Supplementary Figure 1. Copy Number Alterations TP53 Mutation Type. C-class TP53 WT. TP53 mut. Nature Genetics: doi: /ng.

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1 Supplementary Figure a Copy Number Alterations in M-class b TP53 Mutation Type Recurrent Copy Number Alterations TP53 WT TP53 mut TP53-mutated samples (%) Missense Truncating M-class :2.45 :3.85 C-class Supplementary Figure : TP53-mutated tumors a, TP53-mutated tumors within the M-class have a higher number of recurrent copy number alterations (for all SFEs) than TP53 wild type samples. b, While both missense (residue-changing) and truncating TP53 mutations are more frequent in the C-class than in the M-class, this enrichment is significantly stronger for truncating mutations. Nature Genetics: doi:.38/ng.2762

2 Supplementary Figure 2 No. of recurrent mutations Only Tumor from Mutated class Supplementary Figure 2: Mutations versus copy number alterations. Tumors with more recurrent mutations than copy number alterations predominantly are in the M-class (increasing intensity of green), while tumors with more recurrent copy number alterations mostly are in the Cclass (increasing intensity of red). Similar levels of both type of alterations are in tumors at the border between the two classes (grey). Ratio of tumors from the two classes Both are present Only tumors from CN-Altered class Supplementary Figure 3: Distribution of mutations and copy number changes across different tumor types. Samples from different tumor types and subtypes vary in the number of recurrent copy number alterations (X-axis) and number of recurrent mutations (Y-axis). No. of recurrent CNAs Supplementary Figure 3 BLCA LUSC OV UCEC 3 4 Nature Genetics: doi:.38/ng LUAD LAML 2 KIRC 4 4 HNSC GBM COADREAD BRCA 4 ALL TUMORS

3 Supplementary Figure 4 a Independent TCGA Dataset (ITD) b PANCAN8 Hyperbola Thyroid Papillary Carcinoma (4) Pancreas Adenocarcinoma (27) Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (35) Skin Cutaneous Melanoma (58) Prostate Adenocarcinoma (7) # of Recurrent Mutations PANCAN2 ITD Stomach Adenocarcinoma (29) # of Recurrent Copy Number Alterations c PANCAN8 BRAF-mutant Thyroid-enriched class (378) (734) Characterized by somatic mutations M-class (269) Characterized by CNAs C-class d Enrichment [-log(q)] M-class vs C-class (PANCAN8) APC KRAS PIK3CA ARIDA τ =.9* 3q26 8q24 (MYC) TP53 (q = 8E-29) High Amp. Hom. Del. Mutations Alterations Enriched in M-class Alterations Enriched in C-class Supplementary Figure 4: Robustness of classes and features - validation in enlarged dataset. a, An independent dataset consisting of 99 samples from 6 tumor types was integrated with our original dataset (PANCAN2). b, Samples from the resulting set of 8 tumor types (PANCAN8) confirmed the inverse relationships between copy number alterations and mutations, with the newly added samples following the same inverse trend (red squares) we originally observed (gray squares). c, A stratification of the PANCAN8 dataset identifies two main modules of similar size and a small subgroups enriched in BRAF-mutant thyroid samples. These thyroid tumors emerged separately as strongly characterized by BRAF V6E mutations and otherwise depleted of any other SFE. Nonetheless, these tumors do not violate the distinction between tumors primarily characterized by copy number alterations (C-class) and tumors characterized by mutations (M-class), of which thyroid samples are a subset. d, The ranked list of SFEs, with the first of the list being the most enriched in the M-class and the last the most enriched in C-class, is almost perfectly concordant with the same ranked list obtained in the PANCAN2 dataset (Kendall correlation coefficient tau =.9). Nature Genetics: doi:.38/ng.2762

4 Supplementary Figure 5 TUMOUR HIERARCHICAL CLASSIFICATION CLUSTER SIZE MOST FREQUENT SFEs MOST REPRESENTED TUMOR TYPES M M2 M3 M4 M5 M6 M7 M Mutations on APC (5%), PTEN (47%), POLE (46%), ATM (43%) MLH-methylation (7%), BRAF mutations (57%), 6p deletion (46%) ARIDA (9%) and CTNNB (32%) mutations PTEN (94%) and PIK3R (3%) mutations PTEN (79%), PIK3CA (64%), ARIDA (6%), CTCF (4%), CTNNB (3%) mutations and MLH methylation (46%) PIK3CA (99%) mutations PIK3CA (96%), KRAS (72%), APC (53%) mutations and MGMT (46%) methylation PIK3CA (97%) and TP53 (75%) mutations Ultra mutators UCEC and COADREAD (57-6%) Micro-satellite instable COADREAD (56-79%) and UCEC (3-6%) Mixed (BLCA - 2%, LUAD - 5%, UCEC low CNA - 5%) Mixed (GBM - 3%, UCEC Low CNA - 24%) UCEC MSI (43%), UCEC Low CNA (33%), BRCA Lum A (%) BRCA Lum A (48%), HNSC (4%), KIRC (%) COADREAD MSS (4%) and MSI (2%), UCEC Low CNA (%) Mixed (HNSC - 25%, COADREAD MSS - 3%, GBM - 3%, BLCA -2%) M M9 M M M2 M3 M APC (76%), TP53 (57%) mutations and 2q amplification (84%) APC (88%) and NRAS (9%) mutations TP53 (93%), APC (83%) mutations and MGMT (34%) methylation APC (86%), KRAS (86%), and TP53 (52%) mutations KRAS (99%), TP53 (45%), APC (4%) mutations and MGMT (48%) methylation MGMT methylation (84%), TP53 mutations (56%), and 9q2 (CDKN2A) deletion (35%) COADREAD MSS (56-79%), LUAD (%) COADREAD MSS (53-78%) COADREAD MSS (48-8%) COADREAD MSS (48-85%) COADREAD MSS (37-56%), LUAD (34%) GBM (4%), AML (6%), HNSC (3%) M5 26 9q2 (CDKN2A) deletion (76%) and 7p (EGFR) amplification (48%) GBM (6%), LUAD (2%), HNSC (%) M6 5 FLT3 (38%), NPM (29%), and DNMT3A (27%) mutations AML (9%) M7 35 VHL (63%), PBRM (4%) mutations and GSTP methylation (36%) KIRC (92%) ALL TUMORS C C2 C3 C4 C5 C TP53 mutations (99%) TP53 mutations (96%) and 9q2 (CCNE - 4%), 9p3 (BRD4* - 32%), 3q26 (ZNF639*, PIK3CA - 3%) amplification TP53 mutations (92%), 3q26 (ZNF639*, PIK3CA) amplification (64%) and 9q2 (CDKN2A) deletion (32%) TP53 (84%), CDKN2A (34%) mutations, q3 (CCND) amplification (82%), 9q2 (CDKN2A) deletion (25%) TP53 mutations (53%), q3 (CCND - 79%), q4 (PAK - 38%), 8p (WHSCL, FGFR - 3%) amplification q2 (SETDB* - 8%), q34 (PPPR5B*, MDM4-56%) amplification and TP53 mutations (54%) Mixed (HNSC -2%, OV - 2%, LUAD - 5%) OV (66%), LUSC (%), UCEC Serous (6%) LUSC (4%), HNSC (25%) HNSC (5%), LUSC (6%) HNSC (3%), BRCA Lum A (25%) and Lum B (6%) Mixed (BRCA Lum A - 9%, OV - 6%, LUAD - 5%, UCEC Serous - %) C C7 75 TP53 mutations (76%), 8p2 (PPP2R2A* - 56%), 8p23 (FBXO25* - 48%) deletion, and q2 (SETDB* - 4%), 8q24 (MYC - 36%) and 3q26 (ZNF639*, PIK3CA - 35%) amplification OV (56%), BRCA Basal (5%) C8 C9 C C C2 C3 C TP53 mutations (72%) and 8p23 (FBXO25* - 8%), 8p23 (PPP2R2A* - 64%) deletion 8q24 (MYC - 93%), 8q22 (YWHAZ* - 9%), 8p (IKBKB - 55%), 8p2 (WHSCL, FGFR - 45%) amplification and TP53 mutations (36%) TP53 mutations (%) and 8q24 (MYC - 95%), 8q22 (YWHAZ* - %) amplification 8q24 (MYC) amplification (99%), TP53 (89%) and BRCA2 (25%) mutations 7q23-25 (RPS6KB, mir-2-67%), 7q2 (ERBB2-28%), 8q24 (MYC - 56%), 8q22 (YWHAZ* - 42%), q2 (SETDB* - 35%), q34 (PPPR5B*, MDM4-33%) amplification and TP53 mutations (36%) 6p22-23 (E2F3-88%), 8q24 (MYC - 7%), 3q26 (ZNF639*, PIK3CA - 5%), 8q22 (YWHAZ* - 38%), 7q36 (UBE3C* 33%) amplification and TP53 (75%), BRCA2 (3%), BRCA (29%) mutations 8q24 (MYC - 88%), 3q26 (ZNF639* - 78%), 2q3 (AURKA - 52%), 8q22 (YWHAZ* - 5%), q2 (SETDB* - 44%), 5p5 (CLPTML* - 33%), 9p3 (BRD4* - 27%) amplification and TP53 mutations (78%) Mixed (HNSC - 2%, OV - 6%, BRCA Lum A - 5%, LUSC - 3%) BRCA Lum A (33%) and Lum B (5%), BLCA (7%) OV (4%), HNSC (2%), BRCA Basal (%) OV (5%), UCEC Serous (8%), BRCA Basal (8%), LUAD (8%) BRCA Lum A (2%), LumB (9%), Her2+ (%), Basal (9%), OV (8%) OV (75%), BRCA Basal (8%) OV (68%), BRCA Basal (9%) * Most differentially expressed gene in the region when compared to diploid samples Nature Genetics: doi:.38/ng.2762 Supplementary Figure 5: Hierarchical stratification. The hierarchical stratification of tumors based on selected functional events identifies 3 oncogenic signature sub-classes (dendrogram on the left). For each sub-class, we report the most frequent SFEs and the most represented tumor types. For each recurrent copy number alteration, we report known oncogenes or tumor suppressors in the region (if present). For large regions spanning multiple genes, we also report the gene with the most significant differential mrna expression between altered and diploid cases.

5 Supplementary Figure 6 ALL TUMORS 795 samples 445 samples M C M/C classes st-level modules 2nd-level modules M M2 M3 M4 M5 M6 M7 M8 M9MMM2M3M4 M5 M6 M7 C C2 C3 C4 C5 C6 C7C8C9CCC2C3C4 Jaccard Coefficient Jaccard Coefficient Jaccard Coefficient Top Classes (5%) Top Classes (2%) Top Classes (5%) st-level modules (5%) st-level modules (2%) 2nd-level modules (5%) 2nd-level modules (2%) M-M7 (5%) M-M7 (2%) st-level modules (5%) st-level modules (2%) 2nd-level modules (5%) 2nd-level modules (2%) C-C4 (5%) C-C4 (2%) M/C-classed M subclasses C subclasses Random Classification Supplementary Figure 6: Robustness of cluster assignments. Subclasses at all levels of the hierarchical stratification were separately tested for robustness to random sample removal. The top classes M and C (black dots) show almost perfect reproducibility upon removal of 5%, 2%, and 5% of the samples. Similarly, the M subclasses (green dots) maintain a constantly high robustness descending the classification. C subclasses (red dots) at the bottom the classification are the most affected by sample removals, despite a robustness significantly higher than expected (gray dots). The non-focal nature of copy number alterations and the difficulty in identifying the corresponding functional targets are likely to impact the definition of these groups, weakening their robustness. Nature Genetics: doi:.38/ng.2762

6 Supplementary Figure 7 a ARIDA Mutated Samples (%) b ARIDA Hotspot Mutations % Q334 IF-Del (x4) Q334 IF-Ins (x2) R335* (x5) R693* (x5) 5% c M M3 M5 CTCF Mutated Samples (%) e CTCF Hotspot Mutations UCEC BRCA 2285 POLE / ultra-mutators R283C H284N/Y/P R72* (x2) R722* (x5) d 5% 25% R989* (x4) G26-splice (x3) R377C (x2) R377H (x2) P378L (x2) P378A R448* (x7) H32R N34fs (x3) Zinc-Finger domains (ZF-ZF) KIRC HNSC M5 CTCF C2-H2 Zinc Finger f 727 CTCF Splice-site Mutation Wild-type His- (H284/H32) EX 3 Cys- EX 5 G26-splice (TCGA-A2-AYF) Zn His-2 EX 4 ZF ZF2 Cys-2 EX 3 EX 4 EX 5 Exon Skipping Supplementary Figure 7: Recurrent mutations identified by cross-cancer analysis. a, ARIDA mutations are observed in sub-classes M, M3, and M5, which include diverse tumor subtypes (colored stacked bars). b, The frequency of mutations of ARIDA across all tumors indicates hotspot regions (colored according to the tumor type of the mutated samples). c, CTCF mutations are characteristic of sub-class M5 and d, hotspot somatic mutations target different zinc-finger domains (white boxes). e, hotspot mutations frequently occur at the zinc-binding histidine. f, This splice-site mutation causes an inframe exon-skipping event. The skipped exon codes for zinc-finger and 2. Nature Genetics: doi:.38/ng.2762

7 Supplementary Figure 8 TCGA-A2-AYF CTCF Chr. 6 p2.3 p2.2 p2. p.2 p. q.2 q2. q2.2 q3 q2 q22. q22.2 p3.3 p3.2p3.3 p3. p2.3 p2.2 p2. p.2 p. q.2 q2. q2.2 q3 q2 q22. q22.2 q23. q23.2 q23.3 q24.q kb 67,65 kb Exon4 Skipping Exon 3 Exon 4 Exon 5 CTCF Exon 6 Exon 7 Supplementary Figure 8: Splice-site mutation in CTCF. Splice-site mutation on G26 on CTCF (located on 6q22) caused the skipping of Exon 4 in the TCGA-A2-AYF sample. Multiple RNA-seq reads (grey thick lines, one sample per row) span sequences starting from Exon 3 to Exon 5, therefore skipping Exon 4 (endpoints of reads spanning more than one exon are connected by blue lines). Nature Genetics: doi:.38/ng.2762

8 Supplementary Figure 9 q AMP 3q AMP 8p DEL 9p AMP combined q-values GISTIC q-values q2 q32 3q26 8p23 8p2 9p3 SETDB ZNF639 FBXO25 MFN PIK3CA PPPR5B PPP2R2A MDM4 BRD4 Supplementary Figure 9: Significant loci within chromosomal events. Recurrent gains and losses on chromosomes q, 3q, 8p, and 9p span multiple genes. The Gistic algorithm identified the most significant loci in these regions (peaks of q-value histograms). We tested each gene in these peaks for differential mrna expression concordant with the copy number change (over-expressed if amplified, down-regulated if deleted, relative to diploid cases). Combined q-values [-log(q)] serve to determine the most likely functional targets (labeled by corresponding gene symbol). Nature Genetics: doi:.38/ng.2762

9 Supplementary Figure a 4 E545A/D/G/K/Q H47L/Q/R/Y 2 # Mutations H542A/G/K/Q/V R88Q N345I/K/T G8D Q546E/K/P/R E726K M43I/V b # Mutations Cyclin Box E28del T286I P287S PEST PIK3CA 68 aa CCND 295 aa Supplementary Figure : Hotspot mutations identified by cross-cancer analysis. a, PIK3CA hotspot mutations. b, Hotspot mutations in CCND cluster in the PEST domain of the protein, preventing degradation and stabilizing the protein. Mutations are indicated by vertical bars (bar height proportional to the number of mutations in the specified residue, summed over all affected samples in all tumor types). Nature Genetics: doi:.38/ng.2762

10 Supplementary Figure C C2 C3 C4 C5 C6 C7 C8 C9 C C C2 C3 C4 M M2 M3 M4 M5 M6 M7 M8 M9 M M M2 M3 M4 M5 M6 M7 Average Pathway Drug family EGFR EGFR ERBB2 ERBB2 ERBB3 ERBB3 FGFR FGFR2 FGFR3 FGFR3 MET PDGFRA/KIT/KDR NF NF KRAS KRAS HRAS NRAS BRAF RTK/Ras/Raf RTKs NF Ras Raf RTK inhibition BRAF/MAPKi PIK3CA PIK3CA PIK3R PTEN PTEN AKT STK STK TSC TSC/2 MTOR PI(3)K PTEN Akt STK TSCcomplex mtor PI(3)Ki AKTi mtori PI(3)K/AKT/MTOR CDKN2A CDKN2A CDKN2A CDKNA CDKNB CCND CCND CDK6 CDK4 CCNE RB RB E2F3 AURKA Cell Cycle p6-ink4a p2/p27 Cyclin D - CDK4/6 Cyclin E Rb E2F-3 AURK CDK4/6i CDK2i AURKi BRCA BRCA BRCA2 ATM MDM2 MDM4 TP BRCA/2 ATM Mdm2/4 p53 PARPi MDMi p53/dna-repair Samples (%) 5 Homozygous deletion Somatic mutation High-level amplification DNA hyper-methylation % altered Inactivating Activating # pathways altered No Direct Indirect Currently targetable Supplementary Figure : Map of functional and actionable alterations across 3 tumor subclasses. Four major oncogenic pathways (RTK/Ras/Raf, PI(3)K/Akt/mTOR, Rb, and DNA-repair/p53 signaling simplified in the Pathway column) are altered by multiple different mechanisms (arranged vertically) across tumor types and subtypes (from left to right). Alterations to at least one of these pathways are observed in almost all samples of almost all tumor types (stacked barplots at the bottom). Several of these alterations are directly or indirectly therapeutically actionable ( Drug Class column). Nature Genetics: doi:.38/ng.2762

11 Supplementary Figure 2 Subclass A Subclass B Event Woman Supplementary Figure 2: Exercise to test algorithm: network subclasses identified in the Southern Women Club Attendance network. We identified two main classes (blue and red) and within each main class we identified smaller groups of women, who attended the same set of events. Grouping by dotted lines. These results are consistent with the ones in the original publications (see Methods). Nature Genetics: doi:.38/ng.2762

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