HistogramRaw-trimmedmean25perc 20 2D-HistogramRaw-harmmean 21 2D-HistogramRaw-robustmin 22 2D-HistogramRaw-robustmax 23 2D-HistogramRaw-robustskewness 24 2D-HistogramRaw-robustkurtosis 25 2D-HistogramRaw-entropy 26 2D-EdgeSharpnessWindow-min 27 2D-EdgeSharpnessWindow-mean 28 2D-EdgeSharpnessWindow-median 29 2D-EdgeSharpnessWindow-max 30 2D-EdgeSharpnessWindow-var 31 2D-EdgeSharpnessWindow-skewness 32 2D-EdgeSharpnessWindow-kurtosis 33 2D-EdgeSharpnessWindow-madmean 34 2D-EdgeSharpnessWindow-madmedian 35 2D-EdgeSharpnessWindow-iqr 36 2D-EdgeSharpnessWindow-mode 37 2D-EdgeSharpnessWindow-range 38 2D-EdgeSharpnessWindow-trimmedmean25perc 39 2D-EdgeSharpnessWindow-harmmean

9 40 2D-EdgeSharpnessWindow-robustmin 41 2D-EdgeSharpnessWindow-robustmax 42 2D-EdgeSharpnessWindow-robustskewness 43 2D-EdgeSharpnessWindow-robustkurtosis 44 2D-EdgeSharpnessWindow-entropy 45 2D-EdgeSharpnessScale-min 46 2D-EdgeSharpnessScale-mean 47 2D-EdgeSharpnessScale-median 48 2D-EdgeSharpnessScale-max 49 2D-EdgeSharpnessScale-var 50 2D-EdgeSharpnessScale-skewness 51 2D-EdgeSharpnessScale-kurtosis 52 2D-EdgeSharpnessScale-madmean 53 2D-EdgeSharpnessScale-madmedian 54 2D-EdgeSharpnessScale-iqr 55 2D-EdgeSharpnessScale-mode 56 2D-EdgeSharpnessScale-range 57 2D-EdgeSharpnessScale-trimmedmean25perc 58 2D-EdgeSharpnessScale-harmmean 59 2D-EdgeSharpnessScale-robustmin 60 2D-EdgeSharpnessScale-robustmax 61 2D-EdgeSharpnessScale-robustskewness 62 2D-EdgeSharpnessScale-robustkurtosis 63 2D-EdgeSharpnessScale-entropy 64 2D-EdgeSharpnessBlurryness-min 65 2D-EdgeSharpnessBlurryness-mean 66 2D-EdgeSharpnessBlurryness-median 67 2D-EdgeSharpnessBlurryness-max 68 2D-EdgeSharpnessBlurryness-var 69 2D-EdgeSharpnessBlurryness-skewness 70 2D-EdgeSharpnessBlurryness-kurtosis 71 2D-EdgeSharpnessBlurryness-madmean 72 2D-EdgeSharpnessBlurryness-madmedian 73 2D-EdgeSharpnessBlurryness-iqr 74 2D-EdgeSharpnessBlurryness-mode 75 2D-EdgeSharpnessBlurryness-range 76 2D-EdgeSharpnessBlurryness-trimmedmean25perc 77 2D-EdgeSharpnessBlurryness-harmmean 78 2D-EdgeSharpnessBlurryness-robustmin 79 2D-EdgeSharpnessBlurryness-robustmax 80 2D-EdgeSharpnessBlurryness-robustskewness 81 2D-EdgeSharpnessBlurryness-robustkurtosis 82 2D-EdgeSharpnessBlurryness-entropy 83 2D-RDS-min

10 84 2D-RDS-mean 85 2D-RDS-median 86 2D-RDS-var 87 2D-RDS-skewness 88 2D-RDS-kurtosis 89 2D-RDS-madmean 90 2D-RDS-madmedian 91 2D-RDS-iqr 92 2D-RDS-range 93 2D-RDS-trimmedmean25perc 94 2D-RDS-harmmean 95 2D-RDS-robustmin 96 2D-RDS-robustskewness 97 2D-RDS-robustkurtosis 98 2D-RDS-entropy 99 2D-LAII2R10-min 100 2D-LAII2R10-mean 101 2D-LAII2R10-median 102 2D-LAII2R10-max 103 2D-LAII2R10-var 104 2D-LAII2R10-skewness 105 2D-LAII2R10-kurtosis 106 2D-LAII2R10-madmean 107 2D-LAII2R10-madmedian 108 2D-LAII2R10-iqr 109 2D-LAII2R10-mode 110 2D-LAII2R10-range 111 2D-LAII2R10-trimmedmean25perc 112 2D-LAII2R10-harmmean 113 2D-LAII2R10-robustmin 114 2D-LAII2R10-robustmax 115 2D-LAII2R10-robustskewness 116 2D-LAII2R10-robustkurtosis 117 2D-LAII2R10-entropy 118 2D-LAII2R8-min 119 2D-LAII2R8-mean 120 2D-LAII2R8-median 121 2D-LAII2R8-max 122 2D-LAII2R8-var 123 2D-LAII2R8-skewness 124 2D-LAII2R8-kurtosis 125 2D-LAII2R8-madmean 126 2D-LAII2R8-madmedian 127 2D-LAII2R8-iqr

11 128 2D-LAII2R8-mode 129 2D-LAII2R8-range 130 2D-LAII2R8-trimmedmean25perc 131 2D-LAII2R8-harmmean 132 2D-LAII2R8-robustmin 133 2D-LAII2R8-robustmax 134 2D-LAII2R8-robustskewness 135 2D-LAII2R8-robustkurtosis 136 2D-LAII2R8-entropy 137 2D-LAII2R5-min 138 2D-LAII2R5-mean 139 2D-LAII2R5-median 140 2D-LAII2R5-max 141 2D-LAII2R5-var 142 2D-LAII2R5-skewness 143 2D-LAII2R5-kurtosis 144 2D-LAII2R5-madmean 145 2D-LAII2R5-madmedian 146 2D-LAII2R5-iqr 147 2D-LAII2R5-mode 148 2D-LAII2R5-range 149 2D-LAII2R5-trimmedmean25perc 150 2D-LAII2R5-harmmean 151 2D-LAII2R5-robustmin 152 2D-LAII2R5-robustmax 153 2D-LAII2R5-robustskewness 154 2D-LAII2R5-robustkurtosis 155 2D-LAII2R5-entropy 156 2D-LAII2R3-min 157 2D-LAII2R3-mean 158 2D-LAII2R3-median 159 2D-LAII2R3-max 160 2D-LAII2R3-var 161 2D-LAII2R3-skewness 162 2D-LAII2R3-kurtosis 163 2D-LAII2R3-madmean 164 2D-LAII2R3-madmedian 165 2D-LAII2R3-iqr 166 2D-LAII2R3-mode 167 2D-LAII2R3-range 168 2D-LAII2R3-trimmedmean25perc 169 2D-LAII2R3-harmmean 170 2D-LAII2R3-robustmin 171 2D-LAII2R3-robustmax

12 172 2D-LAII2R3-robustskewness 173 2D-LAII2R3-robustkurtosis 174 2D-LAII2R3-entropy 175 2D-LAII2R2-min 176 2D-LAII2R2-mean 177 2D-LAII2R2-median 178 2D-LAII2R2-max 179 2D-LAII2R2-var 180 2D-LAII2R2-skewness 181 2D-LAII2R2-kurtosis 182 2D-LAII2R2-madmean 183 2D-LAII2R2-madmedian 184 2D-LAII2R2-iqr 185 2D-LAII2R2-mode 186 2D-LAII2R2-range 187 2D-LAII2R2-trimmedmean25perc 188 2D-LAII2R2-harmmean 189 2D-LAII2R2-robustmin 190 2D-LAII2R2-robustmax 191 2D-LAII2R2-robustskewness 192 2D-LAII2R2-robustkurtosis 193 2D-LAII2R2-entropy 194 2D-MultiSlice-spherecity 195 2D-MultiSlice-volume 196 2D-MultiSlice-surfaceArea 197 2D-MultiSlice-roughness2dmean 198 2D-MultiSlice-roughness2dvar 199 2D-MultiSlice-compactness2dmean 200 2D-MultiSlice-compactness2dvar 201 2D-MultiSlice-LowIntensityProportion 202 2D-MultiSlice-HistogramRaw-min 203 2D-MultiSlice-HistogramRaw-mean 204 2D-MultiSlice-HistogramRaw-median 205 2D-MultiSlice-HistogramRaw-max 206 2D-MultiSlice-HistogramRaw-var 207 2D-MultiSlice-HistogramRaw-skewness 208 2D-MultiSlice-HistogramRaw-kurtosis 209 2D-MultiSlice-HistogramRaw-madmean 210 2D-MultiSlice-HistogramRaw-madmedian 211 2D-MultiSlice-HistogramRaw-iqr 212 2D-MultiSlice-HistogramRaw-mode 213 2D-MultiSlice-HistogramRaw-range 214 2D-MultiSlice-HistogramRaw-trimmedmean25perc 215 2D-MultiSlice-HistogramRaw-harmmean

13 216 2D-MultiSlice-HistogramRaw-robustmin 217 2D-MultiSlice-HistogramRaw-robustmax 218 2D-MultiSlice-HistogramRaw-robustskewness 219 2D-MultiSlice-HistogramRaw-robustkurtosis 220 2D-MultiSlice-HistogramRaw-entropy 221 2D-MultiSlice-EdgeSharpnessWindow-min 222 2D-MultiSlice-EdgeSharpnessWindow-mean 223 2D-MultiSlice-EdgeSharpnessWindow-median 224 2D-MultiSlice-EdgeSharpnessWindow-max 225 2D-MultiSlice-EdgeSharpnessWindow-var 226 2D-MultiSlice-EdgeSharpnessWindow-skewness 227 2D-MultiSlice-EdgeSharpnessWindow-kurtosis 228 2D-MultiSlice-EdgeSharpnessWindow-madmean 229 2D-MultiSlice-EdgeSharpnessWindow-madmedian 230 2D-MultiSlice-EdgeSharpnessWindow-iqr 231 2D-MultiSlice-EdgeSharpnessWindow-mode 232 2D-MultiSlice-EdgeSharpnessWindow-range 233 2D-MultiSlice-EdgeSharpnessWindow-trimmedmean25perc 234 2D-MultiSlice-EdgeSharpnessWindow-harmmean 235 2D-MultiSlice-EdgeSharpnessWindow-robustmin 236 2D-MultiSlice-EdgeSharpnessWindow-robustmax 237 2D-MultiSlice-EdgeSharpnessWindow-robustskewness 238 2D-MultiSlice-EdgeSharpnessWindow-robustkurtosis 239 2D-MultiSlice-EdgeSharpnessWindow-entropy 240 2D-MultiSlice-EdgeSharpnessScale-min 241 2D-MultiSlice-EdgeSharpnessScale-mean 242 2D-MultiSlice-EdgeSharpnessScale-median 243 2D-MultiSlice-EdgeSharpnessScale-max 244 2D-MultiSlice-EdgeSharpnessScale-var 245 2D-MultiSlice-EdgeSharpnessScale-skewness 246 2D-MultiSlice-EdgeSharpnessScale-kurtosis 247 2D-MultiSlice-EdgeSharpnessScale-madmean 248 2D-MultiSlice-EdgeSharpnessScale-madmedian 249 2D-MultiSlice-EdgeSharpnessScale-iqr 250 2D-MultiSlice-EdgeSharpnessScale-mode 251 2D-MultiSlice-EdgeSharpnessScale-range 252 2D-MultiSlice-EdgeSharpnessScale-trimmedmean25perc 253 2D-MultiSlice-EdgeSharpnessScale-harmmean 254 2D-MultiSlice-EdgeSharpnessScale-robustmin 255 2D-MultiSlice-EdgeSharpnessScale-robustmax 256 2D-MultiSlice-EdgeSharpnessScale-robustskewness 257 2D-MultiSlice-EdgeSharpnessScale-robustkurtosis 258 2D-MultiSlice-EdgeSharpnessScale-entropy 259 2D-MultiSlice-EdgeSharpnessBlurryness-min

14 260 2D-MultiSlice-EdgeSharpnessBlurryness-mean 261 2D-MultiSlice-EdgeSharpnessBlurryness-median 262 2D-MultiSlice-EdgeSharpnessBlurryness-max 263 2D-MultiSlice-EdgeSharpnessBlurryness-var 264 2D-MultiSlice-EdgeSharpnessBlurryness-skewness 265 2D-MultiSlice-EdgeSharpnessBlurryness-kurtosis 266 2D-MultiSlice-EdgeSharpnessBlurryness-madmean 267 2D-MultiSlice-EdgeSharpnessBlurryness-madmedian 268 2D-MultiSlice-EdgeSharpnessBlurryness-iqr 269 2D-MultiSlice-EdgeSharpnessBlurryness-mode 270 2D-MultiSlice-EdgeSharpnessBlurryness-range 271 2D-MultiSlice-EdgeSharpnessBlurrynesstrimmedmean25perc 272 2D-MultiSlice-EdgeSharpnessBlurryness-harmmean 273 2D-MultiSlice-EdgeSharpnessBlurryness-robustmin 274 2D-MultiSlice-EdgeSharpnessBlurryness-robustmax 275 2D-MultiSlice-EdgeSharpnessBlurryness-robustskewness 276 2D-MultiSlice-EdgeSharpnessBlurryness-robustkurtosis 277 2D-MultiSlice-EdgeSharpnessBlurryness-entropy 278 2D-MultiSlice-RDS-min 279 2D-MultiSlice-RDS-mean 280 2D-MultiSlice-RDS-median 281 2D-MultiSlice-RDS-var 282 2D-MultiSlice-RDS-skewness 283 2D-MultiSlice-RDS-kurtosis 284 2D-MultiSlice-RDS-madmean 285 2D-MultiSlice-RDS-madmedian 286 2D-MultiSlice-RDS-iqr 287 2D-MultiSlice-RDS-range 288 2D-MultiSlice-RDS-trimmedmean25perc 289 2D-MultiSlice-RDS-harmmean 290 2D-MultiSlice-RDS-robustmin 291 2D-MultiSlice-RDS-robustskewness 292 2D-MultiSlice-RDS-robustkurtosis 293 2D-MultiSlice-RDS-entropy 294 2D-MultiSlice-LAII2R10-min 295 2D-MultiSlice-LAII2R10-mean 296 2D-MultiSlice-LAII2R10-median 297 2D-MultiSlice-LAII2R10-max 298 2D-MultiSlice-LAII2R10-var 299 2D-MultiSlice-LAII2R10-skewness 300 2D-MultiSlice-LAII2R10-kurtosis 301 2D-MultiSlice-LAII2R10-madmean 302 2D-MultiSlice-LAII2R10-madmedian

15 303 2D-MultiSlice-LAII2R10-iqr 304 2D-MultiSlice-LAII2R10-mode 305 2D-MultiSlice-LAII2R10-range 306 2D-MultiSlice-LAII2R10-trimmedmean25perc 307 2D-MultiSlice-LAII2R10-harmmean 308 2D-MultiSlice-LAII2R10-robustmin 309 2D-MultiSlice-LAII2R10-robustmax 310 2D-MultiSlice-LAII2R10-robustskewness 311 2D-MultiSlice-LAII2R10-robustkurtosis 312 2D-MultiSlice-LAII2R10-entropy 313 2D-MultiSlice-LAII2R8-min 314 2D-MultiSlice-LAII2R8-mean 315 2D-MultiSlice-LAII2R8-median 316 2D-MultiSlice-LAII2R8-max 317 2D-MultiSlice-LAII2R8-var 318 2D-MultiSlice-LAII2R8-skewness 319 2D-MultiSlice-LAII2R8-kurtosis 320 2D-MultiSlice-LAII2R8-madmean 321 2D-MultiSlice-LAII2R8-madmedian 322 2D-MultiSlice-LAII2R8-iqr 323 2D-MultiSlice-LAII2R8-mode 324 2D-MultiSlice-LAII2R8-range 325 2D-MultiSlice-LAII2R8-trimmedmean25perc 326 2D-MultiSlice-LAII2R8-harmmean 327 2D-MultiSlice-LAII2R8-robustmin 328 2D-MultiSlice-LAII2R8-robustmax 329 2D-MultiSlice-LAII2R8-robustskewness 330 2D-MultiSlice-LAII2R8-robustkurtosis 331 2D-MultiSlice-LAII2R8-entropy 332 2D-MultiSlice-LAII2R5-min 333 2D-MultiSlice-LAII2R5-mean 334 2D-MultiSlice-LAII2R5-median 335 2D-MultiSlice-LAII2R5-max 336 2D-MultiSlice-LAII2R5-var 337 2D-MultiSlice-LAII2R5-skewness 338 2D-MultiSlice-LAII2R5-kurtosis 339 2D-MultiSlice-LAII2R5-madmean 340 2D-MultiSlice-LAII2R5-madmedian 341 2D-MultiSlice-LAII2R5-iqr 342 2D-MultiSlice-LAII2R5-mode 343 2D-MultiSlice-LAII2R5-range 344 2D-MultiSlice-LAII2R5-trimmedmean25perc 345 2D-MultiSlice-LAII2R5-harmmean 346 2D-MultiSlice-LAII2R5-robustmin

16 347 2D-MultiSlice-LAII2R5-robustmax 348 2D-MultiSlice-LAII2R5-robustskewness 349 2D-MultiSlice-LAII2R5-robustkurtosis 350 2D-MultiSlice-LAII2R5-entropy 351 2D-MultiSlice-LAII2R3-min 352 2D-MultiSlice-LAII2R3-mean 353 2D-MultiSlice-LAII2R3-median 354 2D-MultiSlice-LAII2R3-max 355 2D-MultiSlice-LAII2R3-var 356 2D-MultiSlice-LAII2R3-skewness 357 2D-MultiSlice-LAII2R3-kurtosis 358 2D-MultiSlice-LAII2R3-madmean 359 2D-MultiSlice-LAII2R3-madmedian 360 2D-MultiSlice-LAII2R3-iqr 361 2D-MultiSlice-LAII2R3-mode 362 2D-MultiSlice-LAII2R3-range 363 2D-MultiSlice-LAII2R3-trimmedmean25perc 364 2D-MultiSlice-LAII2R3-harmmean 365 2D-MultiSlice-LAII2R3-robustmin 366 2D-MultiSlice-LAII2R3-robustmax 367 2D-MultiSlice-LAII2R3-robustskewness 368 2D-MultiSlice-LAII2R3-robustkurtosis 369 2D-MultiSlice-LAII2R3-entropy 370 2D-MultiSlice-LAII2R2-min 371 2D-MultiSlice-LAII2R2-mean 372 2D-MultiSlice-LAII2R2-median 373 2D-MultiSlice-LAII2R2-max 374 2D-MultiSlice-LAII2R2-var 375 2D-MultiSlice-LAII2R2-skewness 376 2D-MultiSlice-LAII2R2-kurtosis 377 2D-MultiSlice-LAII2R2-madmean 378 2D-MultiSlice-LAII2R2-madmedian 379 2D-MultiSlice-LAII2R2-iqr 380 2D-MultiSlice-LAII2R2-mode 381 2D-MultiSlice-LAII2R2-range 382 2D-MultiSlice-LAII2R2-trimmedmean25perc 383 2D-MultiSlice-LAII2R2-harmmean 384 2D-MultiSlice-LAII2R2-robustmin 385 2D-MultiSlice-LAII2R2-robustmax 386 2D-MultiSlice-LAII2R2-robustskewness 387 2D-MultiSlice-LAII2R2-robustkurtosis 388 2D-MultiSlice-LAII2R2-entropy

17 Table S4. Two-dimensional and multislice 2D quantitative MR image features significantly associated with each cluster. For each feature the fold change is reported and defined as the number of times the feature is expressed in samples in the cluster versus in samples not in the cluster. For example, a 3.1-fold increase was observed for the top feature in Cluster 1 compared with patients not in Cluster 1. The features are ranked by descending order of fold changes. Cluster 1 Image feature Fold change 2D-MultiSlice-LAII2R3-iqr D-MultiSlice-LAII2R3-madmedian D-LAII2R5-madmean D-MultiSlice-LAII2R5-iqr D-MultiSlice-LAII2R5-madmedian D-LAII2R3-madmean D-LAII2R5-iqr D-LAII2R3-iqr D-MultiSlice-LAII2R8-robustmax D-MultiSlice-LAII2R3-robustmax D-LAII2R3-madmedian D-LAII2R2-var D-MultiSlice-LAII2R5-madmean D-LAII2R5-madmedian D-MultiSlice-LAII2R5-robustmax D-MultiSlice-LAII2R8-iqr D-LAII2R8-madmean D-MultiSlice-LAII2R3-madmean D-LAII2R2-madmean D-RDS-range D-MultiSlice-LAII2R2-madmedian D-RDS-var D-MultiSlice-LAII2R8-madmedian D-MultiSlice-LAII2R8-madmean D-MultiSlice-LAII2R2-iqr D-MultiSlice-LAII2R10-madmedian D-MultiSlice-LAII2R5-var D-LAII2R3-range D-MultiSlice-RDS-madmean D-LAII2R3-var D-RDS-madmean D-LAII2R5-var D-MultiSlice-RDS-iqr D-LAII2R10-madmean D-LAII2R2-madmedian 2.67

18 2D-LAII2R8-var D-MultiSlice-RDS-var D-LAII2R3-robustmax D-LAII2R5-robustmax D-MultiSlice-RDS-madmedian D-LAII2R8-robustmax D-MultiSlice-LAII2R3-var D-LAII2R2-iqr D-MultiSlice-LAII2R10-robustmax D-MultiSlice-LAII2R10-madmean D-LAII2R10-robustmax D-LAII2R2-range D-LAII2R5-range D-MultiSlice-LAII2R10-iqr D-RDS-iqr D-MultiSlice-LAII2R2-madmean D-LAII2R10-var D-MultiSlice-LAII2R8-var D-LAII2R8-range D-LAII2R8-madmedian D-LAII2R8-iqr D-RDS-madmedian D-LAII2R10-range D-MultiSlice-LAII2R10-var D-roughness2dmean D-LAII2R3-max D-MultiSlice-roughness2dmean D-MultiSlice-LAII2R2-var D-LAII2R10-iqr D-LAII2R5-max D-MultiSlice-LAII2R10-entropy D-MultiSlice-LAII2R2-entropy D-LAII2R8-max D-MultiSlice-LAII2R2-robustmax D-LAII2R10-max D-LAII2R10-madmedian D-MultiSlice-LAII2R8-entropy D-MultiSlice-LAII2R5-entropy D-MultiSlice-LAII2R3-entropy D-MultiSlice-roughness2dvar D-MultiSlice-RDS-entropy D-MultiSlice-compactness2dvar D-MultiSlice-LAII2R5-range D-MultiSlice-LAII2R3-robustskewness 1.84

19 2D-MultiSlice-LAII2R3-range D-MultiSlice-HistogramRaw-robustkurtosis D-LAII2R2-robustmax D-MultiSlice-RDS-skewness D-MultiSlice-LAII2R2-robustskewness D-MultiSlice-LAII2R8-range D-MultiSlice-LAII2R10-range D-MultiSlice-RDS-range D-MultiSlice-RDS-robustskewness D-MultiSlice-LAII2R5-max D-LAII2R2-entropy D-LAII2R2-max D-MultiSlice-HistogramRaw-kurtosis D-EdgeSharpnessWindow-robustskewness D-MultiSlice-LAII2R3-max D-MultiSlice-EdgeSharpnessWindow-robustskewness D-LAII2R3-robustskewness D-MultiSlice-EdgeSharpnessBlurrynessrobustskewness D-compactness2dmean D-MultiSlice-RDS-mean D-MultiSlice-RDS-trimmedmean25perc D-RDS-robustmin D-RDS-min D-RDS-harmmean D-MultiSlice-RDS-harmmean D-MultiSlice-RDS-median D-RDS-mean D-MultiSlice-LAII2R2-median D-MultiSlice-compactness2dmean D-MultiSlice-LAII2R2-trimmedmean25perc D-LAII2R2-median D-LAII2R2-robustmin D-RDS-trimmedmean25perc D-LAII2R2-min D-LAII2R2-harmmean D-LAII2R5-robustmin D-LAII2R3-robustmin D-LAII2R2-trimmedmean25perc D-MultiSlice-LAII2R2-mean D-LAII2R5-harmmean D-LAII2R5-min D-RDS-median D-LAII2R3-median 0.40

20 2D-LAII2R3-min D-LAII2R3-harmmean D-LAII2R8-robustmin D-MultiSlice-LAII2R3-median D-MultiSlice-LAII2R3-trimmedmean25perc D-LAII2R8-min D-MultiSlice-LAII2R5-robustmin D-LAII2R2-mean D-LAII2R10-robustmin D-MultiSlice-LAII2R3-harmmean D-LAII2R10-min D-spherecity D-MultiSlice-LAII2R2-harmmean D-LAII2R3-trimmedmean25perc D-LAII2R8-harmmean D-MultiSlice-LAII2R8-robustmin D-MultiSlice-LAII2R3-mean D-MultiSlice-LAII2R3-robustmin D-MultiSlice-spherecity D-MultiSlice-LAII2R10-robustmin D-MultiSlice-RDS-robustmin D-MultiSlice-LAII2R2-robustkurtosis D-MultiSlice-LAII2R3-robustkurtosis D-LAII2R5-median D-MultiSlice-LAII2R5-trimmedmean25perc D-LAII2R10-harmmean D-MultiSlice-LAII2R5-median D-MultiSlice-LAII2R2-robustmin D-MultiSlice-RDS-robustkurtosis D-MultiSlice-LAII2R3-min D-MultiSlice-LAII2R2-kurtosis D-MultiSlice-LAII2R5-min D-MultiSlice-LAII2R2-mode D-MultiSlice-RDS-kurtosis D-LAII2R3-mode D-LAII2R2-mode D-MultiSlice-LAII2R5-harmmean D-MultiSlice-LAII2R2-min D-LAII2R3-mean D-MultiSlice-LAII2R3-kurtosis D-MultiSlice-LAII2R5-kurtosis D-LAII2R5-trimmedmean25perc D-HistogramRaw-robustskewness D-MultiSlice-HistogramRaw-robustskewness 0.61

21 2D-MultiSlice-LAII2R5-mean D-MultiSlice-LAII2R3-mode D-MultiSlice-RDS-min D-MultiSlice-HistogramRaw-skewness D-HistogramRaw-skewness D-MultiSlice-LAII2R8-min 0.67 Cluster 2 Image feature Fold change 2D-MultiSlice-compactness2dmean D-MultiSlice-RDS-min D-MultiSlice-RDS-robustmin D-MultiSlice-LAII2R3-min D-MultiSlice-RDS-harmmean D-compactness2dmean D-MultiSlice-LAII2R2-robustmin D-MultiSlice-LAII2R3-robustmin D-MultiSlice-LAII2R2-min D-MultiSlice-RDS-mean D-RDS-min D-RDS-robustmin D-LAII2R5-min D-LAII2R8-min D-LAII2R3-min D-LAII2R5-robustmin D-LAII2R8-robustmin D-LAII2R3-robustmin D-MultiSlice-RDS-trimmedmean25perc D-LAII2R2-min D-LAII2R2-robustmin D-MultiSlice-LAII2R5-robustmin D-RDS-harmmean D-RDS-mean D-RDS-trimmedmean25perc D-MultiSlice-RDS-median D-RDS-median D-LAII2R10-robustmin D-MultiSlice-LAII2R2-harmmean D-LAII2R10-min D-MultiSlice-LAII2R2-trimmedmean25perc D-MultiSlice-LAII2R2-median D-MultiSlice-LAII2R2-mean D-MultiSlice-LAII2R5-min D-MultiSlice-LAII2R3-harmmean 1.77

22 2D-MultiSlice-LAII2R8-robustmin D-LAII2R2-harmmean D-MultiSlice-EdgeSharpnessBlurryness-entropy D-LAII2R2-trimmedmean25perc D-LAII2R3-harmmean D-LAII2R2-median D-LAII2R3-median D-MultiSlice-EdgeSharpnessWindow-min D-MultiSlice-EdgeSharpnessWindow-mode D-MultiSlice-EdgeSharpnessWindow-robustmin D-LAII2R2-mean D-MultiSlice-EdgeSharpnessScale-robustmin D-LAII2R5-harmmean D-MultiSlice-EdgeSharpnessScale-min D-MultiSlice-EdgeSharpnessScale-mode D-MultiSlice-LAII2R3-trimmedmean25perc D-MultiSlice-LAII2R3-median D-MultiSlice-EdgeSharpnessBlurryness-robustmin D-MultiSlice-spherecity D-MultiSlice-LAII2R10-robustmin D-EdgeSharpnessWindow-min D-EdgeSharpnessWindow-mode D-EdgeSharpnessWindow-robustmin D-LAII2R3-trimmedmean25perc D-MultiSlice-LAII2R3-mean D-LAII2R8-range D-LAII2R5-range D-MultiSlice-LAII2R3-var D-MultiSlice-LAII2R3-madmean D-MultiSlice-LAII2R3-range D-LAII2R10-range D-LAII2R8-max D-MultiSlice-LAII2R5-range D-MultiSlice-LAII2R8-robustmax D-MultiSlice-RDS-range D-LAII2R3-range D-MultiSlice-RDS-var D-MultiSlice-LAII2R5-madmean D-LAII2R10-max D-MultiSlice-LAII2R5-var D-MultiSlice-RDS-madmean D-MultiSlice-roughness2dmean D-LAII2R5-max D-MultiSlice-LAII2R2-madmean 0.47

23 2D-MultiSlice-LAII2R2-range D-LAII2R5-madmean D-MultiSlice-LAII2R5-robustmax D-MultiSlice-LAII2R2-var D-MultiSlice-LAII2R3-robustmax D-RDS-range D-MultiSlice-LAII2R8-max D-LAII2R2-range D-MultiSlice-LAII2R3-iqr D-MultiSlice-LAII2R3-madmedian D-MultiSlice-compactness2dvar D-LAII2R3-madmean D-MultiSlice-LAII2R5-max D-MultiSlice-LAII2R5-iqr D-MultiSlice-LAII2R2-madmedian D-MultiSlice-LAII2R5-madmedian D-MultiSlice-LAII2R8-range D-LAII2R2-var D-LAII2R8-madmean D-MultiSlice-RDS-iqr D-LAII2R5-var D-MultiSlice-LAII2R10-robustmax D-LAII2R3-max D-MultiSlice-LAII2R2-iqr D-LAII2R2-madmean D-MultiSlice-LAII2R10-max D-MultiSlice-RDS-madmedian D-LAII2R8-var D-RDS-madmean D-RDS-var D-surfaceArea D-LAII2R3-var D-MultiSlice-LAII2R10-range D-MultiSlice-LAII2R8-iqr D-MultiSlice-LAII2R8-madmean D-MultiSlice-LAII2R2-robustmax D-MultiSlice-LAII2R3-max D-LAII2R3-madmedian D-LAII2R10-kurtosis D-LAII2R3-iqr D-LAII2R8-kurtosis D-MultiSlice-LAII2R8-madmedian D-LAII2R10-madmean D-LAII2R10-var 0.56

24 2D-MultiSlice-LAII2R8-var D-MultiSlice-roughness2dvar D-LAII2R3-robustmax D-LAII2R5-madmedian D-roughness2dmean D-LAII2R10-robustmax D-LAII2R5-iqr D-RDS-iqr D-MultiSlice-surfaceArea D-RDS-madmedian D-LAII2R8-robustmax D-LAII2R2-iqr D-LAII2R5-robustmax D-LAII2R2-madmedian D-EdgeSharpnessScale-madmedian D-LAII2R10-robustkurtosis D-MultiSlice-LAII2R10-madmedian D-LAII2R8-robustkurtosis D-volume D-MultiSlice-EdgeSharpnessScale-range D-EdgeSharpnessScale-range D-MultiSlice-LAII2R10-madmean D-EdgeSharpnessScale-iqr D-EdgeSharpnessScale-madmean D-MultiSlice-EdgeSharpnessScale-madmean D-LAII2R5-kurtosis D-MultiSlice-volume D-MultiSlice-EdgeSharpnessScale-iqr D-MultiSlice-EdgeSharpnessScale-madmedian D-MultiSlice-EdgeSharpnessScale-var D-EdgeSharpnessScale-var D-LAII2R8-iqr D-MultiSlice-LAII2R10-iqr D-MultiSlice-LAII2R10-var D-LAII2R8-madmedian D-MultiSlice-EdgeSharpnessBlurryness-madmean D-MultiSlice-HistogramRaw-range D-LAII2R10-iqr D-LAII2R5-robustkurtosis D-LAII2R10-madmedian D-HistogramRaw-range D-MultiSlice-EdgeSharpnessBlurryness-range D-MultiSlice-EdgeSharpnessBlurryness-robustkurtosis D-MultiSlice-LAII2R2-max 0.70

25 2D-LAII2R2-max D-LAII2R2-robustmax D-MultiSlice-EdgeSharpnessBlurryness-iqr D-LAII2R3-kurtosis D-MultiSlice-EdgeSharpnessWindow-range D-MultiSlice-HistogramRaw-max D-MultiSlice-EdgeSharpnessScale-robustmax D-MultiSlice-EdgeSharpnessBlurryness-max D-EdgeSharpnessWindow-range D-MultiSlice-EdgeSharpnessBlurryness-kurtosis D-HistogramRaw-max D-MultiSlice-EdgeSharpnessBlurryness-madmedian D-LAII2R10-mean D-MultiSlice-EdgeSharpnessScale-max D-EdgeSharpnessScale-max 0.74 Cluster 3 Image feature Fold change 2D-EdgeSharpnessScale-madmedian D-EdgeSharpnessScale-iqr D-EdgeSharpnessScale-range D-EdgeSharpnessScale-madmean D-EdgeSharpnessScale-var D-MultiSlice-EdgeSharpnessScale-madmean D-MultiSlice-HistogramRaw-robustskewness D-MultiSlice-EdgeSharpnessScale-madmedian D-MultiSlice-EdgeSharpnessScale-range D-MultiSlice-EdgeSharpnessScale-var D-MultiSlice-EdgeSharpnessScale-iqr D-spherecity D-HistogramRaw-robustskewness D-MultiSlice-HistogramRaw-skewness D-HistogramRaw-skewness D-volume D-MultiSlice-volume D-MultiSlice-EdgeSharpnessBlurryness-madmean D-LAII2R8-kurtosis D-MultiSlice-HistogramRaw-madmean D-LAII2R5-kurtosis D-HistogramRaw-range D-MultiSlice-LowIntensityProportion D-MultiSlice-EdgeSharpnessBlurryness-robustkurtosis D-MultiSlice-HistogramRaw-iqr D-MultiSlice-HistogramRaw-range 1.86

26 2D-LowIntensityProportion D-HistogramRaw-madmean D-MultiSlice-RDS-robustkurtosis D-MultiSlice-LAII2R2-robustkurtosis D-MultiSlice-EdgeSharpnessBlurryness-range D-LAII2R10-kurtosis D-MultiSlice-LAII2R2-range D-MultiSlice-surfaceArea D-MultiSlice-HistogramRaw-var D-MultiSlice-LAII2R3-robustkurtosis D-MultiSlice-LAII2R10-trimmedmean25perc D-HistogramRaw-var D-MultiSlice-LAII2R10-median D-MultiSlice-LAII2R10-mean D-MultiSlice-LAII2R3-kurtosis D-MultiSlice-LAII2R8-trimmedmean25perc D-HistogramRaw-max D-MultiSlice-HistogramRaw-max D-MultiSlice-LAII2R2-kurtosis D-MultiSlice-EdgeSharpnessWindow-range D-MultiSlice-LAII2R8-mean D-MultiSlice-LAII2R8-median D-HistogramRaw-iqr D-MultiSlice-RDS-kurtosis D-MultiSlice-EdgeSharpnessBlurryness-max D-MultiSlice-HistogramRaw-madmedian D-MultiSlice-LAII2R5-kurtosis D-MultiSlice-HistogramRaw-robustmax D-MultiSlice-EdgeSharpnessWindow-robustkurtosis D-LAII2R3-kurtosis D-MultiSlice-LAII2R2-max D-MultiSlice-EdgeSharpnessBlurryness-madmedian D-MultiSlice-EdgeSharpnessBlurryness-iqr D-surfaceArea D-MultiSlice-LAII2R5-median D-MultiSlice-LAII2R5-trimmedmean25perc D-MultiSlice-EdgeSharpnessBlurryness-var D-HistogramRaw-robustmax D-LAII2R10-harmmean D-MultiSlice-EdgeSharpnessScale-robustmax D-MultiSlice-LAII2R8-max D-MultiSlice-EdgeSharpnessScale-harmmean D-EdgeSharpnessScale-robustmax D-MultiSlice-EdgeSharpnessBlurryness-kurtosis 1.57

27 2D-MultiSlice-RDS-range D-MultiSlice-LAII2R5-mean D-LAII2R8-harmmean D-EdgeSharpnessBlurryness-robustkurtosis D-EdgeSharpnessBlurryness-kurtosis D-LAII2R8-robustkurtosis D-EdgeSharpnessWindow-robustkurtosis D-EdgeSharpnessScale-max D-MultiSlice-EdgeSharpnessBlurryness-robustmax D-MultiSlice-EdgeSharpnessScale-max D-LAII2R3-robustkurtosis D-LAII2R5-median D-MultiSlice-LAII2R10-max D-LAII2R2-kurtosis D-LAII2R10-median D-LAII2R2-median D-LAII2R10-mean D-LAII2R5-robustkurtosis D-MultiSlice-LAII2R3-range D-MultiSlice-LAII2R5-max D-MultiSlice-EdgeSharpnessWindow-min D-MultiSlice-EdgeSharpnessWindow-mode D-MultiSlice-EdgeSharpnessWindow-robustmin D-EdgeSharpnessWindow-min D-EdgeSharpnessWindow-mode D-EdgeSharpnessWindow-robustmin D-MultiSlice-EdgeSharpnessScale-robustmin D-MultiSlice-EdgeSharpnessScale-min D-MultiSlice-EdgeSharpnessScale-mode D-EdgeSharpnessScale-robustmin D-MultiSlice-EdgeSharpnessBlurryness-robustmin D-MultiSlice-EdgeSharpnessWindow-robustskewness D-EdgeSharpnessScale-min D-EdgeSharpnessScale-mode D-MultiSlice-LAII2R10-entropy D-LAII2R8-entropy D-EdgeSharpnessBlurryness-entropy D-MultiSlice-LAII2R8-entropy D-LAII2R10-entropy D-MultiSlice-EdgeSharpnessBlurryness-entropy D-MultiSlice-LAII2R2-entropy D-MultiSlice-RDS-entropy D-LAII2R5-entropy D-MultiSlice-LAII2R3-entropy 0.55

28 2D-MultiSlice-LAII2R5-entropy D-MultiSlice-EdgeSharpnessBlurryness-min D-MultiSlice-EdgeSharpnessBlurryness-mode D-MultiSlice-RDS-skewness D-MultiSlice-RDS-robustskewness D-MultiSlice-EdgeSharpnessBlurrynessrobustskewness D-EdgeSharpnessWindow-entropy D-MultiSlice-EdgeSharpnessWindow-skewness D-MultiSlice-LAII2R2-robustskewness D-LAII2R3-entropy D-MultiSlice-RDS-min D-LAII2R5-iqr 0.64 Table S5. Cluster assignment by subjects in the development cohort with and without midline-crossing lesions. With midline-crossing, n = 140; without midline crossing, n = 121. With midlinecrossing lesions Cluster Without midlinecrossing lesions Cluster Patient_033 1 Patient_033 1 Patient_047 3 Patient_047 1 Patient_054 2 Patient_054 2 Patient_056 2 Patient_056 2 Patient_066 2 Patient_066 2 Patient_080 1 Patient_080 1 Patient_083 3 Patient_083 3 Patient_084 2 Patient_084 2 Patient_085 3 Patient_085 3 Patient_086 2 Patient_086 2 Patient_088 2 Patient_088 2 Patient_091 2 Patient_091 2 Patient_092 2 Patient_092 2 Patient_094 2 Patient_094 2 Patient_097 3 Patient_097 3 Patient_098 3 Patient_098 3 Patient_099 3 Patient_099 3 Patient_104 2 Patient_104 2 Patient_105 3 Patient_105 2 Patient_106 1 Patient_106 1 Patient_109 1 Patient_109 1 Patient_110 1 Patient_110 1 Patient_114 1 Patient_114 1 Patient_116 3 Patient_116 1

29 Patient_117 2 Patient_117 2 Patient_121 1 Patient_121 1 Patient_124 1 Patient_124 1 Patient_125 1 Patient_125 1 Patient_129 3 Patient_129 3 Patient_133 2 Patient_133 2 Patient_135 1 Patient_135 1 Patient_136 2 Patient_136 2 Patient_137 3 Patient_137 3 Patient_142 1 Patient_142 1 Patient_144 1 Patient_144 1 Patient_145 3 Patient_145 3 Patient_146 2 Patient_146 2 Patient_147 2 Patient_147 2 Patient_149 3 Patient_149 3 Patient_150 2 Patient_150 2 Patient_151 2 Patient_151 2 Patient_154 1 Patient_154 1 Patient_155 1 Patient_155 1 Patient_156 3 Patient_156 3 Patient_157 3 Patient_157 3 Patient_158 3 Patient_158 3 Patient_159 2 Patient_159 2 Patient_160 2 Patient_160 2 Patient_161 2 Patient_161 2 Patient_164 3 Patient_164 3 Patient_166 3 Patient_166 3 Patient_167 2 Patient_167 2 Patient_168 3 Patient_168 3 Patient_169 1 Patient_169 1 Patient_170 1 Patient_170 1 Patient_175 2 Patient_175 2 Patient_178 3 Patient_178 3 Patient_182 2 Patient_182 1 Patient_189 1 Patient_189 1 Patient_190 3 Patient_190 3 Patient_201 2 Patient_201 2 Patient_203 1 Patient_203 1 Patient_204 2 Patient_204 2 Patient_206 2 Patient_206 2 Patient_218 2 Patient_218 2 Patient_220 2 Patient_220 2 Patient_222 3 Patient_222 3 Patient_223 1 Patient_223 1 Patient_224 3 Patient_224 3 Patient_225 3 Patient_225 3 Patient_235 2 Patient_235 2 Patient_236 1 Patient_236 1

30 Patient_238 2 Patient_238 2 Patient_240 2 Patient_240 2 Patient_242 2 Patient_242 2 Patient_243 2 Patient_243 2 Patient_248 1 Patient_248 1 Patient_251 3 Patient_251 3 Patient_252 1 Patient_252 1 Patient_267 1 Patient_267 1 Patient_268 3 Patient_268 3 Patient_272 1 Patient_272 1 Patient_273 1 Patient_273 1 Patient_274 2 Patient_274 2 Patient_275 3 Patient_275 3 Patient_277 2 Patient_277 2 Patient_279 2 Patient_279 2 Patient_283 3 Patient_283 3 Patient_287 2 Patient_287 2 Patient_289 3 Patient_289 3 Patient_290 3 Patient_290 3 Patient_297 2 Patient_297 2 Patient_300 3 Patient_300 3 Patient_305 3 Patient_305 3 Patient_307 1 Patient_307 1 Patient_309 2 Patient_309 2 Patient_315 2 Patient_315 2 Patient_317 2 Patient_317 2 Patient_323 2 Patient_323 2 Patient_324 1 Patient_324 1 Patient_327 1 Patient_327 1 Patient_333 2 Patient_333 2 Patient_335 1 Patient_335 1 Patient_338 3 Patient_338 3 Patient_345 2 Patient_345 2 Patient_356 2 Patient_356 2 Patient_357 3 Patient_357 3 Patient_358 2 Patient_358 2 Patient_362 1 Patient_362 1 Patient_364 1 Patient_364 1 Patient_367 3 Patient_367 3 Patient_375 1 Patient_375 1 Patient_385 2 Patient_385 2 Patient_386 2 Patient_386 2 Patient_387 3 Patient_387 3 Patient_388 2 Patient_388 2 Patient_395 2 Patient_395 2 Patient_400 1 Patient_400 1 Patient_403 1 Patient_403 1 Patient_409 3 Patient_409 1

31 Patient_413 1 Patient_413 1 Patient_128 2 Patient_130 3 Patient_152 3 Patient_165 3 Patient_231 1 Patient_234 3 Patient_241 3 Patient_257 2 Patient_270 2 Patient_271 2 Patient_285 3 Patient_291 1 Patient_293 3 Patient_302 2 Patient_311 1 Patient_312 3 Patient_342 2 Patient_343 2 Patient_379 2

32 Table S6. Regulatory signaling pathways significantly associated with each cluster. Each cluster is associated with up-regulated ( 1.0 fold change) or down-regulated (< 1.0 fold change) signaling pathways as determined by individual gene expression and copy number variation data (CNV) integrated using the Pathway Recognition Algorithm Using Data Integration on Genomic Models (PARADIGM). Only signaling pathways with a false discovery rate (FDR or q-value) <5% are included. Signaling pathways are ranked in descending order of fold changes. Signaling pathway Fold change Cluster 1 Signaling events mediated by stem cell factor receptor (c-kit) Cluster 2 Insulin-mediated glucose transport q-value (%) Signaling events mediated by prolactin (PRL) Platelet-derived growth factor receptor-alpha (PDGFR-α) signaling pathway Reelin signaling pathway Vascular endothelial growth factor receptor 1 (VEGFR1) specific signals Polo-like kinase 1 (PLK1) signaling events Regulation of nuclear mothers against decapentaplegic homolog /3 (SMAD2/3) signaling Signaling events mediated by protein-tyrosine phosphatase 1B (PTP1B) Osteopontin-mediated events Signaling events activated by hepatocyte growth factor receptor (c-met) Alpha-M beta-2 (αmβ2) Integrin signaling Syndecan-1 mediated signaling events Erythropoietin (EPO) signaling pathway Endothelins Forkhead box protein A2 (FOXA2) and FOXA3 transcription factor networks Signaling events mediated by vascular endothelial growth factor receptor 1 (VEGFR1) and VEGFR2 Interleukin 6 (IL6) mediated signaling events Angiopoietin receptor Tie2-mediated signaling IL23-mediated signaling events Signaling events mediated by c-kit Forkhead box protein M1 (FOXM1) transcription factor network Cluster 3 FOXA2 and FOXA3 transcription factor networks PDGFR-β signaling pathway Endothelins

33 Thromboxane A2 receptor signaling Syndecan-4 mediated signaling events Syndecan-1 mediated signaling events IL6 mediated signaling events Osteopontin-mediated events Fc-ε receptor I signaling in mast cells αmβ2 Integrin signaling Angiopoietin receptor Tie2-mediated signaling PTP1B B cell receptor (BCR) signaling pathway Retinoic acid receptor and retinoid X receptor (RXR and RAR) heterodimerization with other nuclear receptor Atypical nuclear factor-κ B pathway PLK1 signaling events Ceramide signaling pathway Noncanonical Wnt signaling pathway SMAD2/3 signaling T cell receptor (TCR) signaling in naïve CD8 + T cells IL1 mediated signaling events Calcium signaling in the CD4 + TCR pathway Ras signaling in the CD4 + TCR pathway Nongenotropic androgen signaling Regulation of p38-α and p38-β VEGFR1 specific signals E-cadherin signaling in the nascent adherens junction PRL PDGFR-α signaling pathway IL27 mediated signaling events Canonical Wnt signaling pathway