1 Supplementary Materials Loss-of-function mutations

Supplementary Materials Loss-of-function mutations in ATP6AP1 and ATP6AP2 in granular cell tumors

Pareja et al.

Supplementary Methods Supplementary Figures 1-8 Supplementary Tables 1-5 Supplementary References

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SUPPLEMENTARY METHODS The Cancer Genome Atlas (TCGA) studies re-analyzed in this study For the analysis of the prevalence of ATP6AP1 and ATP6AP2 somatic mutations, whole-exome sequencing results pertaining to 6,285 non-hypermutated common cancer samples were retrieved from TCGA studies of 14 common cancer types, including Acute Myeloid Leukemia1, Bladder Urothelial Carcinoma2, Breast Invasive Carcinoma3, Colorectal Adenocarcinoma4, Head and Neck Squamous Cell Carcinoma5, Kidney Renal Clear Cell Carcinoma6, Kidney Chromophobe7, LowGrade Glioma/Glioblastoma Multiforme8, Pan-Lung Cancer9, Ovarian Serous Cystadenocarcinoma10, Prostate Adenocarcinoma11, Stomach Adenocarcinoma12, Uterine Corpus Endometrial Carcinoma13 and Papillary Thyroid Carcinoma14.

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Supplementary Figure 1

Supplementary Figure 1: Copy number profiles and clonality of recurrent non-synonymous mutations identified in granular cell tumors by whole-exome sequencing, Sanger sequencing validation of ATP6AP1 and ATP6AP2 mutations and evolutionary conservation of ATP6AP1 in-frame indels. (a) Copy number profiles of granular cell tumors (GCTs) subjected to whole-exome sequencing (WES; n=17). Samples are shown in rows, chromosomes are depicted along the x-axis, and copy number alterations are color-coded according to the legend. (b) Cancer cell fraction (CCF) and clonality of each recurrent non-synonymous somatic mutation identified in GCTs by WES (n=17). CCFs are color-coded according to the legend. Clonal mutations are depicted by an orange box. *, sequencing depth not appropriate for clonality assessment. (c) Representative sequence 3

electropherograms of normal and tumor samples from GCTs found to harbor ATP6AP1 or ATP6AP2 mutations by WES (n=12). The gene affected, mutation type, base and amino acid change are indicated for each case. Arrows point to the altered base. (d) Multiple alignment of the amino acid sequence of human ATP6AP1 with the orthologous proteins of Gallus gallus, Danio rerio, Xenopus laevis, Bos taurus, Delphinus delphis, Equus caballus, Mus musculus, Rattus norvegicus and Pan troglodytes for GCTs harboring ATP6AP1 in-frame small insertion and deletion (indel) mutations (n=5). The residues altered by in-frame indels are indicated by black boxes. “*”, single fully conserved residue; “:”, conservation between groups of strongly similar properties; “.”, conservation between groups of weakly similar properties. The physicochemical properties of the residues are color-coded as follows: small (red), acidic (blue), basic (magenta), and hydroxyl + sulfhydril + amine + G (green).

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Supplementary Figure 2: ATP6AP1 loss-of-function mutations and X chromosome inactivation, and expression of mutant ATP6AP1 and ATP6AP2 transcripts in granular cell tumors (GCTs).

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(a) Representative bisulfite sequencing electropherograms of GCTs from female patients harboring ATP6AP1 mutations in the vicinity of CpG islands (n=5). Following bisulfite treatment, DNA was PCR amplified with primer sets specific for methylated DNA (upper) and non-methylated DNA (lower). The gene affected, mutation type, base and amino acid change are indicated in each case. Arrows depict the altered base. Blue (*), methylated non-converted cytosine residues, red (*), nonmethylated cytosine residues converted to thymidine. (b) Modified HUMARA assay representative sequence electropherograms of GCTs from female patients harboring ATP6AP1 mutations in the vicinity of CpG islands (n=3), following restriction digestion with HhaI (upper) or control mockdigestion (lower). The gene affected, mutation type, base and amino acid change are indicated in each case. Arrows depict the altered base. (c) Integrative Genomics Viewer (IGV) pileups of the mRNA expression of ATP6AP1 and ATP6AP2 mutated forms identified by RNA-sequencing in GCTs from male (n=3) and female (n=4) patients. The gender, gene affected, base and amino acid changes are indicated for each case. (d) Representative sequence electropherograms of cDNA derived from RNA extracted from GCTs found to harbor ATP6AP1 or ATP6AP2 mutations by wholeexome sequencing (n=1) or targeted capture sequencing (n=13), including male (n=2) and female (n=12) patients. The gene affected, mutation type, base and amino acid change are indicated in each case. Arrows and brackets point to the altered base. F, female; M, male.

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Supplementary Figure 3: ATP6AP1 and ATP6AP2 silencing and loss of function mutations result in loss of protein expression in granular cell tumors. (a) Confocal fluorescence micrographs of formalin-fixed paraffin-embedded (FFPE) immortalized Schwann cell pellets where ATP6AP1 or ATP6AP2 had been stably silenced, or control cells. Scale bars, 25 µm. (b) Western blot analysis of ATP6AP1 and ATP6AP2 in human granular cell tumors (GCTs). Protein extracts from frozen ATP6AP1MUT GCTs (n=3) and a pool of matching normal tissue were blotted for ATP6AP1. Protein extracts from FFPE ATP6AP2MUT (n=3) and ATP6AP1/2WT (n=1) GCTs were blotted for ATP6AP2. GAPDH was used as loading control. Experiments are representative of three replicates.

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Supplementary Figure 4: Functional impact of ATP6AP1 or ATP6AP2 silencing on the phenotype, distribution of endosomal compartments, lysosomal acidification and activity, and endocytic flux. (a) ATP6AP1 and ATP6AP2 western blot analysis of primary Schwann cells, HEK293 cells and MCF10A cells following transfection with validated short-interfering RNAs (siRNAs) targeting ATP6AP1 or ATP6AP2, or non-targeting control siRNA pools. Tubulin was used as loading control. 8

(b) Transmission-electron micrographs of MCF10A cells transfected with siRNAs targeting ATP6AP1 or ATP6AP2, or with non-targeting control siRNAs (top). Scale bars, 5 m and 1 m. Quantification of the number of GCT-like intracytoplasmic granules per image area of primary Schwann (from Fig. 4b), HEK293 (from Fig. 4b) and MCF10A cells following transfection with siRNAs targeting ATP6AP1 or ATP6AP2, or non-targeting control siRNAs (bottom). Quantification was performed using ImageJ in at least 10 representative images per condition (error bars, mean ± SD). (c) ATP6AP1 and ATP6AP2 western blot analysis of immortalized Schwann and HEK293 cells with stable short-hairpin (sh)RNA silencing of ATP6AP1 or ATP6AP2, or control shRNAs. Tubulin was used as loading control. (d) Quantification of pHrodo Red dextran fluorescence intensity per cell-covered area in immortalized Schwann cells and HEK293 cells with stable silencing of ATP6AP1 or ATP6AP2, using 2 different shRNA constructs per gene, or control non-targeting shRNA species (n=3, mean ± SD). Quantification was performed using ImageJ in at least 3 representative images per sample. (e) Quantification of pHrodo Red dextran fluorescence intensity per cell-covered area in primary Schwann and HEK293 cells following transient silencing of ATP6AP1 and ATP6AP2, singly or in combination, or non-targeting control (n=3, mean ± SD). Quantification was performed using ImageJ in at least 5 representative images per sample. (f) Quantification of the number of EEA1-positive (early endosomes), Rab13-positive (recycling endosomes) and LAMP-1 positive (lysosomes) foci in primary Schwann and HEK293 cells following transient silencing of ATP6AP1 and ATP6AP2, singly or in combination, or with non-targeting control siRNAs (n≥7, mean ± SD). The average number of foci per cell (DAPI stained nuclei) was analyzed using ImageJ in at least 10 representative images per condition. (g) Lysosomal activity assay in immortalized Schwann cells and HEK293 cells transfected with siRNAs against ATP6AP1 or ATP6AP2, or non-targeting control siRNAs. Flow cytometry histograms of immortalized Schwann cells and HEK293 cells incubated with Lysosomal-Specific Self-Quenched Substrate (SQS; n=3). (h) Flow cytometry histograms of primary Schwann cells and HEK293 cells incubated with pHrodo Red Transferrin conjugate. Quantification of the median fluorescence intensity (MFI) of the pHrodo Red signal (n=3; mean ± SD). (i) Quantification of the MFI of the pHrodo Red signal in immortalized Schwann cells and HEK293 cells with stable silencing of ATP6AP1 or ATP6AP2 and non-targeting shRNA control following incubation with pHrodo Red Transferrin conjugate and flow cytometry analysis (n=3; mean ± SD). P-values were determined using Student’s t-test (***=p≤0.001, **=p≤0.01, *=p≤0.05, n.s.=p>0.05).

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Supplementary Figure 5: Functional impact of ATP6AP1 or ATP6AP2 silencing on the assembly of the V-ATPase complex, autophagy, cell viability, cellular migration and anchorage independent growth, and susceptibility to pharmacologic inhibition. (a) Western blot analysis of ATP6V1A and ATP6V0D expression in the membrane (M) and cytosolic (C) fractions of immortalized Schwann cells and HEK293 cells with stable short-hairpin (sh)RNA 10

silencing of ATP6AP1 or ATP6AP2, or non-targeting control shRNA. MEK1/2 and NRG1 were used as markers of the cytosolic and membrane fractions, respectively. Quantification of ATP6V1A membrane to cytosolic ratio (top), a surrogate of V-ATPase assembly, and total ATP6V0D1 and ATP6V1A expression (bottom) are shown (n=6; mean ± SD). (b) Western blot analysis of LC3B in immortalized Schwann cells and HEK293 cells at baseline conditions and following treatment with the Bafilomycin-1A. Whole cell lysates from immortalized Schwann cells (left) and HEK293 cells (right) with stable silencing of ATP6AP1 or ATP6AP2, and non-targeting controls were immunoblotted for LC3B following autophagy induction with Bafilomycin-1A or EtOH (vehicle control). Quantification LC3B-II (arrowheads)/tubulin ratios is depicted relative to control cells (Immortalized Schwann cells, n=5; HEK293 cells, n=4). (c) Cell proliferation assay of immortalized Schwann cells and HEK293 cells with stable ATP6AP1 or ATP6AP2 silencing over a period of 7 days (n=3, mean ± SD). (d) Cell proliferation assay of immortalized Schwann cells and HEK293 cells with single silencing of ATP6AP1 short-interfering RNA (siRNA, ATP6AP1) or ATP6AP2 (shRNA ATP6AP2), combined silencing of ATP6AP1 and ATP6AP2 (siRNA ATP6AP1 + shRNA ATP6AP2) or control (shRNA Control + siRNA Control) over a period of 3 days (n=3, mean ± SD). (e) Cell viability assay of immortalized Schwann cells and HEK293 cells with stable silencing of ATP6AP1 or ATP6AP2 with validated shRNAs, or control shRNA following treatment with different concentrations of Nethylmaleimide (NEM) or control (DMSO) for 72 hours (n=5; mean ± SD). (f) Wound healing assay of primary Schwann cells following transfection with 2 individual siRNA oligonucleotides targeting ATP6AP1 or ATP6AP2 or non-targeting control siRNAs (n=3; mean ± SD). Wound area was quantified using ImageJ at 0 hours and 16 hours, and the percent of wound healed after 16 hours was determined (mean ± SD). (g) Soft agar colony formation assay of immortalized Schwann cells and HEK293 cells with stable silencing of ATP6AP1, ATP6AP2 or non-targeting control (Schwann cells, n=4; HEK293 cells, n=6; mean ± SD). Quantification of average colony size is shown. (h) Wound healing assay of immortalized Schwann cells with stable silencing of ATP6AP1, ATP6AP2 or non-targeting control, following treatment with the indicated concentrations of PD166285, PP2, CAS285986-31-4 or vehicle (DMSO). Quantification of the percent of wound healed after 16 hours is shown (n=3; mean ± SD). P-values were determined using Student’s t-test (***=p≤0.001, **=p≤0.01, *=p≤0.05, n.s.=p>0.05). CAS, CAS285986-31-4.

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Supplementary Figure 6: Unprocessed images of western blots. Unprocessed images of scanned immunoblots shown in (a) Supplementary Figure 4d, (b) Supplementary Figure 3b and (c) Supplementary Figure 4a of the manuscript are provided. Molecular weight ladders are indicated by an asterisk (*).

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Supplementary Figure 7: Unprocessed images of western blots. Unprocessed images of scanned immunoblots shown in (a) Supplementary Figure 4c, (b) Supplementary Figure 5a and (c) Supplementary Figure 5b of the manuscript are provided. Molecular weight ladders are indicated by an asterisk (*).

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Supplementary Figure 8: Depiction of gating strategies employed for flow cytometry assays. Sequential plots illustrating the gating strategies used in (a) Supplementary Figure 4h-4i and (b) Figure 5c and Supplementary Figure 4g of the manuscript are provided.

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Supplementary Table 1 Page 1

Supplementary Table 1: Clinicopathologic and sequencing information of the granular cell tumors included in this study.

Case ID

Sex

Anatomic location

Mitosis >2

Spindling

Increased nuclear/cytoplasmic ratio

Vesicular nuclei and prominent nucleoli

Nuclear pleomorphism

Necrosis

Fanburg-Smith histologic classification

DNA sequencing platform

RNA sequencing

ATP6AP1 mutation

ATP6AP2 mutation

Mutation type

Validation by Sanger sequencing and/ or repeat targeted capture

GCT1 GCT2 GCT3 GCT4 GCT5 GCT6 GCT8 GCT9 GCT10 GCT11 GCT12 GCT13 GCT14 GCT15 GCT16 GCT18 GCT20 GCT21 GCT22 GCT23 GCT25 GCT28 GCT32 GCT35 GCT36 GCT37 GCT38 GCT39 GCT40 GCT41 GCT42 GCT43 GCT44 GCT45 GCT46 GCT47 GCT48 GCT49 GCT52 GCT53 GCT54 GCT55 GCT57 GCT58 GCT59 GCT60 GCT61 GCT62 GCT63 GCT64 GCT65 GCT66 GCT67 GCT68 GCT69 GCT70 GCT71 GCT72 GCT73 GCT74 GCT75 GCT78 GCT79 GCT80 GCT81 GCT82 GCT83 GCT84 GCT85

M F F M F F F F F F M M F F F F F F F F F F F F F M F F F F M F F F F F F M F F F F F F M F F F M F F M F F F F F F F F M F F F F F F F F

Soft tissue Gastrointestinal tract Skin Soft tissue Soft tissue Bladder Soft tissue Gastrointestinal tract Gastrointestinal tract Skin Skin Soft tissue Soft tissue Soft tissue Soft tissue Skin Soft tissue Skin Soft tissue Skin Breast Gastrointestinal tract Skin Lung Soft tissue Skin Breast Soft tissue Gastrointestinal tract Tongue Soft tissue Gastrointestinal tract Soft tissue Gastrointestinal tract Gastrointestinal tract Breast Breast Gastrointestinal tract Tongue Breast Tongue Skin Skin Skin Skin Gastrointestinal tract Skin Skin Skin Skin Skin Skin Skin Skin Skin Skin Skin Soft tissue Skin Skin Skin Skin Skin Skin Breast Skin Skin Skin Gastrointestinal tract

No Yes No No No Yes No No No No No No No No No No No No No No No No No No No Yes No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No Yes No No No No No No No No No

Yes Yes No No No Yes No No Yes No No No No Yes No No No No No No No No No No No Yes Yes No Yes Yes No Yes No Yes Yes No No Yes No No No No No No No Yes No Yes No No No No No No No No No Yes No Yes Yes No No No Yes No No Yes Yes

No Yes No No No Yes No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No Yes No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No Yes Yes

Yes Yes No No No Yes No No No No Yes No No Yes No No No No No No Yes No No No No No No No No No No No No No Yes Yes Yes Yes No No No No No No No No No No No No No No Yes No Yes No No No Yes No No No No No Yes Yes No No No

No Yes No No No Yes No No No No No No No No No No No No No No Yes No Yes No No No No Yes No No No No No No No Yes Yes Yes No No No No No No No No No Yes No No No No No No No No No Yes No No No No No No No No No Yes No

No Yes No No No Yes No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No

Atypical Malignant Benign Benign Benign Malignant Benign Benign Atypical Benign Atypical Benign Benign Atypical Benign Benign Benign Benign Benign Benign Atypical Benign Atypical Benign Benign Atypical Atypical Atypical Atypical Atypical Benign Atypical Benign Atypical Atypical Atypical Malignant Malignant Benign Benign Benign Benign Benign Benign Benign Atypical Benign Atypical Benign Benign Benign Benign Atypical Benign Atypical Benign Benign Atypical Atypical Atypical Atypical Benign Benign Benign Atypical Atypical Benign Malignant Atypical

WES WES WES WES WES WES WES WES WES WES WES WES WES WES WES Targeted capture WES Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture

Yes Yes No Yes Yes No No No Yes Yes Yes Yes No Yes Yes No No No No Yes No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No No

WT p.L345Qfs*32 p.Q293* WT p.T388Sfs*7 p.W138* WT WT p.L377* WT WT p.L430Cfs*17 WT p.Q403Rfs*5 p.W393* WT WT p.Q401Rfs*7 p.Y147* WT p.S368del p.H67Sfs*11 p.L82Wfs*16 WT p.W50* WT WT p.F274Sfs*12 WT p.X324_splice p.X76_splice p.X82_splice p.F274del p.L331Pfs*46 WT p.W21Vfs*29 p.Q44Rfs*39 p.S382Gfs*72 WT p.P46Afs*5 WT p.G425Rfs*33 WT p.F422Sfs*10 WT p.Q403Pfs*3 p.L72Cfs*7 WT p.F356Sfs*22 p.X200_splice p.W427* p.N296Ifs*4 p.Y414_S416del WT WT p.S335_E343del p.W427Hfs*22 p.W57* p.X308_splice WT p.S129Pfs*16 p.A354Lfs*20 p.N111Tfs*10 WT p.R87Sfs*6 p.S70Afs*9 p.Y414Sfs*25 WT WT

p.Q188* WT WT p.I313Dfs*22 WT WT WT p.P90Qfs*48 WT WT WT WT WT WT WT p.Q160* WT WT WT WT WT WT WT WT WT WT p.R31* WT WT WT WT WT WT WT WT WT WT WT WT WT p.D107Vfs*29 WT p.N258Sfs*47 WT p.L68Cfs*11 WT WT WT WT WT WT WT WT WT WT WT WT WT WT WT WT WT WT WT WT WT WT WT WT

Truncating SNV Frame-shift indel Truncating SNV Frame-shift indel Frame-shift indel Truncating SNV N/A Frame-shift indel Frame-shift indel N/A N/A Frame-shift indel N/A Frame-shift indel Truncating SNV Truncating SNV N/A Frame-shift indel Truncating SNV N/A In-frame indel Frame-shift indel Frame-shift indel N/A Truncating SNV N/A Truncating SNV Frame-shift indel N/A Splice site SNV Splice site SNV Splice site SNV In-frame indel Frame-shift indel N/A Frame-shift indel Frame-shift indel Frame-shift indel N/A Frame-shift indel Frame-shift indel Frame-shift indel Frame-shift indel Frame-shift indel Frame-shift indel Frame-shift indel Frame-shift indel N/A Frame-shift indel Splice site SNV Truncating SNV Frame-shift indel In-frame indel N/A N/A In-frame indel Frame-shift indel Truncating SNV Splice site SNV N/A Frame-shift indel Frame-shift indel Frame-shift indel N/A Frame-shift indel Frame-shift indel Frame-shift indel N/A N/A

ATP6AP2 (p.Q188*) ATP6AP1 (p.L345Qfs*32) ATP6AP1 (p.Q293*) ATP6AP2 (p.I313Dfs*22) ATP6AP1 (p.T388Sfs*7) ATP6AP1 (p.W138*) N/A ATP6AP2 (p.P90Qfs*48) ATP6AP1 (p.L377*) N/A N/A ATP6AP1 (p.L430Cfs*17) N/A ATP6AP1 (p.Q403Rfs*5) ATP6AP1 (p.W393*) ATP6AP2 (p.Q160*) N/A ATP6AP1 (p.Q401Rfs*7) ATP6AP1 (p.Y147*) N/A ATP6AP1 (p.S368del) ATP6AP1 (p.H67Sfs*11) ATP6AP1 (p.L82Wfs*16) N/A ATP6AP1 (p.W50*) N/A ATP6AP2 (p.R31*) ATP6AP1 (p.F274Sfs*12) N/A ATP6AP1 (p.X324_splice) ATP6AP1 (p.X76_splice) ATP6AP1 (p.X82_splice) ATP6AP1 (p.F274del) ATP6AP1 (p.L331Pfs*46) N/A ATP6AP1 (p.W21Vfs*29) ATP6AP1 (p.Q44Rfs*39) ATP6AP1 (p.S382Gfs*72) N/A ATP6AP1 (p.P46Afs*5) ATP6AP2 (p.D107Vfs*29) ATP6AP1 (p.G425Rfs*33) ATP6AP2 (p.N258Sfs*47) ATP6AP1 (p.F422Sfs*10) ATP6AP2 (p.L68Cfs*11) ATP6AP1 (p.Q403Pfs*3) ATP6AP1 (p.L72Cfs*7) N/A ATP6AP1 (p.F356Sfs*22) ATP6AP1 (p.X200_splice) ATP6AP1 (p.W427*) ATP6AP1 (p.N296Ifs*4) ATP6AP1 (p.Y414_S416del) N/A N/A ATP6AP1 (p.S335_E343del) ATP6AP1 (p.W427Hfs*22) ATP6AP1 (p.W57*) ATP6AP1 (p.X308_splice) N/A ATP6AP1 (p.S129Pfs*16) ATP6AP1 (p.A354Lfs*20) ATP6AP1 (p.N111Tfs*10) N/A ATP6AP1 (p.R87Sfs*6) ATP6AP1 (p.S70Afs*9) ATP6AP1 (p.Y414Sfs*25) N/A N/A

Supplementary Table 1 Page 2 GCT86 F Gastrointestinal tract No Yes Yes GCT87 F Skin No No No GCT88 F Skin No No No GCT89 F Skin Yes Yes No GCT90 F Skin No No No GCT91 F Skin No No No GCT92 F Gastrointestinal tract No Yes No GCT93 F Parotid gland No No No GCT95 M Tongue No No No GCT96 F Skin No No No GCT97 M Skin No No Yes GCT98 F Skin No No No GCT99 F Tongue No Yes No F, female; M, male; N/A, not applicable; WES, whole-exome sequencing; WT, wild-type

No No Yes Yes No Yes No No No No No No No

No No Yes Yes No No No No No No No No No

No No No No No No No No No No No No No

Atypical Benign Atypical Malignant Benign Atypical Atypical Benign Benign Benign Atypical Benign Atypical

Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture WES Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture Targeted capture

No No No No No No No No No No No No No

p.R315* WT p.V48Tfs*26 p.X200_splice WT p.S382Vfs*14 p.W302* WT WT WT WT p.M395del p.A135Pfs*10

WT WT WT WT WT WT WT WT WT WT p.X95_splice WT WT

Truncating SNV N/A Frame-shift indel Splice site SNV N/A Frame-shift indel Truncating SNV N/A N/A N/A Splice site SNV In-frame indel Frame-shift indel

ATP6AP1 (p.R315*) N/A ATP6AP1 (p.V48Tfs*26) ATP6AP1 (p.X200_splice) N/A ATP6AP1 (p.S382Vfs*14) ATP6AP1 (p.W302*) N/A N/A N/A ATP6AP2 (p.X95_splice) ATP6AP1 (p.M395del) ATP6AP1 (p.A135Pfs*10)

Supplementary Table 2: List of fusion genes and/or readthroughs identified by RNA-sequencing analysis of granular cell tumors. Sample

Gene 5'

Gene 3'

Mapping 5'

Mapping 3'

Total reads

Spanning reads

In-frame

Read-through

GCT15T GCT23T GCT2T GCT1T GCT23T GCT23T

DHTKD1 ZNF841 FAM214A RRP7B RRP7B 7SK/IL1RAP

SEC61A2 ZNF432 ARPP19 KCTD19 KCTD19 KCTD19

chr10:12162267 chr19:52592189 chr15:52876940 chr22:42961107 chr22:42961107 chr3:190360198

chr10:12175239 chr19:52550314 chr15:52849419 chr16:67355624 chr16:67355624 chr16:67355618

4 17 4 9 9 8

2 5 2 4 4 5

No Yes No No No No

No No Yes No No Yes

Driver Probability (Oncofuse) 0.0168 0.9737 0.0416 0.0471 0.0471 0.1134

Supplementary Table 3: Sequencing statistics of the granular cell tumors subjected to whole-exome sequencing. Case GCT1 GCT2 GCT3 GCT4 GCT5 GCT6 GCT8 GCT9 GCT10 GCT11 GCT12 GCT13 GCT14 GCT15 GCT16 GCT20 GCT92

Tissue Type (Sample ID)

Total Reads

Tumor (GCT1T) Normal (GCT1N) Tumor (GCT2T) Normal (GCT2N) Tumor (GCT3T) Normal (GCT3N) Tumor (GCT4T) Normal (GCT4N) Tumor (GCT5T) Normal (GCT5N4) Tumor (GCT6T) Normal (GCT6N) Tumor (GCT8T) Normal (GCT8N) Tumor (GCT9T) Normal (GCT9N) Tumor (GCT10T) Normal (GCT10N) Tumor (GCT11T3) Normal (GCT11N3) Tumor (GCT12T3) Normal (GCT12N3) Tumor (GCT13T2) Normal (GCT13N2) Tumor (GCT14T2) Normal (GCT14N2) Tumor (GCT15T2) Normal (GCT15N2) Tumor (GCT16T2) Normal (GCT16N2) Tumor (GCT20T2) Normal (GCT20N2) Tumor (GCT92T) Normal (GCT92N)

85,063,839 77,362,194 128,101,984 162,779,641 79,728,767 65,949,245 109,135,641 86,170,100 122,861,678 91,559,376 109,400,409 75,155,499 123,061,507 78,553,308 99,405,995 96,023,264 129,047,709 77,971,965 105,270,395 94,293,572 117,359,514 109,533,044 103,400,606 93,364,190 102,990,531 107,306,446 157,583,873 102,265,966 113,352,436 95,610,219 108,812,267 75,437,421 79,293,291 94,268,623

Mean Target Coverage 99.21 92.60 150.61 193.52 96.03 73.98 114.36 93.40 157.33 78.83 125.72 86.84 151.53 94.83 117.89 117.44 111.21 92.88 102.91 72.85 106.59 115.10 98.60 86.17 75.37 96.19 118.84 86.67 115.10 82.69 119.65 66.22 91.63 118.34

Target Bases 2X 99.63% 99.65% 99.71% 99.81% 99.78% 99.71% 99.55% 99.67% 99.78% 99.58% 99.78% 99.74% 99.79% 99.74% 99.77% 99.79% 99.78% 99.77% 99.68% 99.48% 99.63% 99.66% 99.47% 99.43% 99.40% 99.56% 99.67% 99.61% 99.71% 99.56% 99.57% 99.33% 99.69% 99.64%

Target Bases 50X 83.01% 79.95% 90.05% 92.35% 81.29% 71.35% 87.29% 81.55% 91.56% 72.69% 78.74% 66.29% 90.63% 76.46% 85.17% 79.47% 76.88% 69.11% 75.61% 70.98% 81.15% 81.62% 83.17% 78.04% 72.51% 68.84% 84.52% 60.47% 77.41% 72.11% 87.08% 65.43% 78.34% 86.88%

Target Bases 100X 43.44% 38.34% 65.69% 75.98% 40.22% 22.44% 51.90% 38.69% 69.28% 27.14% 49.44% 31.43% 66.16% 36.71% 51.96% 46.40% 43.78% 34.64% 40.05% 22.06% 45.35% 48.59% 44.71% 34.38% 24.46% 36.82% 51.95% 31.52% 45.35% 30.48% 56.94% 16.04% 36.57% 55.27%


Supplementary Table 4: List of non-synonymous somatic mutations identified in granular cell tumors by whole-exome sequencing.

Sample

Gene

Amino Acid Change

Chromosome

Position

Reference Allele

Alternate Allele

Effect

Tumor MAF

Normal MAF

GCT10T GCT10T GCT10T GCT10T GCT10T GCT10T GCT11T3 GCT11T3 GCT11T3 GCT11T3 GCT11T3 GCT11T3 GCT11T3 GCT11T3 GCT11T3 GCT11T3 GCT11T3 GCT11T3 GCT11T3 GCT11T3 GCT12T3 GCT12T3 GCT12T3 GCT12T3 GCT12T3 GCT12T3 GCT12T3 GCT12T3 GCT12T3 GCT12T3 GCT12T3 GCT13T2 GCT13T2 GCT13T2 GCT13T2 GCT13T2 GCT13T2 GCT13T2 GCT13T2 GCT13T2 GCT13T2 GCT13T2 GCT13T2 GCT13T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT14T2 GCT15T2 GCT15T2 GCT15T2 GCT15T2 GCT15T2 GCT15T2 GCT15T2 GCT15T2 GCT15T2 GCT15T2 GCT15T2 GCT15T2 GCT15T2

ATP6AP1 TPRXL NAMPTL HSPB8 ATP5EP2 CCDC40 IK ZC3H3 FAM155A UBE2J2 PLXND1 SMC4 FAM71B DENND1A OR5AS1 FAT3 AHNAK2 ITGB1BP2 FRMPD3 NAALAD2 RHBG KCTD16 GRM1 SRRM3 GID4 LMAN1 TTC13 PVRIG MAP3K9 SEZ6L ZRANB2 ASXL2 ATP6AP1 RMDN3 NANOS1 BPTF NAP1L2 DNAH14 SEMA3G GIMAP1 ZNF317 CYP2A6 DDX53 SLC9A2 KCNN3 IFNA2 LMAN1 COBLL1 TTK EP400 HOXB3 ALS2CL GOLIM4 FAM8A1 NFE2L3 DAB2IP IRF2BPL EIF5 ALG1 DNM3 NEB SNCAIP C7orf55-LUC7L2 RIMBP2 NAGLU P2RX6 PABPC3 NUTM1 ATP6AP1 GTF3C3 SMAP1 MYO6 FLCN RXRB IRX5 SLC9A5 MED15 ZBED6 GFPT1

p.L377* p.S212P p.V77F p.N184S p.V22A p.T931M p.E94Afs*21 p.S881del p.Q86del p.I130V p.Y978C p.R932K p.R141C p.R448H p.L29F p.V547F p.T1283M p.T232N p.R1268W p.X678_splice p.R425Dfs*35 p.A384Lfs*20 p.P842Lfs*76 p.G326Afs*323 p.D81Tfs*61 p.E305Rfs*20 p.C11del p.R95H p.A39E p.T405M p.R33* p.A636Pfs*135 p.L430Cfs*17 p.T386Nfs*7 p.D112del p.E148del p.E221del p.P1095L p.P97L p.V13F p.G424R p.F384Y p.A43T p.R480* p.P112Lfs*64 p.I170Tfs*2 p.E305Rfs*22 p.L907Ffs*25 p.R854Kfs*11 p.H31Pfs*34 p.Q34Pfs*68 p.L89del p.Q453del p.R115del p.D229del p.A89del p.A164del p.P185del p.L20del p.I667L p.R2691C p.G480R p.S2L p.R119W p.G506R p.V339I p.F335Lfs*19 p.R345Afs*24 p.Q403Rfs*5 p.T361Nfs*11 p.E173Gfs*19 p.Q918Tfs*24 p.H429Pfs*27 p.A52del p.A78del p.E708del p.Q188del p.K121Q p.R452C

23 3 10 12 13 17 5 8 13 1 3 3 5 9 11 11 14 23 23 11 1 5 6 7 17 18 1 7 14 22 1 2 23 15 10 17 23 1 3 7 19 19 23 2 1 9 18 2 6 12 17 3 3 6 7 9 14 14 16 1 2 5 7 12 17 22 13 15 23 2 6 6 17 6 16 16 22 1 2

153663775 14106310 36812934 119631623 28519461 78063643 140032592 144522386 108518686 1192446 129291689 160146730 156592759 126212985 55797981 92086917 105417940 70524092 106844972 89916178 156354347 143853530 146720698 75896717 17943014 57013193 231114542 99817902 71275773 26695001 71544351 25967216 153664111 41029893 120789634 65822266 72433663 225270398 52476624 150416172 9271591 41351209 23018301 103310885 154842105 21384819 57013193 165551295 80751896 132445252 46629736 46729621 167747641 17600982 26217668 124461707 77493647 103804756 5121897 172348263 152499753 121780273 139045012 130935838 40695540 21380330 25671332 34646682 153664029 197649613 71508369 76599857 17119708 33168096 54965326 67300016 20918816 203767011 69565158

GC T C A T C TGA TGAG TCTG T T G G C G G G C C T TC CA GC CG CG C AAGC G G C G CT GC G GGAC CGAG GTCC C G G G A G C AG GA CT C G G T CGCA CCTG CCGG AATG GCGC AGCG ACAC CGCT A G G C G G G CA GC TC G G G T ACCG GGCC TGAG ACAG A G

G C A G C T T T T C C A A T C T A A T A T C G C C CT A A T T A C G GT G C G T A T A T A T A G C CA GA GC TG C C C A G A A C C A A T A A A C G T GT GA GA TG A G T A C A

Frame_Shift_Del Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Frame_Shift_Del In_Frame_Del In_Frame_Del Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Splice_Site Frame_Shift_Del Frame_Shift_Del Frame_Shift_Del Frame_Shift_Del Frame_Shift_Del Frame_Shift_Ins In_Frame_Del Missense_Mutation Missense_Mutation Missense_Mutation Nonsense_Mutation Frame_Shift_Del Frame_Shift_Del Frame_Shift_Ins In_Frame_Del In_Frame_Del In_Frame_Del Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Nonsense_Mutation Frame_Shift_Del Frame_Shift_Del Frame_Shift_Del Frame_Shift_Ins Frame_Shift_Ins Frame_Shift_Ins Frame_Shift_Ins In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Frame_Shift_Del Frame_Shift_Del Frame_Shift_Del Frame_Shift_Ins Frame_Shift_Ins Frame_Shift_Ins Frame_Shift_Ins In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del Missense_Mutation Missense_Mutation

0.333333333 0.090909091 0.114285714 0.069767442 0.072072072 0.246575342 0.157894737 0.173913043 0.086956522 0.104477612 0.147058824 0.070175439 0.134020619 0.204545455 0.192307692 0.150943396 0.266666667 0.131578947 0.203488372 0.098360656 0.096774194 0.102564103 0.118421053 0.111111111 0.1 0.08 0.117647059 0.105263158 0.115384615 0.104166667 0.166666667 0.102362205 0.4 0.083333333 0.142857143 0.081081081 0.133333333 0.1 0.073170732 0.181818182 0.118421053 0.166666667 0.076923077 0.27027027 0.125 0.161290323 0.125 0.185185185 0.178571429 0.125 0.129032258 0.095238095 0.108108108 0.121212121 0.105263158 0.176470588 0.25 0.066666667 0.086956522 0.083333333 0.088235294 0.176470588 0.096774194 0.083333333 0.176470588 0.09375 0.117647059 0.090909091 0.206751055 0.090909091 0.097560976 0.089285714 0.102564103 0.125 0.096774194 0.114285714 0.151515152 0.095652174 0.056179775

0 0 0 0 0 0 0 0 0 0 0 0 0.016949153 0 0 0 0 0 0 0.016666667 0 0 0.010526316 0 0 0 0 0 0 0 0 0 0.012987013 0 0 0 0 0 0 0 0.02173913 0.03125 0 0 0 0 0 0 0 0 0 0 0 0.006849315 0 0.01754386 0 0 0 0 0 0 0 0.011494253 0 0 0 0 0.004716981 0 0 0 0 0 0 0 0 0 0

Tumor Depth Normal Depth

270 44 35 43 111 73 19 23 23 67 102 57 97 44 52 53 30 76 172 61 31 39 76 18 20 25 17 38 26 48 18 127 80 24 14 37 45 30 41 55 76 30 52 37 16 31 16 27 28 16 31 21 37 33 19 17 8 30 23 60 34 17 31 36 17 32 17 22 237 33 41 56 39 24 31 35 33 115 89

232 50 44 35 90 55 12 8 9 33 57 52 59 45 58 62 19 49 63 60 33 39 95 21 22 23 23 32 41 59 16 91 77 28 10 25 41 31 17 39 46 32 42 57 70 10 22 15 8 16 123 38 55 146 13 57 13 53 41 19 30 20 56 87 36 109 14 18 212 16 10 22 40 27 31 24 21 42 46

Cancer Cell Fraction

Clonal Probability

95% Confidence Interval High

95% Confidence Interval Low

Clonality

Exac Score

1 0.54 0.68 0.42 0.43 1 1 1 0.76 0.91 1 0.61 1 1 1 1 1 1 1 0.86 0.67 0.71 0.82 0.88 0.79 0.55 0.81 0.83 0.8 0.72 1 1 1 0.83 1 0.81 1 1 0.73 1 1 1 0.77 1 1 1 1 1 1 1 1 0.79 0.89 1 0.87 1 1 0.55 0.72 0.69 0.73 1 0.8 0.69 1 0.77 1 0.95 1 0.95 1 0.94 1 1 1 1 1 1 0.59

0.97403 0.283 0.4316 0.16482 0.02192 0.85751 0.75421 0.79972 0.5782 0.6792 0.84705 0.45409 0.8147 0.90376 0.89942 0.81593 0.90179 0.87407 0.91957 0.64391 0.44692 0.46824 0.55849 0.5481 0.51601 0.38416 0.52527 0.54559 0.52311 0.47209 0.64853 0.77873 0.54448 0.61868 0.73442 0.61462 0.80663 0.68297 0.57462 0.9156 0.79874 0.84383 0.59542 0.86763 0.65715 0.78222 0.65715 0.81738 0.80873 0.65715 0.70191 0.58392 0.64163 0.68188 0.61316 0.76041 0.75984 0.45213 0.55474 0.51312 0.55579 0.76041 0.59264 0.5307 0.76041 0.58045 0.69156 0.63521 0.91221 0.65037 0.68612 0.66634 0.70188 0.73468 0.66915 0.73359 0.82199 0.7441 0.39519

1 0.96047682 0.978386113 0.928331337 0.801573918 1 0.989909629 1 0.981211758 0.988751121 1 0.972117205 1 1 1 1 1 1 1 0.98682284 0.978124025 0.980069696 0.986197096 0.983721653 0.982074013 0.971689826 0.982564098 0.9850921 0.98334483 0.980503969 0.988693968 1 1 0.982843023 0.987914254 0.983588241 1 0.986999958 0.981063602 1 1 1 0.982879527 1 0.9855833 1 0.9855833 1 1 0.9855833 0.989147329 0.981940849 0.986514294 0.988356998 0.98353568 1 0.989554337 0.971626987 0.98012725 0.978240295 0.98098742 1 0.983341195 0.979174662 1 0.982603077 0.98699784 0.9846676 1 0.986397535 0.988573474 0.988148869 0.989173688 0.989525995 0.987197374 1 1 1 0.966508135

0.936201946 0.210705647 0.253973488 0.144339435 0.219054293 0.707663136 0.303173376 0.375851262 0.177179513 0.399028588 0.632127852 0.230663687 0.580422007 0.588003847 0.602363549 0.509269539 0.592758526 0.583555682 0.860156443 0.358373065 0.213207815 0.260006725 0.413339347 0.191652668 0.181953057 0.14653981 0.185156693 0.288350817 0.238880762 0.293506996 0.286711032 0.539572495 0.867169355 0.185456693 0.22757665 0.238524679 0.446692097 0.26598345 0.224093738 0.612230092 0.509267992 0.437275847 0.272083844 0.656863697 0.205060083 0.40939742 0.205060083 0.429342127 0.42425105 0.205060083 0.328786045 0.181114562 0.299945221 0.318918512 0.190359329 0.309672904 0.250182753 0.145556848 0.172361845 0.282164783 0.224646815 0.309672904 0.237808951 0.216361068 0.309672904 0.2333184 0.217444822 0.197305375 0.894948129 0.260111102 0.320408847 0.345105891 0.328045674 0.296720575 0.267844095 0.343780965 0.430977224 0.50395304 0.247557263

Clonal Subclonal Subclonal Subclonal Subclonal Clonal Clonal Clonal Clonal Clonal Clonal Subclonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Subclonal Subclonal Clonal Clonal Clonal Subclonal Clonal Clonal Clonal Subclonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Subclonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Subclonal

. . . . . 1.89E-05 . . . . . . 5.65E-05 9.42E-06 9.43E-06 . 5.50E-05 . . . . 9.70E-04 . . . 1.13E-04 4.63E-04 9.75E-06 . 5.65E-05 . . . . . . . 5.25E-05 9.42E-06 . . . . . . . . . . . . . 0.002759 . 2.83E-05 . . . 9.48E-06 . 4.73E-05 . . 9.42E-06 . . . . . . . . . . 1.49E-04 0.009918 . . 9.42E-06


GCT15T2 GCT15T2 GCT15T2 GCT15T2 GCT15T2 GCT16T2 GCT16T2 GCT16T2 GCT16T2 GCT16T2 GCT16T2 GCT16T2 GCT16T2 GCT16T2 GCT16T2 GCT16T2 GCT16T2 GCT1T GCT1T GCT1T GCT1T GCT1T GCT1T GCT1T GCT1T GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT20T2 GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT2T GCT3T GCT3T GCT3T GCT3T GCT3T GCT3T GCT3T GCT3T GCT3T GCT3T GCT3T GCT4T GCT4T GCT4T GCT4T GCT4T GCT4T GCT4T GCT4T GCT4T GCT4T GCT4T GCT5T GCT5T GCT5T

RP11-766F14.2 FOPNL FITM2 TSPEAR CD36 FRAS1 KCNN3 YEATS2 AARD FOXB2 SFMBT2 ZIC2 ERN1 ABCG5 MUC2 FAT3 ATP6AP1 KMT2C SYT8 ANKRD11 ZNF419 NRAS LY9 ATP6AP2 RNF17 GRINA LCORL KRTAP5-7 AMOT CASZ1 CSF3R CHDH GIN1 RPP40 ADCY8 TOPORS SPIN1 OR1B1 CDC42BPG ZFHX2 HSPA2 KIAA1199 USP36 COL18A1 ZNF175 ATP6AP1 SLC35F3 KCNJ3 HNRNPDL SIL1 PCDHA6 TRIM7 WRNIP1 BNC2 MARK2 PHGR1 RFFL CACNG1 PITPNC1 CLASRP C20orf78 RBMXL3 PTCHD2 DNAH5 RDH10 EGFL7 NAT10 TENM4 RBBP8NL TTC3 KIAA1210 ANKRD16 ATP6AP1 ATP6AP2 TPRXL A4GNT KIAA0947 COPS6 CEP78 UVRAG KBTBD6 PYGL FANCA RTTN PARP12 SHANK1 ATP6AP1

p.T444K p.R40C p.G232R p.T270M p.S1743Pfs*10 p.Q41del p.G814del p.A88del p.A234del p.V452_E457del p.A33del p.L10del p.P161L p.T1758I p.V611A p.W393* p.Q419R p.R75H p.G1630R p.T255A p.G12D p.C320* p.Q188* p.X1299_splice p.F109Lfs*18 p.A22del p.G27_S33del p.A926del p.S783L p.R583H p.A79T p.R20Q p.P304L p.T1167M p.S1032L p.R191C p.T285I p.P380L p.S2034Y p.T207N p.S805N p.K956R p.P1155S p.X24_splice p.L345Qfs*32 p.V189I p.M458L p.S17A p.N122S p.P17Q p.L361F p.R211P p.R536Q p.D322N p.H37P p.E313D p.L197F p.E201K p.R431C p.L73Q p.C662R p.T448I p.V3173M p.A337T p.R112Q p.R966L p.H1464Y p.A437V p.W848C p.R523Q p.Q154* p.Q293* p.W312fs p.S150T p.Y271C p.N1423T p.H44R p.T645I p.D658G p.T403K p.E731K p.S1088F p.L1708I p.G19Afs*16 p.R493Gfs*70 p.T388Sfs*7

4 16 20 21 7 4 1 3 8 9 10 13 17 2 11 11 23 7 11 16 19 1 1 23 13 8 4 11 23 1 1 3 5 6 8 9 9 9 11 14 14 15 17 21 19 23 1 2 4 5 5 5 6 9 11 15 17 17 17 19 20 23 1 5 8 9 11 11 20 21 23 10 23 23 3 3 5 7 9 11 13 14 16 18 7 19 23

100574475 G 15977973 G 42935360 C 45948448 G 80293813 G 79359731 CT 154842330 TTGC 183493743 CGGA 117950724 AGGC 79635238 TGGC 7247850 ACATCAACAATG 100634393 CGCG 62207359 TCAG 44058927 G 1093454 C 92087110 T 153663826 G 151960144 T 1856613 G 89348062 C 58004685 A 115258747 C 160784439 C 40457960 C 25436850 G 145065711 G 18023309 AGCG 71238370 GTGGCTCCGGCT 112022604 GGCA 10713766 G 36933539 C 53857801 C 102444353 C 4995493 G 131792892 G 32541428 G 91083502 C 125390961 G 64605621 G 23993050 G 65008187 C 81218090 G 76798561 T 46925102 C 52076655 G 153663681 CTCGA 234367444 G 155711691 A 83350795 A 138378397 T 140207726 C 180622621 G 2766488 G 16436585 C 63668327 G 40648365 A 33339140 C 65052307 C 65665762 G 45567770 C 18790658 A 114425988 T 11574473 C 13770946 C 74235254 G 139564387 G 34165003 G 78413268 G 60989097 G 38525381 G 118223625 C 5929885 G 153662746 C 40464890 GATAAT 14106124 T 137843317 T 5463715 A 99686967 A 80881443 C 75852330 A 41705440 G 51375660 C 89815152 G 67721430 G 139762591 GC 51206832 CG 153663802 TGGCC

T A T A GGTAA C T C A T T C T A T C A C A T G T A T T GC A A G A T T T A A A T A A T A A C T A C A T C C A A C T A C G T A T T C T T A A T A A T T A T G A C C G T G T T A T G C T

Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Nonsense_Mutation Frame_Shift_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del Missense_Mutation Missense_Mutation Missense_Mutation Nonsense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation_Hotspo Nonsense_Mutation Nonsense_Mutation Splice_Site Frame_Shift_Ins In_Frame_Del In_Frame_Del In_Frame_Del Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Splice_Site Frame_Shift_Del Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Nonsense_Mutation Nonsense_Mutation Frame_Shift_Del Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Frame_Shift_Del Frame_Shift_Del Frame_Shift_Del

0.108333333 0.085106383 0.076923077 0.096774194 0.387755102 0.131147541 0.107142857 0.24 0.121212121 0.095238095 0.06779661 0.114285714 0.166666667 0.063492063 0.068965517 0.113207547 0.210526316 0.108108108 0.042105263 0.051612903 0.109589041 0.273972603 0.162790698 0.7 0.166666667 0.12962963 0.086956522 0.117647059 0.0625 0.078431373 0.063291139 0.235294118 0.061538462 0.051948052 0.149253731 0.126984127 0.054347826 0.053763441 0.078947368 0.075268817 0.072463768 0.052083333 0.102564103 0.09375 0.095238095 0.380319149 0.295566502 0.301886792 0.42 0.273584906 0.352941176 0.324840764 0.160493827 0.301724138 0.28 0.181818182 0.339869281 0.285714286 0.175925926 0.294117647 0.298342541 0.08086785 0.140495868 0.178571429 0.15625 0.1 0.159090909 0.126582278 0.112359551 0.191919192 0.272222222 0.132743363 0.289156627 1 0.166666667 0.260638298 0.349056604 0.251396648 0.260504202 0.365079365 0.052980132 0.25 0.096774194 0.253012048 0.095238095 0.090909091 0.148148148

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.020689655 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.015957447 0 0 0 0 0 0.020408163 0 0 0 0.01 0 0 0 0 0.009153318 0 0 0 0 0 0 0 0 0 0 0 0 0.052631579 0.01183432 0.017647059 0.010526316 0 0 0 0.030769231 0 0.014705882 0 0 0

120 47 104 93 49 61 56 25 33 21 59 35 12 63 87 53 247 37 95 155 73 73 86 10 18 54 23 17 32 51 79 34 65 77 134 63 92 93 38 93 138 96 39 32 42 376 203 53 50 106 85 157 81 232 225 33 306 266 216 68 181 507 121 112 64 50 44 158 89 99 180 113 83 4 42 188 212 179 119 126 151 36 62 83 21 22 270

120 22 78 92 16 58 19 23 13 13 61 21 11 30 52 48 145 10 72 168 62 71 100 10 19 25 10 12 13 21 35 10 35 83 83 39 55 66 28 56 75 61 21 18 32 431 188 32 43 94 67 270 49 172 211 54 100 422 129 89 120 437 100 93 64 28 30 123 59 82 141 68 69 7 19 169 170 95 104 130 129 65 51 68 10 11 107

1 0.89 0.81 1 1 1 0.86 1 0.97 0.76 0.54 0.91 1 0.51 0.55 0.9 1 0.61 0.24 0.29 0.62 1 0.93 1 0.95 0.87 0.58 0.79 0.48 0.53 0.42 1 0.41 0.35 1 0.85 0.36 0.36 0.53 0.5 0.49 0.35 0.69 0.63 0.64 1 1 1 1 0.99 1 1 0.58 1 1 0.66 1 1 0.64 1 1 0.37 1 1 1 0.84 1 1 0.95 1 1 1 1 1 0.56 0.87 1 1 0.87 1 0.18 0.84 0.32 0.85 1 1 1

0.80093 0.63867 0.61015 0.73383 0.05708 0.70989 0.60187 0.86294 0.63552 0.53487 0.32388 0.61352 0.67822 0.27462 0.263 0.62851 0.96375 0.40094 0.0009 0.00006 0.31685 0.89436 0.68915 0.84018 0.60833 0.54493 0.36338 0.4709 0.28479 0.23954 0.07106 0.81331 0.09475 0.03382 0.71112 0.53815 0.02298 0.02092 0.28284 0.1087 0.03358 0.01571 0.40696 0.37302 0.36413 0.89152 0.91422 0.83483 0.88353 0.83653 0.89335 0.92 0.12278 0.9267 0.8941 0.46733 0.97603 0.91337 0.01229 0.84369 0.91155 0 0.85038 0.90479 0.84332 0.65217 0.82698 0.83561 0.73806 0.92698 0.81064 0.82792 0.82316 0.32256 0.18555 0.62077 0.91439 0.87088 0.64073 0.89188 0 0.58683 0.00143 0.6017 0.71557 0.70603 0.96652

1 0.986463449 0.985462262 1 1 1 0.986817671 1 0.987877639 0.981306022 0.960812407 0.98691458 0.987604812 0.95185581 0.950259987 0.988146441 1 0.971822682 0.581616864 0.555131923 0.961612915 1 1 1 0.986504915 0.987693878 0.97384173 0.982010353 0.963994089 0.956490653 0.878766928 1 0.897703755 0.815807981 1 0.987394004 0.793185714 0.786342448 0.964063917 0.91251138 0.842611155 0.765936708 0.978670387 0.97536917 0.974740404 1 1 1 1 1 1 1 0.90085206 1 1 0.972424101 1 1 0.838925128 1 1 0.495339609 1 1 1 0.985976026 1 1 1 1 1 1 1 1 0.934722991 0.988705923 1 1 0.989547848 1 0.33351704 0.986990595 0.650356072 0.987769662 0.986101942 0.985684147 1

0.570742128 0.298171414 0.387194956 0.470865756 0.807171676 0.459848457 0.359007459 0.502498738 0.313618027 0.177979595 0.208605723 0.303773517 0.224498551 0.196678008 0.251534186 0.371804481 0.886216884 0.23354779 0.092207265 0.146653034 0.315217357 0.738409194 0.526375369 0.602413183 0.264122652 0.390449577 0.151980269 0.182309339 0.131878701 0.203784361 0.182222149 0.547846637 0.161952443 0.136419944 0.609869638 0.406547113 0.155968269 0.154235287 0.178128629 0.245053324 0.264062625 0.149438709 0.254064775 0.203813181 0.240185389 0.954927697 0.802130499 0.622763217 0.759858122 0.676914192 0.775079435 0.81972092 0.345584804 0.827023621 0.781811183 0.302315783 0.942582685 0.810925477 0.471226987 0.651325578 0.794332956 0.273856788 0.635207154 0.722943223 0.558203987 0.325710312 0.48468537 0.630112243 0.472680671 0.727240501 0.90115028 0.595785965 0.822613583 0.475491064 0.274147818 0.669920303 0.858534635 0.770479385 0.621525856 0.821413784 0.086525613 0.432761309 0.148463503 0.559345436 0.208726388 0.205047303 0.860686508

Clonal Clonal Clonal Clonal Subclonal Clonal Clonal Clonal Clonal Clonal Subclonal Clonal Clonal Subclonal Subclonal Clonal Clonal Subclonal Subclonal Subclonal Subclonal Clonal Clonal Clonal Clonal Clonal Subclonal Subclonal Subclonal Subclonal Subclonal Clonal Subclonal Subclonal Clonal Clonal Subclonal Subclonal Subclonal Subclonal Subclonal Subclonal Subclonal Subclonal Subclonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Subclonal Clonal Clonal Subclonal Clonal Clonal Subclonal Clonal Clonal Subclonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Not assessable Subclonal Clonal Clonal Clonal Clonal Clonal Subclonal Clonal Subclonal Clonal Clonal Clonal Clonal

. 1.88E-05 9.42E-06 5.08E-04 0.004567 . . . . . . . 8.61E-04 . 8.70E-05 . . . 9.44E-06 . . 1.88E-05 . . . . . 1.51E-04 . . 6.12E-04 . . 9.42E-06 . . . . 1.07E-05 . . . . 9.58E-06 . . . . . . . . . 8.47E-05 . . . . . . . 8.77E-05 . 3.77E-05 . 0.003549 . . . . 2.83E-05 9.42E-06 . . . . . . . . 3.77E-05 9.42E-06 0.047 . . . .


GCT5T GCT5T GCT5T GCT5T GCT5T GCT5T GCT5T GCT5T GCT5T GCT5T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT6T GCT8T GCT8T GCT8T GCT8T GCT8T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT92T GCT9T GCT9T GCT9T GCT9T GCT9T GCT9T GCT9T GCT9T GCT9T GCT9T GCT9T

KMT2A MPZ NBEAL1 KBTBD8 ZNF367 ALAD OR5AK2 MMP7 C12orf60 MORC4 NFKB2 FGR FMN2 SNX17 IL1B PLCXD3 FAM53C DIAPH1 UTRN ZNF804B LMOD2 TLE1 DNAJC25 PLCE1 PLCE1 CNTROB USP32 ZNF556 ILVBL ZXDB PCDH19 F8 ATP6AP1 PPP4R1L FA2H GPR124 MED13L ATP6V0C CYLC1 SLC7A4 CLASP2 SPTA1 OR7C1 OSGEPL1 TYSND1 PPP1R9B NCL HNF4A DBNDD2 MYH9 CARD10 FGF10 C6orf132 ARID1B MLLT3 RBM10 CYP4Z1 TET1 CCDC92 THSD4 HS3ST2 IGF2BP1 CEP44 P4HA2 ALKBH4 MSR1 DIAPH2 ATP6AP1 ATP6AP2 RNF123 INSRR GRHL1 ALS2CL GPER1 OR5B2 PLBD1 DGKA LTA4H AMER2

p.A67del p.M222I p.E1687A p.E449K p.R168H p.L123Q p.S291R p.C87R p.F21L p.E806K p.G634Dfs*7 p.K287Q p.G941A p.R317C p.Q257K p.A113V p.R266C p.A325V p.I2908V p.I1160N p.D154N p.D750Y p.I286V p.Q16L p.K18E p.E792V p.I253T p.T336M p.P215L p.G206R p.D412N p.R1671H p.W138* p.F254Lfs*27 p.G893E p.S635G p.E139K p.K201T p.G236Afs*55 p.M965Wfs*33 p.L1370Afs*10 p.T105Hfs*17 p.K13* p.L138del p.P257del p.G698del p.L341del p.S223del p.E1350del p.K272_E273del p.C23del p.L176_P184del p.Q131del p.S190del p.R85del p.R374C p.S879L p.E306K p.L733H p.T216M p.N353I p.R11Q p.E438K p.S205L p.V387I p.P558Q p.W302* p.P90Qfs*48 p.L608Pfs*12 p.A1011D p.T272M p.Q206K p.T66I p.S62R p.L202V p.E278K p.A173T p.I362F

11 1 2 3 9 9 11 11 12 23 10 1 1 2 2 5 5 5 6 7 7 9 9 10 10 17 17 19 19 23 23 23 23 20 16 8 12 16 23 22 3 1 19 2 10 17 2 20 20 22 22 5 6 6 9 23 1 10 12 15 16 17 4 5 7 8 23 23 23 3 1 2 3 7 11 12 12 12 13

118307413 CGCG 161275747 C 204009621 A 67058348 G 99160514 C 116153107 A 56757259 A 102398564 A 14975932 T 106185412 C 104160508 AG 27942104 T 240370934 G 27598547 C 113587979 G 41382402 G 137681173 C 140958152 G 145103147 A 88965775 T 123302100 G 84199178 C 114412099 A 95790850 A 95790855 A 7851640 A 58346864 A 2877963 C 15233576 G 57619097 G 99662362 C 154157053 C 153660662 G 56814715 C 74752909 CG 37698298 G 116446315 T 2569693 G 83128318 A 21385396 CG 33602360 AT 158615065 C 14910637 G 190626330 T 71905928 TCAG 48227102 GGGC 232319941 ACCT 43052772 AGCT 44038637 ACCT 36689418 GCCT 37906308 GCTCCTT 44388714 AAGC 42075104 GTTCCAGCAGCA 157099426 ACAG 20414343 ACTG 47030466 AGGC 47571852 C 70405122 C 124421685 C 72039338 T 22926426 C 47119720 A 175220304 G 131533958 C 102098136 G 15977990 C 96212885 C 153662775 G 40450581 AC 49740923 T 156812890 G 10104083 C 46727848 G 1131561 C 58190549 A 14689599 G 56334131 G 96415993 C 25744674 T

C G C A T T C G G T A G C T T A T A G A A A G T G T G T A A T T A T C A C A C C A CT GA TA T G A A A G G A G A A A T T T A T T A T A T A A A TG T T T T T C A T A

In_Frame_Del Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Frame_Shift_Del Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Nonsense_Mutation Splice_Site Frame_Shift_Del Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Frame_Shift_Del Frame_Shift_Del Frame_Shift_Ins Frame_Shift_Ins Frame_Shift_Ins In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del In_Frame_Del Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Nonsense_Mutation Frame_Shift_Del Frame_Shift_Ins Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation Missense_Mutation

0.115384615 0.122866894 0.108333333 0.160714286 0.073170732 0.108910891 0.392857143 0.082524272 0.24 0.189873418 0.211111111 0.212962963 0.43220339 0.510373444 0.179245283 0.209677419 0.2109375 0.304347826 0.23880597 0.194285714 0.072727273 0.258064516 0.263157895 0.473684211 0.491525424 0.34562212 0.298245614 0.182857143 0.054545455 0.052631579 0.140151515 0.255555556 0.563380282 0.380434783 0.22 0.095238095 0.048192771 0.18490566 0.230769231 0.204819277 0.057692308 0.085714286 0.114285714 0.081081081 0.053333333 0.050847458 0.050847458 0.050632911 0.093023256 0.052631579 0.075 0.052631579 0.25 0.068627451 0.125 0.055555556 0.111111111 0.090909091 0.121212121 0.255319149 0.119496855 0.212765957 0.0625 0.102564103 0.078431373 0.25 0.204081633 0.25 0.382352941 0.160493827 0.27027027 0.145454545 0.169230769 0.198412698 0.178082192 0.134328358 0.232067511 0.266666667 0.25443787

0 0 0 0.029411765 0 0 0 0 0 0 0 0 0.016666667 0 0 0 0.004807692 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.022727273 0 0 0 0 0 0 0 0 0 0 0.011235955 0 0.007194245 0 0 0 0 0.005181347 0 0 0 0 0 0 0.02173913 0 0 0 0 0 0 0 0 0.003333333 0 0

26 293 120 56 164 101 28 206 25 79 90 216 118 241 106 62 256 46 67 175 55 93 19 57 59 217 57 175 165 76 264 90 213 92 100 63 166 265 39 83 52 35 70 37 75 59 59 79 43 76 40 76 8 102 16 90 27 44 33 47 159 47 64 39 51 80 49 48 68 162 111 55 65 252 146 67 237 60 169

11 106 68 34 90 52 21 100 19 16 71 201 60 146 56 40 208 27 49 138 27 85 20 43 45 100 39 82 77 35 124 47 100 67 69 31 112 165 23 98 74 53 88 47 74 59 72 106 49 91 49 104 7 89 13 139 37 72 44 52 193 79 82 67 69 109 49 46 56 182 120 47 64 360 103 46 300 43 221

1 1 1 1 0.85 1 1 0.96 1 1 0.91 0.92 1 1 0.77 0.9 0.91 1 1 1 0.39 1 1 1 1 1 1 0.97 0.29 0.38 1 1 1 1 1 0.63 0.32 1 1 1 0.62 0.91 1 0.86 0.57 0.54 0.54 0.54 0.99 0.56 0.8 0.56 1 0.73 1 0.59 1 0.97 1 1 1 1 0.67 1 0.84 1 1 1 1 0.67 1 0.61 0.71 0.83 0.75 0.56 0.97 1 1

0.77864 0.87581 0.85383 0.91894 0.69769 0.84605 0.15723 0.78736 0.86093 0.8958 0.74577 0.7825 0.96805 0.95158 0.53575 0.72335 0.76986 0.8574 0.80759 0.85812 0.09781 0.86466 0.8087 0.9638 0.96158 0.96541 0.91284 0.81961 0.00001 0.10523 0.85488 0.95309 0.47717 0.96568 0.86119 0.35935 0.0003 0.88654 0.88247 0.93854 0.49097 0.65276 0.79746 0.63444 0.41422 0.41929 0.41929 0.375 0.69067 0.40443 0.60675 0.40443 0.76869 0.55733 0.72074 0.41535 0.72568 0.68303 0.76715 0.85954 0.86219 0.91503 0.5185 0.72119 0.62871 0.85505 0.91941 0.87116 0.95367 0.10316 0.83874 0.24783 0.37727 0.45979 0.30503 0.13906 0.79526 0.77418 0.84564

0.989627012 1 1 1 0.987929767 1 1 1 1 1 1 1 1 1 0.979160036 1 1 1 1 1 0.86358698 1 1 1 1 1 1 1 0.528027506 0.869602788 1 1 1 1 1 0.968815685 0.60047883 1 1 1 0.974709329 0.985775524 1 0.984863471 0.966707264 0.967015618 0.967015618 0.961355146 0.988150744 0.965461092 0.983336304 0.965461092 1 0.980835923 0.987498656 0.967062763 0.988743094 0.987821916 1 1 1 1 0.977455992 0.98934767 0.985117548 1 1 1 1 0.920749165 1 0.955280778 0.973922216 0.981590639 0.967023891 0.924498063 1 1 1

0.298014986 0.799809723 0.595703036 0.589767104 0.463411038 0.563621172 0.708570574 0.560453134 0.532014402 0.733819385 0.571812859 0.687155896 0.895296215 0.959214636 0.49772999 0.511598152 0.698116212 0.643268886 0.593888127 0.70415361 0.151697087 0.688728976 0.425201438 0.832957184 0.845964266 0.921100092 0.714136783 0.668750547 0.150367832 0.150914045 0.70655667 0.784395685 0.964524537 0.858922408 0.735953947 0.283258531 0.158734295 0.808224612 0.588119027 0.744437573 0.199193299 0.254452732 0.491034335 0.247166534 0.216951104 0.180732323 0.180732323 0.207527791 0.315248405 0.214514477 0.236595533 0.214514477 0.258968278 0.34086242 0.222715531 0.248632975 0.28572146 0.311617297 0.353850049 0.69661376 0.671710308 0.639108808 0.246084011 0.330402832 0.286856799 0.791132929 0.634403319 0.694800345 0.819038354 0.464674723 0.730685855 0.311472006 0.39811213 0.637969086 0.515823525 0.299468357 0.740210112 0.623669874 0.75577534

Clonal Clonal Clonal Clonal Clonal Clonal Subclonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Subclonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Subclonal Subclonal Clonal Clonal Clonal Clonal Clonal Subclonal Subclonal Clonal Clonal Clonal Subclonal Clonal Clonal Clonal Subclonal Subclonal Subclonal Subclonal Clonal Subclonal Clonal Subclonal Clonal Clonal Clonal Subclonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Clonal Subclonal Clonal Subclonal Subclonal Subclonal Subclonal Subclonal Clonal Clonal Clonal

. . . 2.84E-05 . . . . . . . . . 9.42E-06 . . 2.83E-05 1.89E-05 . . . . . . . . . 1.88E-05 1.88E-05 0.001766 . . . . . . . . . . 1.89E-05 . . . 6.22E-04 1.76E-04 1.88E-05 0.004049 0.001643 1.32E-04 . 4.71E-04 0.018 . . 5.10E-04 7.53E-05 9.42E-06 3.77E-05 . 1.88E-05 . 4.14E-04 . . 9.42E-06 . . . 9.42E-06 . . . . . . . . .

Supplementary Table 5: Histologic features of granular cell tumors according to ATP6AP1 and ATP6AP2 mutational status. WT

ATP6AP1 /ATP6AP2 (n=23) No 23 (100%) Necrosis Yes 0 (0%) No 16 (69.6%) Spindling Yes 7 (30.4%) Vesicular nuclei and No 20 (87%) prominent nucleoli Yes 3 (13%) 0-2 21 (91.3%) Mitoses/10 HPF >2 2 (8.7%) Increased nuclear/ No 21 (91.3%) cytoplasmic ratio Yes 2 (8.7%) No 21 (91.3%) Nuclear pleomorphism Yes 2 (8.7%) Benign 14 (60.9%) Fanburg-Smith histologic Atypical 8 (34.8%) category Malignant 1 (4.3%) a Fisher's exact test. HPF, high power fields; MUT, mutant; WT, wild-type Fanburg-Smith histologic criteria

WT

ATP6AP1

MUT

(n=50)

48 (96%) 2 (4%) 34 (68%) 16 (32%) 36 (72%) 14 (28%) 47 (94%) 3 (6%) 46 (92%) 4 (8%) 39 (78%) 11 (22%) 24 (48%) 21 (42%) 5 (10%)

ATP6AP2

MUT

(n=9)

9 (100%) 0 (0%) 7 (77.8%) 2 (22.2%) 8 (88.9%) 1 (11.1%) 9 (100%) 0 (0%) 8 (88.9%) 1 (11.1%) 9 (100%) 0 (0%) 6 (66.7%) 3 (33.3%) 0 (0%)

a

p value 0.999 0.939 0.344 0.806 0.859 0.181 0.787

SUPPLEMENTARY REFERENCES 1.

Cancer Genome Atlas Research Network, et al. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 368, 2059-2074 (2013).

2.

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507, 315-322 (2014).

3.

Ciriello G, et al. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell 163, 506-519 (2015).

4.

Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330-337 (2012).

5.

Cancer Genome Atlas Network. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 517, 576-582 (2015).

6.

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 499, 43-49 (2013).

7.

Davis CF, et al. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell 26, 319-330 (2014).

8.

Ceccarelli M, et al. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell 164, 550-563 (2016).

9.

Campbell JD, et al. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nat Genet 48, 607-616 (2016).

10.

Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011).

11.

Cancer Genome Atlas Research Network. The Molecular Taxonomy of Primary Prostate Cancer. Cell 163, 1011-1025 (2015).

12.

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513, 202-209 (2014).

23

13.

Cancer Genome Atlas Research Network, et al. Integrated genomic characterization of endometrial carcinoma. Nature 497, 67-73 (2013).

14.

Cancer Genome Atlas Research Network. Integrated genomic characterization of papillary thyroid carcinoma. Cell 159, 676-690 (2014).

24