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Supplementary Information

Recurrent PAX3-MAML3 Fusion in Biphenotypic Sinonasal Sarcoma

Xiaoke Wang1,, Krista L. Bledsoe2,, Rondell P. Graham1,, Yan W. Asmann3, David S. Viswanatha1,

Jean E. Lewis1, Jason T. Lewis1, Margaret M. Chou4, Michael J. Yaszemski5, Jin Jen6, Jennifer J.

Westendorf5, André M. Oliveira1, 5

1 Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 2 Mayo Graduate School, Rochester, Minnesota 3 Department of Health Sciences Research, Mayo Clinic, Jacksonville, Florida 4 Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and the

Perelman School of Medicine, Philadelphia, Pennsylvania 5 Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota 6 Medical Genome Facility, Center of Individualized Medicine, Mayo Clinic, Rochester, Minnesota

These authors contributed equally to this work.

Supplementary Figure 1 ................................................................................................................... 2


Supplementary Figure 3…. .............................................................................................................. 4



Supplementary Table 1 .................................................................................................................... 7

Supplementary Table 2 .................................................................................................................... 8

Supplementary Table 3 .................................................................................................................. 13



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Nature Genetics: doi:10.1038/ng.2989

Supplementary Figure 1. Cytogenetics and molecular genetic findings for the PAX3-MAML3 fusion. (a) Partial karyogram showing the chromosomal translocation t(2;4)(q35;q31.1). (b) and (c) FISH break apart strategy shows rearrangements of PAX3 and MAML3 loci, respectively (see also Fig. 1b). The percentage of rearranged cells for these loci ranged from 25 to 78% (median, 60%). Endothelial cells, inflammatory cells, sinonasal epithelial cells and other non-neoplastic cells showed no rearrangement of these loci. (d) Representative RT-PCR gel showing the fusion PAX3-MAML3 in three examples of SNS (lanes 1-3). Several other tumors (lanes 4-8: alveolar rhabdomyosarcoma, dermatofibrosarcoma protuberans, melanoma, malignant peripheral nerve sheath tumor and synovial sarcoma, respectively) and normal sinonasal tissue (lane 9) were negative for the fusion product; lanes 10-11: no template; see also Supplementary Table 2). (e) Confirmatory chromatogram showing the PAX3-MAML3 sequence at the fusion breakpoint in case 1.

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Supplementary Figure 2. The PAX3-MAML3 fusion protein localizes to the nucleus and binds DNA. (a) Western blots were performed with anti-PAX3 or tubulin antibodies on lysates of HEK293T cells expressing pcDNA3 (Co), FLAG-PAX3-MAML3 (P-M) or HA-PAX3. (b) Immunofluorescence images showing nuclear expression of FLAG-PAX3-MAML3 in C2C12 cells. Cells were counterstained with phalloidin to detect cytoplasmic F-actin and with DAPI to detect DNA. (c) Electrophoretic mobility shift assay (EMSA) of FLAG-PAX3-MAML3 binding to double-stranded DNA containing a PAX3 binding element. Lysates from COS-7 cells expressing FLAG-PAX3-MAML3 (P-M) or HA-PAX3 were incubated with a 32P-labeled PAX3 DNA probe in the presence or absence of 100-fold excess of the wildtype (WT) probe, a mutated (Mut) probe, control IgG, anti-HA or anti-FLAG. The arrow points to PAX3-MAML3/DNA complexes. The arrowhead indicates PAX3/DNA complexes. The asterisk indicates the free probe. (d) Transient transcription assays demonstrating the effect of PAX3-MAML3 on a Notch reporter, Hes5p-Luc, in C2C12 cells in the presence or absence of the Notch 1 intracellular domain 1 (NICD1). * p < 0.01, ** p < 0.0001 relative to control in unpaired t-tests. 3


Supplementary Figure 3. Pathway enrichment analysis. (a) Gene ontology analysis shows that SNS expression profile is enriched in genes involved in several developmental processes, including skeletal system morphogenesis and general organ development (minimum p = 3.39x10-14 for skeletal system morphogenesis, false discovery rate (FDR) = 1.37x10-10; maximum p = 1.14x10-10 for organ morphogenesis, FDR = 4.64x10-8 ) (b) Enrichment process network analysis shows that SNS exhibits differential expression of several biologic circuits involved in neural, cardiac, bone and other developmental processes (minimum p = 4.19x10-4 for neural development, FDR = 0.058; maximum p = 0.031 for olfactory transduction, FDR = 0.427). Enrichment analyses were performed using the MetaCore gene regulatory network database in order to identify networks that are significantly enriched by differentially expressed genes. Modified gene ontology terms are based on the GO database (www.geneontology.org).

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Supplementary Figure 4. Representative qPCR and immunohistochemistry studies confirm differential gene expression in SNS. (a) and (b) High expression of NTRK3 and MYOD1 were observed in most examples of SNS. (c) MLANA and MITF (not shown) were not expressed in SNS. (d) NTRK3 showed a strong membranous pattern of expression in virtually all SNS (24/25). No staining was observed in the sinonasal epithelium. (e) MYOD1 nuclear expression was focal in a few SNS tumors (4/25); arrow indicating an example cell with focal MYOD1 expression. (f) Melan A and MITF (not shown) were universally negative in all SNS tested (n=22). qPCR and/or immunohistochemistry also confirmed the overexpression of PLUNC, PCP4, GDF7, PIK3C2G, ALX1 and PAX3, and downregulation of HOXB7 (data not shown; see also Supplementary Table 1; additional information about the phenotype of SNS can be found in ref. 1) (RE, relative expression; SNS, sinonasal sarcoma (n=5); NST, normal sinonasal tissue (n=4); ARMS, alveolar rhabdomyosarcoma (n=3); DFSP, dermatofibrosarcoma protuberans (n=3); MPNST, malignant peripheral nerve sheath tumor (n=3); SS, synovial sarcoma (n=3). *** and ** indicate Kruskal-Wallis test p < 0.01 and p < 0.05, respectively, and post hoc Dunett’s test p < 0.05; * indicates Wilcoxon-Mann-Whitney test p < 0.05; error bars represent mean ± SD).

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Supplementary Figure 5. Differential expression of myogenin between SNS and ARMS. (a) Biphenotypic sinonsal sarcoma (SNS) is a monomorphic spindle cell neoplasm that exclusively occurs in the head and neck region of middle aged individuals, most commonly females (HE x100). (b) ARMS is a pediatric small round cell tumor that shows a characteristic pseudoalveolar growth pattern (HE x100). (c-d) qPCR and immunohistochemical analysis show that while all ARMS (n = 11) express high levels of MYOG (myogenin) mRNA (c) and protein (d, inset), SNS (n = 11) is consistently negative for this marker (c/d); * indicates Wilcoxon-Mann-Whitney test p < 0.0001; error bars represent mean ± SD).

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Supplementary Table 1. Summary of Clinical Features, Immunophenotype and Molecular Findings in Biphenotypic Sinonasal Sarcoma

Case Sex Age Location PAX3-MAML3 PAX3 MAML3 Phenotype Profile #

(RT-PCR) (FISH) (FISH) PAX3 S100 Actin NTRK3 MyoD1 Myogenin Desmin Melan A LR LR (mo) OS (mo)1^ † Δ F 47 ethmoid/cribriform + + + + F+ - + F+ - F+ - Y 10 122^ M 74 ethmoid/orbit + + + + + + + - - - - - - -3 F 42 nasal/ethmoid + + + + + + + - - - - N 60 604* F 47 nasal/ethmoid + + - + + + + - - - - - - -5 F 47 ethmoid/nasal cavity + + + + F+ + + - - - - - - -6** F 57 ethmoid - + - + F+ + + - - - - - - -7 F 24 ethmoid/sphenoid + + + + F+ + + - - - - Y 60 608 M 39 nasal cavity + + + + + F+ + - - - - N 32 329** F 26 nasal cavity - + - + F+ - + - - - - N 18 1810 F 85 sphenoid + + + + + + + - - - - Y 12 1211 F 45 nasal cavity + + + + F+ + + F+ - - - N 48 4812 F 51 nasal cavity + + + + + + + - - F+ - N 42 4213* F 32 nasal cavity + + - + + + + F+ - - - N 36 3614** F 47 nasal cavity - + - + + F+ + - - - - - -15** F 46 ethmoid - + - + + + + - - - - N 26 2616 F 58 frontal/ethmoid + + + + F+ + - - - F+ - Y 24 4017 F 56 ethmoid + + + + + + + - - F+ - - - -18 F 52 frontal/ethmoid + + + + F+ + + - - - - N 180 18019** M 76 nasal cavity - + - ND + + + ND ND ND ND N 12 1220 F 49 nasal cavity + + + + + + + - - - - N 25 2521*** M 46 nasal cavity/ethmoid/frontal - - + + F+ + + - - - - N 336 33622* F 38 nasal cavity + + - + + F+ F+ - - - - Y 13 2023 M 56 ethmoid + + + ND + + + ND ND - ND - - -24 F 66 ethmoid + + + + + + + F+ - - - - - -25 M 61 nasal cavity + + + + + ND + ND ND ND ND - - -+, positive; -, negative; Y, yes; N, not observed; LR, local recurrence; OS, overall survival; mo, months; ND, not done due to lack of material; F, focal positivity (<30% of total tumor area).* Findings suggestive of a cryptic MAML3 locus rearrangement (cases 4, 13 and 22).** Findings suggestive of alternate PAX3 fusion genes.*** Findings suggestive of an alternate MAML3 fusion gene.^ Index case for cytogenetics. Karyotypes: 46,XX,t(2;4)(q35;q31.1)[22]/46,XX[7] (case 1) and 46,XX,t(2;4)(q35;q31.1)[cp20]/46,XX[3] (case 2).† Index case used for transcriptome sequencing.Δ An alternate splicing variant of PAX3-MAML3 was found in this case (GenBank accession no. KF727277). #, immunohistochemical analysis for S100, actin (muscle specific actin and smooth muscle actin) and desmin were described in ref.1; all tumors were universally positive for ALX1 and negative for MITF,SILV, HMB45 and HES1.

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Supplementary Table 2. Clinico-Pathologic Features and Molecular Profile of Control Tumors and Tissues Used in this Study

Histologic Diagnosis Age Sex Location Molecular Profile PM(-) GEP qPCR IHC1 Adrenal cortical carcinoma 43 F Adrenal - *

2 Alveolar rhabdomyosarcoma-01 7 F Forearm PAX3-FOXO1 * * * *

3 Alveolar rhabdomyosarcoma-02 21 F Periorbital PAX3-FOXO1 * * * *

4 Alveolar rhabdomyosarcoma-03 1 M Thigh PAX3-FOXO1 * * * *

5 Alveolar rhabdomyosarcoma-04 9 F Lung, met. PAX3-FOXO1 * * *

6 Alveolar rhabdomyosarcoma-05 5 M Abdominal wall PAX3-FOXO1 * * *

7 Alveolar rhabdomyosarcoma-06 51 M Neck PAX3-FOXO1 * * *

8 Alveolar rhabdomyosarcoma-07 5 F Thigh PAX3-FOXO1 * * *

9 Alveolar rhabdomyosarcoma-08 7 M Sinus PAX3-FOXO1 * * *

10 Alveolar rhabdomyosarcoma-09 14 M Thigh PAX3-FOXO1 * * *

11 Alveolar rhabdomyosarcoma-10 7 F Pelvic area PAX3-FOXO1 * * *

12 Alveolar rhabdomyosarcoma-11 12 M Forearm PAX3-FOXO1 * *

13 Alveolar rhabdomyosarcoma-12 16 M Neck, met. PAX3-FOXO1 * *

14 Alveolar rhabdomyosarcoma-13 28 F Neck PAX3-FOXO1 * *

15 Alveolar rhabdomyosarcoma-14 57 F Neck PAX3-FOXO1 * *

16 Alveolar rhabdomyosarcoma-15 13 F Thigh PAX3-FOXO1 * *

17 Alveolar rhabdomyosarcoma-16 9 F Sinus PAX3-FOXO1 * *

18 Alveolar rhabdomyosarcoma-17 9 M Perirenal PAX3-FOXO1 * *

19 Alveolar rhabdomyosarcoma-18 14 F Inguinal area PAX3-FOXO1 * *

20 Alveolar rhabdomyosarcoma-19 7 F Calf PAX7-FOXO1 * *

21 Alveolar rhabdomyosarcoma-20 19 M Groin PAX3-FOXO1 * *

22 Alveolar rhabdomyosarcoma-21 51 M Neck PAX3-FOXO1 * *

23 Alveolar soft part sarcoma 35 F Pelvis ASPSCR1-TFE3 *

24 Angioleiomyoma 45 M Hand - * *

25 Angiomatoid fibrous histiocytoma 22 M Arm EWSR1-CREB1 * *

26 Breast adenocarcinoma, lobular type 48 F Breast - *

27 Chronic myelogenous leukemia cell line K562 - - - BCR-ABL *

28 Colon adenocarcinoma 83 M Colon, ascending - *

29 Colon adenocarcinoma 4 F Colon; FAP - *

30 Dedifferentiated liposarcoma 85 M Retroperitoneum - * *

31 Dermatofibroma/Benign fibrous histiocytoma-01 45 F Arm - * * * *

32 Dermatofibroma/Benign fibrous histiocytoma-02 46 F Arm - * * * *

33 Dermatofibroma/Benign fibrous histiocytoma-03 39 F Shoulder - * * * *

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34 Dermatofibrosarcoma protuberans-01 53 F Chest wall - * *

35 Dermatofibrosarcoma protuberans-02 35 M Upper back - * *

36 Dermatofibrosarcoma protuberans-03 62 F Chest wall - * *

37 Dermatofibrosarcoma protuberans-04 60 M Chin - * *

38 Dermatofibrosarcoma protuberans-05 48 F Lower back COL1A1-PDGFB * *

39 Dermatofibrosarcoma protuberans-06 17 M Thigh - * *

40 Dermatofibrosarcoma protuberans-07 65 M Abdominal wall COL1A1-PDGFB * *

41 Desmoplastic small round cell tumor-01 21 M Abdomen EWSR1-WT1 * * * *



44 Embryonal rhabdomyosarcoma-01 45 F Axilla - * *

45 Embryonal rhabdomyosarcoma-02 7 M Epididymum - * *

46 Embryonal rhabdomyosarcoma-03 5 M Infratemporal - * *

47 Embryonal rhabdomyosarcoma-04 7 M Bladder - * *

48 Embryonal rhabdomyosarcoma-05 18 F Skull base - * *

49 Embryonal rhabdomyosarcoma-06 12 M Paratesticular - * *

50 Embryonal rhabdomyosarcoma-07 12 F Cheek - * *

51 Embryonal rhabdomyosarcoma-08 16 F Maxilla - * *

52 Embryonal rhabdomyosarcoma-09 5 F Skull base - * *

53 Embryonal rhabdomyosarcoma-10 8 M Shoulder - * *

54 Embryonal rhabdomyosarcoma-11 12 M Paratesticular - * *

55 Embryonal rhabdomyosarcoma-12 1 M Prostate - * *

56 Embryonal rhabdomyosarcoma-13 6 M Bladder - * *

57 Endometrial stromal sarcoma 34 F Uterus - * *

58 Ewing sarcoma-01 54 M Leg EWSR1-FLI1 * * * *

59 Ewing sarcoma-02 10 M Paraspinal EWSR1-FLI1 * * * *

60 Ewing sarcoma-03 24 F Abdomen EWSR1-FLI1 * * * *

61 Ewing sarcoma-04 17 F Neck EWSR1-FLI1 *

62 Ewing sarcoma-05 27 F Pelvis EWSR1-FLI1 * *

63 Ewing sarcoma-06 39 M Abdomen EWSR1-ERG * *

64 Ewing sarcoma-07 15 F Sinus EWSR1-FLI1 *

65 Fibroma of tendon sheath-01 69 M Hand - * * * *

66 Fibroma of tendon sheath-02 65 F Hand - * * * *

67 Fibroma of tendon sheath-03 77 M Hand - * * * *

68 Fibrosarcoma, adult-type-01 57 M Groin - * *

69 Fibrosarcoma, adult-type-02 91 F Mandible - *

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70 Gastrointestinal stromal tumor-01 48 F Stomach KIT exon 11 mut. * * * *



73 Infantile fibrosarcoma 8w M Thigh ETV6-NTRK3 * *

74 Leiomyosarcoma-01 53 F Uterus - * *

75 Leiomyosarcoma-02 84 M Leg - * *

76 Leiomyosarcoma-03 71 M Leg * *

77 Malignant peripheral nerve sheath tumor-01 50 F Thigh - * * * *

78 Malignant peripheral nerve sheath tumor-02 42 F Leg - * * * *

79 Malignant peripheral nerve sheath tumor-03 38 M Neck; NF1 - * * * *

80 Malignant peripheral nerve sheath tumor-04 41 M Pelvis - * *

81 Malignant peripheral nerve sheath tumor-05 57 F Groin - * *

82 Malignant peripheral nerve sheath tumor-06 74 F Chest wall - * *

83 Malignant peripheral nerve sheath tumor-07 94 M Neck - * *

84 Malignant peripheral nerve sheath tumor-08 74 F Chest wall - * *

85 Malignant peripheral nerve sheath tumor-09 69 M Shoulder - * *

86 Melanoma-01 52 F Inguinal area, met. - * * * *

87 Melanoma-02 48 M Chest wall, met. - * * * *

88 Melanoma-03 80 M Arm - * * * *

89 Melanoma-04 80 F Arm - *

90 Melanoma-05 71 M Abdominal wall, met. - *

91 Melanoma-06 49 M Groin, met. - *

92 Melanoma-07 36 M Neck - *

93 Melanoma-08 57 M Mesentery, met. - *

94 Mucoepidermoid carcinoma-01 79 F Parotid gland CRCT1-MAML2 * *

95 Mucoepidermoid carcinoma-02 67 M Parotid gland CRCT1-MAML2 *

96 Myofibroblastic sarcoma 51 M Hypopharynx - * *

97 Myofibroma 34 M Chest wall - * *

98 Myxofibrosarcoma 70 M Chest wall - * *

99 Neurofibroma-1 31 F Sciatic nerve; NF1 - * * * *

100 Neurofibroma-2 62 M Chest wall - * * * *

101 Neurofibroma-3 57 F Chest wall - * * * *

102 Normal cardiac skeletal muscle-01 38 F - - * *

103 Normal cardiac skeletal muscle-02 56 M - - *

104 Normal parathyroid gland 70 F - - *

105 Normal sinonasal tissue-01 55 M R - * * *

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106 Normal sinonasal tissue-02 50 F - - * *

107 Normal sinonasal tissue-03 63 M - - * * *


109 Normal sinonasal tissue-05 31 M L - * *

110 Normal sinonasal tissue-06 31 M R - * * *

111 Normal sinonasal tissue-07 63 M - - * *


113 Normal sinonasal tissue-09 68 F - - * *



116 Normal sinonasal tissue-12 37 M - - * *

117 Normal sinonasal tissue-13 55 M L - * * *

118 Normal skeletal muscle-01 59 M - - * * *

119 Normal skeletal muscle-02 65 F - - * * *

120 Osteosarcoma 3 M Femur - * *

121 Pleomorphic adenoma 55 M Submandibular gland - * *

122 Prostatic stromal sarcoma 54 M Prostate - * *

123 Schwannoma-01 35 F Spine, T7 - * * * *

124 Schwannoma-02 51 F Sciatic nerve - * * * *

125 Schwannoma-03 43 M Neck - * * * *

126 Spindle cell rhabdomyosarcoma 1 M Chest wall - * *

127 Synovial sarcoma-01 17 F Forearm SS18-SSX1 * * * *

128 Synovial sarcoma-02 19 M Finger SS18-SSX1 * * * *

129 Synovial sarcoma-03 76 M Thigh SS18-SSX2 * * * *

130 Synovial sarcoma-04 31 M Abdomen SS18-SSX1 * *

131 Synovial sarcoma-05 32 M Lung, met. SS18-SSX1 * *

132 Synovial sarcoma-06 63 F Lung, met. SS18-SSX1 *

133 Synovial sarcoma-07 18 F Hand SS18-SSX1 * *

134 Synovial sarcoma-08 77 F Chest wall SS18-SSX2 * *

135 Synovial sarcoma-09 13 F Shoulder SS18-SSX2 *

136 Synovial sarcoma-10 17 F Forearm SS18+ FISH * *

137 Synovial sarcoma-11 43 M Arm SS18-SSX1 * *

138 Synovial sarcoma-12 14 M Thigh SS18-SSX2 * *

139 Synovial sarcoma-13 48 F Thigh SS18-SSX1 * *

140 Synovial sarcoma-14 35 F Abdominal wall SS18-SSX2 * *

141 Synovial sarcoma-15 23 F Abdominal wall SS18-SSX1 * *

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142 Synovial sarcoma-16 29 F Pleura SS18-SSX1 * *

143 Undifferentiated small round cell sarcoma-01 7 M Ankle - * *

144 Undifferentiated small round cell sarcoma-02 33 F Liver - * *

145 Undifferentiated small round cell sarcoma-03 10m M Mediastinum - * *FAP, familial adenomatous polyposis; NF1, neurofibromatosis type I; PM(-), negative for PAX3-MAML3; GEP, gene expression profling.IHC, immunohistochemistry.

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Supplementary Table 3. Top 150 Overexpressed and Downregulated Genes in Biphenotypic Sinonasal Sarcoma

Upregulated Genes Downregulated GenesGene p-value Ratio Gene p-value Ratio

1 PLUNC 4.39E-17 81.859 HOXB7 1.04E-05 -13.4572 CXCL17 2.91E-08 45.462 KRT1 0.00477499 -11.0813 C20orf114 1.44E-09 43.499 HOXD13 0.00210586 -10.8414 CAPN13 5.97E-07 39.921 HOXB5 9.85E-09 -10.7725 PIGR 2.75E-07 33.284 PMP2 0.00234188 -10.2936 XAGE2B 1.72E-15 29.737 PRG4 2.46E-05 -10.0317 SERPINB3 1.39E-07 29.127 PLA2G2A 3.52E-05 -9.97628 PCP4 1.79E-08 27.85 GABRA2 0.000338385 -9.00269 C13orf30 5.13E-06 27.73 PCOLCE2 0.000319173 -8.4021

10 CTAG1B 1.55E-05 26.232 CDH19 0.000299448 -8.144911 GDF7 8.63E-11 24.295 ADH1B 0.0034806 -7.81312 GALNT17 6.04E-09 22.784 NKAIN2 0.00124955 -7.808413 TEKT1 7.53E-17 22.66 CIDEC 0.000101102 -7.806114 SCGB1A1 1.67E-06 21.586 C1orf68 0.0300937 -7.214715 COL6A6 5.35E-08 20.168 TNMD 0.000501419 -7.17216 BMP5 3.90E-06 19.381 MLANA 0.0175587 -7.04817 PIK3C2G 7.34E-09 19.114 NPTX1 0.00118341 -7.025118 ALX1 6.84E-05 18.932 ANK2 1.58E-10 -6.905619 RSPO1 1.83E-07 18.625 HOXA4 2.12E-06 -6.784520 GABBR2 7.17E-06 17.219 LAMA2 1.66E-06 -6.768621 MUC16 2.14E-08 16.219 HOXA2 2.74E-06 -6.720222 CYP2F1 2.88E-06 16.029 HOXB3 3.05E-05 -6.637123 SV2C 9.73E-07 15.814 MEOX2 9.19E-05 -6.596324 C20orf186 3.97E-06 15.505 LCE6A 0.0277075 -6.421725 CDH8 9.01E-06 15.121 FLG2 0.0192111 -6.404426 LCN2 4.99E-05 15.1 COMP 0.00579508 -6.374927 C1orf194 6.41E-09 15.087 GRIN3A 0.000391851 -6.374128 C11orf88 1.96E-06 14.117 TUBB4 0.00148051 -6.355929 FAM3D 3.20E-05 14.06 SIM1 0.00052901 -6.2702

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30 ERN2 1.46E-06 13.388 STMN2 0.000775597 -6.231831 TCEAL2 0.000111257 13.231 USP9Y 0.0356565 -6.189732 ADH7 8.56E-05 13.22 TOX 0.000266356 -6.161133 AGXT 4.62E-05 13.195 IL17B 0.00106547 -6.15734 DBX1 2.11E-08 13.16 HOXA9 3.81E-05 -6.146535 LYPD2 9.38E-08 12.739 PKIA 6.01E-07 -6.114736 SCGB2A1 0.000102285 12.724 POU3F2 0.000948689 -6.051137 SEC14L3 1.27E-08 12.586 JARID1D 0.0379543 -5.750738 MMP10 2.29E-06 12.541 TK1 0.000695896 -5.721339 GDF10 6.14E-08 12.243 CYorf15A 0.0281793 -5.704540 ASCL1 6.03E-06 12.179 NCAM2 0.000666985 -5.703141 ALX4 0.000110112 12.149 SGCG 0.000288481 -5.657342 FGFR2 1.12E-05 12.052 BHLHE22 2.07E-05 -5.634143 CCDC37 3.90E-07 11.856 BCHE 3.33E-05 -5.615644 C4orf49 6.32E-09 11.824 HOXB8 0.00257608 -5.513445 DNAI1 4.08E-07 11.708 LOR 0.025267 -5.494646 NWD1 3.93E-05 11.611 CXorf57 0.00139664 -5.488647 MME 4.24E-07 11.406 PRL 0.00993249 -5.476748 C10orf92 2.51E-06 11.277 CASP14 0.0156152 -5.473849 SLPI 5.90E-05 11.188 ODZ1 0.000896747 -5.461450 CAPZA3 2.03E-06 11.055 SCRG1 0.00913605 -5.406451 GALNTL6 4.25E-05 11.051 CADM2 0.00493505 -5.384852 GRP 8.90E-05 11.016 KRT2 0.0279916 -5.372153 CCDC33 5.71E-09 11 ISG15 2.64E-06 -5.331854 KRT19 1.34E-06 10.821 PTTG3P 0.00661097 -5.313455 PSCA 4.86E-06 10.511 C5orf46 0.000474402 -5.310956 CLDN3 1.32E-05 10.253 GFRA3 0.0129174 -5.293457 FAM5C 1.16E-05 10.191 NPTX2 0.00339756 -5.274458 TTR 1.42E-05 10.025 CYP4F22 0.00413109 -5.262259 SPRR3 0.00644916 9.9884 LOC730833 0.0359634 -5.219660 SLC18A2 9.60E-06 9.88 TMEFF2 0.00969879 -5.206661 CEACAM5 0.00017398 9.8067 COL9A1 0.000603958 -5.151462 GREM1 0.000102242 9.6702 LOC392395 0.00144798 -5.106163 ATRNL1 1.83E-11 9.5795 CDH12 0.00715154 -5.0859

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64 KRT13 0.00190808 9.4874 HOXA13 0.0133703 -5.070965 PCSK1N 2.61E-05 9.4343 FOXD1 0.000728918 -5.021566 DBC1 4.56E-05 9.4102 SPRR2B 0.00976528 -4.994567 SVOPL 3.57E-06 9.3384 CDCA7 0.00063766 -4.885268 KRT8 1.67E-05 9.3125 SCN7A 0.00071488 -4.848469 LRRC50 3.18E-07 9.3047 PRUNE2 0.000316209 -4.841570 C3orf51 0.000430141 9.2921 POPDC3 0.00213165 -4.805171 GATA2 1.17E-06 9.2514 GABRB1 0.00925977 -4.804972 NTN5 5.20E-07 9.2453 TMEM132D 0.0189635 -4.801473 ALX1 3.59E-05 9.1691 PGBD5 0.00262015 -4.790374 WDR38 4.24E-12 9.1217 MOXD1 1.71E-06 -4.742375 PAX1 1.46E-07 9.0333 FLG 0.0933306 -4.73376 FMO1 1.15E-05 8.9895 LCE2B 0.0464016 -4.710277 DNAH2 1.49E-05 8.9859 SALL3 0.0022649 -4.705478 CEACAM6 0.00404314 8.9042 RXRG 0.000835452 -4.657879 LOC653216 8.18E-13 8.8905 CAMK2N2 0.000430515 -4.629980 MIR1251 0.00103899 8.879 TRPC3 0.00130805 -4.629681 NTRK3 1.02E-06 8.8224 ANGPTL5 0.00192239 -4.611982 SHD 0.00063655 8.8138 SOX6 7.71E-07 -4.607483 ALX3 1.82E-10 8.8001 TCBA1 0.00427285 -4.556984 GABRP 0.000132833 8.7754 SPRR2E 0.101103 -4.549785 UBL4B 0.000124852 8.5023 PLSCR2 0.0183303 -4.521986 SLC27A6 6.00E-10 8.4982 TYRP1 0.0293822 -4.519587 XAGE2 4.36E-12 8.4938 SCGB2A2 0.0207824 -4.505788 ADD2 3.72E-11 8.4592 LIN28B 0.0478772 -4.467189 SFRP2 0.000249023 8.4413 DSC1 0.0320409 -4.461390 PTH2R 7.60E-05 8.4316 PNMA2 0.00301205 -4.450591 MSLN 6.30E-05 8.4251 NELL1 0.0484135 -4.414692 AGR3 2.57E-08 8.3564 RGPD1 0.0109749 -4.37793 PPP1R1A 5.74E-06 8.2719 TMEM195 0.00069676 -4.353694 C20orf85 1.54E-08 8.2506 KIF1A 0.0120386 -4.345295 FOXA1 0.000116756 8.2475 PDZRN4 0.00105691 -4.343396 PAX3 7.29E-05 8.2211 OGN 0.00101552 -4.340897 AGR2 7.77E-05 8.2086 CHGA 0.00613909 -4.326

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98 CCKAR 4.71E-05 8.2013 HOXA5 0.000368769 -4.32399 TCN1 0.000112729 8.1742 HOXB4 0.000147181 -4.3164

100 SERPINB11 3.63E-05 8.1582 SLC7A10 0.000569256 -4.3011101 ENKUR 3.48E-05 8.0988 LOC645993 0.0150569 -4.2949102 POU4F1 0.000853803 8.0529 LPPR5 0.000588422 -4.2883103 POU3F3 7.51E-05 7.9827 BIRC7 0.00232648 -4.2759104 NEUROG2 0.000264238 7.9305 WIT-1 0.00692671 -4.2425105 RASL10B 7.45E-06 7.9278 COL20A1 0.00345151 -4.2269106 VTCN1 0.000979247 7.9278 PCSK1 0.00309818 -4.2073107 C10orf81 0.000556033 7.7769 KRTAP4-7 0.0759449 -4.1958108 MYOCD 0.000206078 7.663 DCT 0.0147734 -4.1955109 EYA1 0.00100156 7.6549 KRT77 0.0324527 -4.1893110 PTPRT 0.000130063 7.6477 PBK 0.0184913 -4.1657111 IL33 1.32E-10 7.6339 RDH12 0.00924201 -4.1431112 C1orf110 0.000346133 7.6184 PKD1L2 0.000465405 -4.1373113 RSPH1 6.02E-08 7.5733 HAS1 0.0108455 -4.1341114 GSTA1 0.000597503 7.5395 DCX 0.010975 -4.103115 TTLL10 0.000313309 7.526 LCE2A 0.0494144 -4.1013116 VSTM2A 1.28E-05 7.5216 HOXA7 0.000450772 -4.0897117 ALDH1A2 1.92E-06 7.4885 HOXA10 9.54E-05 -4.088118 SLC6A14 3.28E-05 7.4712 LYG2 0.00142611 -4.0822119 C1orf92 8.40E-07 7.4203 HOXA11 0.0181798 -4.0822120 EYA4 0.000101901 7.3837 PASD1 0.017145 -4.0743121 ADRA2C 4.04E-08 7.3544 CSRP3 0.0397223 -4.0413122 MYOD1 0.00338096 7.3498 CST6 0.0350487 -4.0375123 NOS1 0.00196216 7.3307 IGSF1 0.00020312 -4.0368124 SLC27A2 8.86E-09 7.2862 KRT27 0.0640569 -4.0353125 MIR1295 7.10E-07 7.2837 NDST4 0.00282094 -4.0171126 CES4 3.79E-05 7.2016 FABP3 3.54E-05 -4.0033127 SPTB 1.34E-06 6.9061 TMEM16D 0.00837574 -3.9957128 C1orf87 9.81E-07 6.8446 IL1F10 0.020815 -3.973129 ADRA2A 2.57E-06 6.7533 CHRDL2 0.0162398 -3.9533130 LRRC26 0.00115479 6.7452 TOP2A 0.00902653 -3.9523131 SEC1 2.75E-05 6.7322 ADIPOQ 0.0169976 -3.9467

16


132 KRT6A 0.0274447 6.7121 PSAT1 0.000145387 -3.9405133 PAX2 0.000700939 6.6691 DSG1 0.0303598 -3.932134 ELF5 0.000124623 6.6192 EBF2 0.00711868 -3.9296135 ALDH3A1 0.00132063 6.5814 BVES 8.11E-05 -3.9225136 USP6 4.71E-05 6.5363 NOG 0.0077547 -3.9156137 MSMB 4.78E-05 6.5217 EDN3 0.0219593 -3.9062138 FOXJ1 6.43E-06 6.5162 LCE2D 0.0183431 -3.9019139 CYP4B1 0.00111263 6.4792 PCDH10 0.00446531 -3.8997140 ACADL 3.41E-05 6.364 ZFY 0.0422992 -3.8948141 PNLDC1 0.000167751 6.3437 LCE1C 0.0340865 -3.8933142 SH3GL3 0.00441108 6.3172 RASGEF1C 0.00635796 -3.8874143 CHRNA6 3.30E-09 6.315 COL25A1 0.000995746 -3.8742144 C20orf185 6.11E-05 6.2814 LZTS1 0.0198336 -3.8675145 FGF9 0.00551208 6.2442 CDCA2 0.000986709 -3.8651146 CA11 0.000439906 6.2398 SERPINA12 0.0259683 -3.8623147 ARSI 1.81E-05 6.1973 CDCA5 0.00765013 -3.8621148 NOV 0.000103639 6.1854 UBE2T 0.00265316 -3.8567149 NCRNA00113 1.08E-10 6.1756 MFAP5 0.00465583 -3.8433150 CYP2B7P1 0.00240509 6.1601 SLN 0.0180046 -3.8399

Note. Genes in boxes (n=6) had their overexpressions confirmed by qPCR and immunohistochemistry, genes in bold (n=4) had their expressions confirmed by qPCR.

17


Supplementary Table 4. Top 500 Differentially Expressed Genes Between Biphenotypic Sinonasal Sarcoma and Alveolar Rhabdomyosarcoma*^

Upregulated Genes in SNS Downregulated Genes in SNSGene p-value Ratio Gene p-value Ratio

1 PLUNC 7.07E-09 108.107 TMEM132D 0.000246646 -126.972 SERPINB3 9.40E-06 89.7604 FGF8 0.00012864 -71.7723 C13orf30 0.00126438 73.0828 SMYD1 0.00608899 -71.1814 CTAG1B 0.00198819 53.4672 ELA2A 0.000555404 -62.5785 C20orf114 4.42E-05 48.4547 DCX 0.00014379 -62.0266 GDF7 5.65E-05 38.466 APOBEC2 0.00135815 -61.1697 C11orf88 0.00176701 32.9217 NELL1 0.00026629 -60.5018 SV2C 0.000834003 32.125 GATA4 0.00102645 -60.0989 SYT1 0.00585911 31.9214 NRTN 0.00142368 -57.791

10 PIGR 0.0213863 30.7632 ACTA1 0.00854447 -56.8411 XAGE2B 4.27E-06 29.8136 ACTC1 0.00651005 -54.81112 TEKT1 1.71E-06 29.4818 MTMR7 8.58E-05 -53.97613 CXCL17 0.0224302 28.3944 FBN3 0.000943276 -51.43514 CAPN13 0.0194503 27.711 MYH8 0.00497254 -50.99615 SLC18A2 0.00183949 27.2424 C20orf200 0.000132883 -48.77616 SELV 0.0210812 25.6551 KBTBD5 0.0038156 -48.74817 PIK3C2G 5.73E-05 25.0835 MYO18B 0.0062162 -45.22618 ADAM33 0.000167624 25.0491 FRMPD1 0.005357 -42.46619 RSPO1 0.0157468 23.9273 TAGLN3 0.00257936 -41.49920 CAPZA3 0.000974623 22.7997 MIMT1 1.73E-05 -39.48921 NOV 0.000877829 20.6772 POPDC3 9.56E-06 -38.62522 TFAP2C 0.000543876 20.6478 RGR 5.65E-05 -38.55123 MYOCD 0.00757379 19.5847 SRRM4 0.00127988 -37.94724 SH3GL3 0.0259415 19.4634 EDN3 0.00115999 -37.22925 ENKUR 0.00142368 19.3349 LOC392395 0.000420696 -36.46926 RSPH1 0.00014379 19.322 C1orf105 8.05E-06 -35.38327 NEGR1 0.00374303 19.2725 PGBD5 6.87E-05 -35.2728 GALNT17 0.00368471 19.2129 OLIG2 5.73E-05 -35.2529 TTR 0.0154405 19.0238 IL17B 0.00374303 -35.013

18


30 ALX4 0.00714315 18.7512 NGB 3.13E-05 -34.29231 GPR81 0.00242539 18.6282 SALL3 0.00118474 -34.20832 MME 0.00521344 17.6025 CKM 0.0494447 -32.23433 SOX2 0.00341445 16.7433 PBK 0.00416909 -30.09534 CES4 0.00375068 16.71 PRDM12 0.00183949 -29.68535 ZIC2 0.0169789 16.1202 CHRNG 8.05E-06 -29.02136 RSPO3 0.000275236 15.5202 DUSP26 0.0184903 -28.57437 C20orf186 0.0552092 15.3705 SLC18A1 7.07E-09 -27.99238 CCKAR 0.0455091 15.2583 TRIM55 1.23E-05 -27.81739 KNDC1 0.00890939 15.1827 CHRND 1.07E-05 -27.12340 PRAME 0.0679781 15.0846 BTBD17 0.00530106 -26.06541 PAX9 0.0049782 14.6384 POU4F2 0.00758612 -25.84642 SVOPL 0.0130128 14.5803 CADM2 0.00445602 -25.543 DLX6AS 0.0451356 14.543 FGFR4 4.27E-06 -25.49644 FAT4 7.63E-06 14.3826 LZTS1 0.00963682 -25.19645 C1orf194 0.0137725 14.2848 CDH12 0.00981869 -25.15946 COL6A6 0.0208391 14.127 MYT1L 0.000529863 -25.08547 FAM5C 0.012062 13.9021 MYOG 1.17E-06 -24.53248 CCDC37 0.0036847 13.7031 DES 0.00925934 -23.65749 MSLN 0.0212893 13.6539 CAPN6 8.44E-05 -23.14450 PTH2R 0.0222658 13.6487 LOC389827 9.56E-06 -23.1351 MMP2 3.29E-06 13.6071 UTS2R 3.54E-06 -22.67352 SNORD94 0.00789484 13.5301 ZSCAN10 0.00266213 -22.57153 ALS2CR11 0.000187836 13.4002 SMPX 0.00239303 -22.55754 C10orf92 0.0194032 13.2028 GPR123 0.000448061 -22.32255 HLA-DRB4 0.0727773 13.1396 DLGAP2 0.000234024 -21.8556 C4orf49 0.000275236 13.0326 MYOM3 0.0100102 -21.54857 GABBR2 0.0321504 12.9927 CBLN2 0.0011904 -21.43558 DNAH12L 0.0111607 12.9609 C10orf71 0.000148141 -21.19959 CYP2F1 0.0404757 12.907 SBK2 0.0104548 -20.67260 AOX1 0.0145664 12.8354 SYN2 1.80E-07 -20.57661 WDR38 0.00014379 12.743 TCF15 0.00509999 -20.55862 PCSK1N 0.0225447 12.6568 MYO7B 0.00558443 -20.27463 CCDC33 0.0038156 12.6436 INA 0.0134378 -20.204

19


64 CYP4B1 0.0359645 12.5494 CSRP3 0.0719089 -20.0865 DUOXA1 0.00527865 12.3579 SOX3 0.000545795 -19.79966 CH25H 0.00106493 12.2933 FAM64A 0.000375799 -19.64667 C1orf192 0.000152943 12.2791 ELA3A 0.00108602 -19.08768 OR2M4 0.0242465 12.1157 KREMEN2 3.82E-05 -19.03369 UBL4B 0.0356771 11.6376 CHGA 0.0251995 -19.00270 LOC10019237 0.00393566 11.4584 PKP1 0.000981495 -18.75971 GDF10 0.000246646 11.4269 LHX1 0.000965818 -18.51672 VIT 0.0407127 11.3238 AURKA 0.00128496 -18.42373 NTNG1 0.0219137 11.3131 ARPP-21 9.61E-05 -18.38574 C9orf4 0.0340917 11.2538 TTN 0.00758612 -18.31575 GRP 0.0352728 11.1353 FAM181A 0.0473495 -18.25676 KRT6A 0.168091 11.0223 PLEKHG4B 0.0053033 -18.18377 HLA-DRB5 0.246056 10.8967 TMSB15A 0.0172877 -18.12778 C20orf85 0.000391551 10.8852 MYLK4 0.00015506 -18.07579 POU3F3 0.0625721 10.8794 SYT4 0.0440483 -18.00980 SERPINB13 0.125638 10.8078 CENPF 0.00698151 -17.90981 PTHLH 0.000463653 10.805 AURKB 0.0100779 -17.84982 CPZ 0.00557187 10.736 PKD2L1 0.00552198 -17.81483 LOC653216 0.000406635 10.7068 MYL4 1.71E-06 -17.67484 ELF5 0.0407127 10.6834 KIFC1 0.00629182 -17.47985 CYS1 0.0122425 10.5882 ZNF488 0.00197293 -17.4286 WIF1 0.0442668 10.5657 MCM2 0.00253985 -17.39587 COLEC12 0.00155659 10.5555 MYH13 0.00474972 -17.30388 TBX3 5.24E-06 10.4762 MIR1289-2 0.017965 -17.29489 C4orf7 0.208044 10.462 MYBPHL 0.0198512 -17.26790 RGS22 0.00520946 10.434 MYH7 0.195376 -17.12391 CP 0.0110733 10.4217 SEZ6 0.00527751 -16.99892 C22orf15 0.0100839 10.4183 CDCA5 0.00245785 -16.79793 COL27A1 0.005357 10.4163 MICAL2 8.05E-06 -16.78494 SCNN1A 0.0241351 10.4145 TNNT3 0.00492918 -16.77495 HPGD 0.0382202 10.382 MYLK2 0.000584416 -16.75496 CYP2B7P1 0.0635272 10.3634 SRPK3 0.0159336 -16.55997 DNAH2 0.00272058 10.3607 CDC45L 0.00238913 -16.291

20


98 SCGB2A1 0.0944868 10.309 CNR1 3.48E-05 -16.22299 CCDC114 0.00683178 10.2613 SLN 0.0077061 -16.184

100 SNORD9 0.0233387 10.2228 MYLPF 0.0834328 -16.18101 MIR874 0.079235 10.136 BEST3 0.0429649 -15.901102 RARG 0.00698151 10.1261 CST2 0.0116279 -15.885103 MXRA8 0.000743037 10.1071 PLCXD3 0.00314084 -15.785104 CEACAM6 0.102294 10.0707 CXorf57 0.0111389 -15.679105 XAGE2 0.000758485 10.0611 LHX4 0.00266213 -15.517106 DNAH3 0.0278656 10.0135 MYL2 0.107952 -15.514107 CYP2A13 0.0106887 9.99812 TROAP 0.00781324 -15.504108 ZIC5 0.0816127 9.9956 PRL 0.0813648 -15.485109 IL33 0.000298164 9.70844 NEUROD2 0.000493172 -15110 GREM2 0.102294 9.56181 CACNG1 0.00331608 -14.951111 OR2M5 0.0473495 9.50801 TEX14 0.00667065 -14.823112 KRT23 0.0965258 9.46753 MYBPH 0.0406591 -14.808113 PSCA 0.0483224 9.43129 FCRLA 0.0351634 -14.753114 BMPER 0.0155432 9.38904 TOP2A 0.0144286 -14.748115 C1QTNF4 0.0149345 9.38813 LIPG 0.00202647 -14.641116 GALNTL6 0.0215319 9.35152 SNTG1 0.0294247 -14.626117 ARSI 0.00248247 9.34971 GTSE1 0.0177741 -14.614118 LEPR 5.24E-06 9.32462 PTTG3P 0.0251995 -14.463119 LMOD1 0.000920138 9.26316 LOC100133545 0.0039169 -14.301120 IGFL2 0.00620245 9.20796 GRM3 0.0158752 -14.234121 FAM181B 0.00931155 9.1858 PKIA 6.69E-05 -14.17122 NKX6-1 0.017965 9.17839 INSM1 8.05E-06 -13.959123 SLC14A1 0.0120158 9.17671 KCNT1 0.0284401 -13.946124 AKAP14 0.0105014 9.16511 BHLHE22 0.00183949 -13.907125 SNORA74A 0.0214982 9.10094 RGPD1 0.0628256 -13.816126 ERN2 0.0472177 9.09972 CDH3 0.0220369 -13.707127 KRT6B 0.269951 9.09223 MYO16 0.0147057 -13.677128 CART1 0.162602 9.06195 C20orf166 0.1001 -13.339129 FADS2 0.00890939 9.03545 CPA5 8.58E-05 -13.338130 TAS1R1 0.0139419 9.03176 KRT33B 0.0282435 -13.336131 C10orf93 0.00601277 9.02984 SGCG 0.00777897 -13.244

21


132 GSTA1 0.127253 8.99287 CCNB2 0.0108065 -13.158133 ADD2 0.00194429 8.91681 PROX1 0.000257545 -13.039134 GABRP 0.0816098 8.85985 SMTNL2 0.00444127 -12.733135 MUC16 0.0392326 8.81608 LOC100128675 0.000482203 -12.396136 C21orf130 0.00115916 8.79975 BUB1 0.0102376 -12.371137 C1orf158 0.0498391 8.64568 TNNC1 0.081791 -12.368138 AGR3 0.0044149 8.60449 PITX3 0.000235586 -12.196139 CEACAM5 0.110621 8.60244 CABP7 5.24E-06 -12.167140 VWA3B 0.00887671 8.54641 SIM1 0.0189609 -12.125141 CHD5 0.0065092 8.53991 DTL 0.00757141 -12.071142 FOXL2 0.0258602 8.52046 CDCA7 0.010396 -12.039143 KRT19 0.0588622 8.4771 DBH 0.0404757 -12.009144 CD200 0.00169042 8.45454 C2orf48 0.0201784 -11.993145 C1orf87 0.00489321 8.41708 SCN4A 0.0147946 -11.833146 TACSTD1 0.0377883 8.39666 KIF1A 0.102294 -11.806147 FAM3D 0.139077 8.3849 TRIM36 0.00168828 -11.797148 PANX2 0.0204284 8.31392 ASPM 0.00870422 -11.795149 C11orf92 0.0526495 8.29751 MYLC2PL 0.0051167 -11.785150 AMTN 0.0513004 8.25237 MGC45800 0.0159734 -11.676151 LYPD2 0.0136607 8.23864 NKAIN4 0.0339158 -11.559152 FOXG1 0.0250166 8.21989 CAMK2B 0.000379559 -11.519153 KLK11 0.162501 8.20454 KIF20A 0.0190618 -11.505154 ODAM 0.20942 8.14329 HSPB3 0.00238913 -11.469155 OPRK1 0.0167622 8.13192 DNAH17 0.0105217 -11.421156 VSTM2A 0.0349503 8.07592 STMN2 0.0121886 -11.381157 KCNN1 0.0145635 8.06143 HRASLS 0.0206304 -11.315158 ARMC3 0.0272916 8.04674 ISG15 0.00499736 -11.28159 CYP1A2 0.0590961 7.99739 KIF19 3.29E-06 -11.239160 PNMA3 0.00374303 7.98842 CHRDL2 0.0191143 -11.239161 SEMA6D 0.00119042 7.96599 TNNI1 0.01663 -11.159162 S1PR2 0.00183949 7.9479 NCAPG 0.00475844 -11.156163 FLJ23834 0.0404757 7.93687 FAM163A 0.0985109 -11.135164 SCUBE3 0.127628 7.92442 LOC389257 0.020474 -11.114165 CD164L2 0.167554 7.90832 BVES 9.09E-05 -11.092

22


166 FLJ10324 0.00915346 7.90172 KRT31 0.00331742 -11.081167 NTRK2 0.000463653 7.86606 KIF24 0.0134927 -11.078168 MMP10 0.0567918 7.85082 LINGO1 0.0206628 -11.042169 ESPN 0.0523775 7.84315 OTOF 0.00140168 -11.038170 NKD1 0.0867874 7.83536 SCN3B 0.00450465 -10.944171 ENPP2 8.05E-06 7.82768 EPHA7 0.0245423 -10.895172 ABCA13 0.0721518 7.75098 ARSF 0.0098606 -10.884173 C1orf92 0.00702106 7.73309 SYT17 0.0225447 -10.848174 LCN2 0.15499 7.71067 MYT1 0.0659801 -10.814175 HPSE2 0.0442654 7.69215 COL25A1 0.00393137 -10.81176 FOXJ1 0.0106302 7.68721 NKAIN1 0.00203338 -10.767177 CCL28 0.000448886 7.65782 C16orf59 0.0930286 -10.76178 ADRA1D 0.0659801 7.65618 ESCO2 0.00759177 -10.733179 SLC6A14 0.0621268 7.64271 HOXD13 0.19704 -10.721180 SNORA60 0.00847146 7.63817 KCNH2 6.06E-05 -10.717181 ALX3 0.000207579 7.61932 MYBPC2 0.0200964 -10.68182 SEC14L3 0.0490796 7.59649 UNC45B 0.0215873 -10.651183 WNT5A 0.0195874 7.52609 TK1 0.0137071 -10.589184 SERPINB11 0.0843453 7.49965 PNMA2 0.0468203 -10.559185 KRT5 0.295017 7.45923 HIST1H1B 0.00510218 -10.53186 WNT7B 0.0576228 7.44624 PCDH8 0.000780778 -10.468187 LOC730347 0.0365952 7.41223 INHBE 6.51E-05 -10.438188 PTPN13 0.00956912 7.36979 LBX1 0.0679781 -10.422189 ZFHX4 0.000246646 7.33829 LOC340156 0.000180339 -10.352190 ASCL1 0.0986927 7.31928 ENPP6 0.0378502 -10.343191 STOML3 0.0392326 7.30737 SPSB4 5.24E-06 -10.339192 TWIST1 0.0149408 7.26853 KIF4A 0.058834 -10.294193 PNLDC1 0.0553282 7.26826 ANKRD2 0.0168016 -10.279194 CNTN1 0.0562559 7.26157 LOC154822 5.24E-06 -10.241195 OR2T4 0.0684334 7.23925 MIR660 0.00255472 -10.166196 DYNLRB2 0.0168241 7.22726 AIPL1 1.86E-06 -10.011197 DLX5 0.0251995 7.20993 KCNF1 0.029823 -9.9969198 WNK4 0.113487 7.17952 SGOL1 0.0113204 -9.9688199 GLIS1 0.0634845 7.17813 SST 0.0479032 -9.9621

23


200 LLGL2 0.0308545 7.17112 ACTN2 0.0591877 -9.9529201 DUOX1 0.00792649 7.15229 CCNE1 0.000957315 -9.9374202 SLC6A4 0.0142732 7.14847 MPO 1.33E-05 -9.8765203 EPHA5 0.0281748 7.12519 ASB10 0.0323086 -9.864204 CCL14 0.00183949 7.07469 HJURP 0.00890939 -9.837205 C6 0.114154 7.07217 GJD4 6.30E-06 -9.6348206 SNORA39 0.00399848 7.05972 RAPSN 2.92E-05 -9.6348207 FOXA1 0.165607 7.05048 COL22A1 0.0983549 -9.6322208 ABCG2 0.00712692 6.97008 COMP 0.032158 -9.592209 MIR27B 0.0198267 6.96941 RHEBL1 0.000493172 -9.567210 C10orf79 0.00375068 6.9337 NHLH1 0.00781324 -9.55211 KRT14 0.275883 6.90906 NKX6-2 0.0124246 -9.5469212 PAX3 0.0756772 6.90061 LRTM1 0.021265 -9.5443213 ALX1 0.0843453 6.85754 LPPR5 0.0118675 -9.5178214 CYTL1 0.0288208 6.84044 DRGX 0.000119658 -9.4566215 LPPR3 0.031246 6.83028 BLM 0.00193701 -9.4355216 DPYS 0.0495627 6.82347 LOC727924 0.170194 -9.4238217 ADAM28 0.00586097 6.81877 C14orf73 0.00313586 -9.4204218 GPX6 0.111356 6.81122 LAMA1 0.0362659 -9.4117219 HOXC10 0.281157 6.80079 MEOX2 0.00623485 -9.3611220 RNF175 0.020904 6.78131 CASQ2 0.00762922 -9.3584221 ANXA8L1 0.283314 6.76991 C13orf33 0.000301003 -9.3566222 PLCH1 0.0378502 6.76351 UBE2T 0.0108338 -9.2911223 CDC42BPG 0.0364579 6.7518 PRKAG3 0.00829392 -9.2794224 C4orf45 0.0033334 6.7035 NES 0.0147946 -9.2168225 C3orf15 0.0508328 6.67439 HAMP 0.0595948 -9.166226 NUDT9P1 0.0120158 6.66036 KIF18A 0.00198569 -9.1446227 C6orf97 0.0200964 6.63768 TMEM132B 0.00769702 -9.1389228 DNAI1 0.0587692 6.62857 PASD1 0.112886 -9.1258229 LRRC50 0.0679781 6.62606 CA9 0.0288256 -9.1088230 LDLRAD1 0.00331608 6.61087 KIAA0367 0.095085 -9.1087231 ASTN1 0.0659824 6.60173 TFRC 0.0716598 -9.1024232 GAL3ST3 0.191014 6.5891 HFE2 0.0845411 -9.0816233 NWD1 0.117204 6.57299 FIT1 4.79E-06 -9.0592

24


234 TC2N 0.0420109 6.56477 IGF2BP3 0.011321 -9.0567235 ADH7 0.282893 6.56298 ZNF311 0.0144641 -9.0204236 MIR1295 0.0233387 6.54327 HRNBP3 0.0213831 -8.9828237 SERPINB4 0.0346129 6.49628 FANCI 0.011321 -8.9738238 CA11 0.0038127 6.48975 MIR133B 0.0150416 -8.9539239 CLDN3 0.0536166 6.48853 KLHL30 0.00527865 -8.93240 LONRF2 0.000854104 6.46795 PEG3 0.0106302 -8.8872241 ATRNL1 0.00665536 6.46305 PEG3AS 1.51E-06 -8.8834242 HORMAD1 0.0100548 6.44928 C13orf3 0.0105221 -8.818243 SNORD90 0.00267054 6.44769 BRSK2 0.000276319 -8.788244 SCGB1A1 0.118601 6.44605 MYL1 0.127654 -8.7858245 SOX21 0.224357 6.44438 ATPGD1 0.0262322 -8.7644246 OR2M3 0.00585448 6.43241 RRP12 0.0763883 -8.7635247 TMPRSS11E2 0.248062 6.43126 KBTBD10 0.0162198 -8.7365248 PTX3 0.0482249 6.41336 NEU4 0.101233 -8.6578249 TTLL10 0.128323 6.37731 STAC3 0.00202498 -8.6454250 TRPM3 0.0320107 6.33847 PPM1E 0.0619712 -8.6037251 MIR125A 0.0662151 6.32487 CENPE 0.00775127 -8.5688252 CCL16 0.000152492 6.30745 INSM2 0.0424381 -8.5515253 WDR86 0.0233387 6.29005 KCNJ5 0.0015469 -8.5268254 CCDC85A 0.00176701 6.27166 KIF11 0.00129353 -8.4913255 B3GNT7 0.045377 6.25137 ANK2 0.000101895 -8.4676256 TMEM215 0.0494447 6.23281 PIPOX 0.0320107 -8.4655257 XG 0.0100102 6.23017 C5orf46 0.0127254 -8.4589258 VEGFC 0.000207579 6.22669 C7orf33 0.0244215 -8.4362259 SLPI 0.0951938 6.2248 BIRC5 0.0178478 -8.4329260 PPP1R1A 0.0659233 6.21106 ZNF695 0.0472121 -8.4207261 UGT2A2 0.13259 6.20645 DDN 0.0166762 -8.4038262 RARB 0.000101895 6.19518 ESRRG 0.00109444 -8.3403263 LRRC26 0.0793988 6.18337 CTNND2 0.00377321 -8.3273264 C11orf21 0.0166539 6.18272 SCT 9.61E-05 -8.2848265 VWA3A 0.0088291 6.18117 ALK 0.00194429 -8.272266 LRRTM4 0.266407 6.17728 N4BP3 0.00446187 -8.265267 GAGE5 0.0234888 6.17674 NPPA 0.0144535 -8.2539

25


268 C21orf121 0.115322 6.17348 HRC 0.0207534 -8.2492269 MIRLET7I 0.00197293 6.16919 VGLL2 0.00445602 -8.2433270 SHANK1 0.0456715 6.16681 KIR3DS1 0.0162789 -8.2131271 GPR27 0.155455 6.13313 SOX11 0.061711 -8.1665272 PAX1 0.0213344 6.13058 CRMP1 0.00743473 -8.1603273 B3GNT9 0.0100102 6.09439 C12orf48 0.0200744 -8.1502274 C1QTNF7 0.0200964 6.09214 ANKRD34B 8.96E-05 -8.119275 GAGE7 0.0200964 6.08567 C1orf135 0.0133559 -8.1177276 B4GALNT4 0.076998 6.07041 MYPN 0.0323886 -8.1086277 FGL1 0.0678679 6.06303 SGCA 0.0309974 -8.0975278 SLC27A2 0.0133559 6.06159 CSMD1 0.0331962 -8.0795279 GRIA3 0.00610532 6.05702 SNTG2 0.217847 -8.0436280 NCRNA00113 0.00299344 6.03884 NXPH2 0.0873093 -8.0435281 BMP6 0.00147047 6.03475 DPP6 0.196031 -8.0264282 SNORD101 0.0682052 6.0003 ELAVL2 0.0639623 -7.9749283 XYLT1 0.0316513 5.98629 SLC26A4 0.0679781 -7.9601284 FAM183A 0.0325667 5.93913 TMEM169 0.00238648 -7.9581285 CTTNBP2 0.0043604 5.93666 EFCBP1 0.120173 -7.8938286 ROPN1L 0.0233387 5.9356 CYP27B1 0.0400638 -7.8696287 TSPAN10 0.0382885 5.92905 SPINT2 0.0662291 -7.8661288 GATA2 0.00692588 5.91366 EPHA8 0.0260871 -7.8561289 TSPAN32 0.0242465 5.91246 COL20A1 0.115076 -7.8198290 ARSE 0.243208 5.89675 GP6 0.0404757 -7.797291 SNORD36B 0.0733641 5.88282 RPL3L 0.0366279 -7.7549292 SNORA13 0.0240736 5.86938 OTX2 0.0131615 -7.7508293 TCN1 0.239387 5.85955 C15orf42 0.0276071 -7.7466294 OR2A7 0.0454479 5.85948 COL9A1 0.0233387 -7.7389295 AQP5 0.132235 5.85309 CKAP2L 0.0462567 -7.719296 C20orf185 0.185747 5.83802 KCNG3 0.00270741 -7.7143297 LRRC4B 0.0561263 5.83302 MLF1IP 0.00781324 -7.6489298 GDNF 0.00789484 5.81647 TSG1 0.031887 -7.6398299 COL24A1 0.0363368 5.81264 MCM10 0.0359767 -7.6121300 ALDH1A2 0.00870422 5.80425 MYBPC1 0.112886 -7.5854301 NME5 0.043135 5.79482 OIP5 0.00299252 -7.581

26


302 BIK 0.0641618 5.78207 PLSCR2 0.087016 -7.5528303 SNORA31 0.0700678 5.77463 CHRNA1 0.0522476 -7.5276304 ZP2 0.105889 5.77391 HMP19 0.00216391 -7.5237305 SNORD83A 0.0930135 5.76064 GPRIN1 0.0681369 -7.5214306 TMEM200B 0.00266977 5.74694 C6orf142 0.0827447 -7.5166307 LTF 0.153197 5.74169 ASF1B 0.00368471 -7.4778308 ADH1C 0.126829 5.73791 GINS4 0.0213344 -7.4472309 COLEC10 0.118891 5.73315 LMNB2 0.0263143 -7.4177310 YSK4 0.0316033 5.72405 RIPPLY1 0.0136273 -7.4045311 GULP1 0.00871132 5.67818 DEPDC1B 0.00276202 -7.3832312 ENPP3 0.0196911 5.67457 CTRC 0.00704223 -7.3774313 MIR24-1 0.0111389 5.66198 LRRC14B 0.00930227 -7.3374314 EFNA5 0.0793988 5.65009 MAPK8IP1 0.0284428 -7.3187315 SNORA27 0.0400638 5.64439 RGAG1 0.0259746 -7.2918316 UGT1A6 0.129194 5.64216 CACNG2 0.0395616 -7.2891317 LRP2 0.196652 5.64063 TRPM8 0.0104678 -7.2562318 SLC25A27 0.0121995 5.63597 KIF2C 0.0219952 -7.2525319 LOC401720 0.00627788 5.63575 GMNN 0.0147946 -7.2444320 FLRT2 0.00246561 5.63185 KCNC2 0.051698 -7.2331321 CNTNAP4 0.0703603 5.63037 TOX 0.0562559 -7.2075322 LOC126075 0.0347866 5.6223 TRIM72 0.000517317 -7.198323 FRMPD2 0.0247575 5.61821 PLA2G2A 0.095526 -7.1587324 EPHX2 0.0469293 5.61453 FAM65B 0.000771667 -7.1128325 GPR109A 0.0283557 5.58363 PBX4 0.0033334 -7.1049326 PITPNC1 2.70E-05 5.57999 PCOLCE2 0.104203 -7.0804327 CCDC11 0.0349543 5.57726 ABLIM3 0.00282798 -7.0711328 ALOX12P2 0.0965913 5.56673 SEMA5B 0.00204674 -7.0476329 GRIK2 0.0562559 5.56364 ST8SIA2 0.0827801 -7.036330 C15orf51 0.00446187 5.55825 NEB 0.0498465 -7.0288331 C1orf133 0.0793988 5.54405 SIRT4 0.0278656 -6.998332 PTGER3 0.0189517 5.52556 GRIN3A 0.0611808 -6.9594333 MYCBPAP 0.00238913 5.49525 CENPN 0.0759485 -6.9565334 LRRIQ4 0.0626705 5.49233 ADAMTS14 0.039212 -6.9344335 MIR429 0.0498447 5.46942 LRFN4 0.0234963 -6.934

27


336 BNC2 0.0113103 5.44902 CBLN1 0.0276071 -6.9183337 HOTAIR 0.382969 5.44112 GSG2 0.102294 -6.9078338 PTPN20A 0.0992135 5.43322 PDLIM4 0.0428732 -6.9055339 RNF180 0.0566172 5.43126 PSAT1 0.0390778 -6.9005340 MMP19 0.00945099 5.41387 SLC29A2 0.00704223 -6.8966341 CDH29 0.108911 5.40366 LCNL1 0.0259746 -6.8898342 YBX2 0.0325667 5.38462 POLQ 0.00314466 -6.8779343 TUBA4 0.075974 5.37592 RBM24 0.000743037 -6.8766344 RADIL 0.0765388 5.34788 NTRK1 0.0416382 -6.8722345 TP53TG3 0.0819454 5.3421 CHEK1 0.00109272 -6.869346 CACNA1C 0.00156123 5.33591 GABRR1 0.132619 -6.8685347 DKFZP564J10 0.0547754 5.32173 CENPA 0.00693492 -6.8403348 RBMS3 1.73E-05 5.31971 ST6GAL2 0.130992 -6.839349 CYP26A1 0.0858287 5.30706 NGFR 0.000623441 -6.8262350 CLSTN3 0.00564259 5.28874 MIR30C2 0.0246205 -6.807351 MMP7 0.0914868 5.2877 FOXA2 0.162 -6.7873352 ABHD12B 0.115908 5.28765 CEP55 0.0371909 -6.7815353 NEK5 0.151488 5.28453 MELK 0.00587413 -6.7316354 LOC340508 0.128279 5.27065 EXO1 0.0142177 -6.7029355 FBLN5 0.00054426 5.26933 P2RX1 0.0595421 -6.6885356 WNT9B 0.012858 5.26647 KIF18B 0.113886 -6.6867357 TMEM204 0.000261274 5.2536 HOXB7 0.130207 -6.6514358 ANXA8L2 0.239541 5.24626 SKA1 0.000610756 -6.6504359 SNORD61 0.0718544 5.23628 XRCC3 0.00702893 -6.649360 SPINT1 0.0477028 5.22484 FOXM1 0.0493867 -6.6483361 SNORD124 0.0469807 5.22175 FRMD3 0.0319828 -6.6396362 SNORA32 0.0158752 5.22166 TACC3 0.0735034 -6.6386363 AGAP11 0.00356317 5.21766 RECQL4 0.0183482 -6.6226364 MAML3 0.00604986 5.215 SLC1A7 0.0512636 -6.6138365 TMEM37 0.019229 5.20847 C9orf61 0.0486047 -6.6007366 SNORD123 0.0284673 5.19854 TTF2 0.0452165 -6.6002367 IQSEC2 0.00203697 5.19115 CDC25A 0.0402258 -6.5981368 FER1L6 0.0827801 5.18922 SLITRK1 0.0575423 -6.597369 AGR2 0.142191 5.17903 FAM89A 0.000288886 -6.5914

28


370 ODZ2 0.0441708 5.17424 CPA1 0.00724056 -6.5883371 MAML2 0.000319503 5.15631 UBE2C 0.0194032 -6.5569372 FLJ44112 0.00724617 5.14565 SATL1 0.0765388 -6.5555373 DMKN 0.143319 5.14119 NUF2 0.00527865 -6.5546374 VTRNA1-1 0.0159069 5.1404 KCNG2 0.0887613 -6.5508375 SNORA36B 0.0147946 5.13016 NPY 0.209769 -6.5504376 MIR100 0.0559234 5.12876 ANK1 0.0138006 -6.531377 PAPPA2 0.0625721 5.12491 TMEM63C 0.0220369 -6.5116378 SORBS2 0.033107 5.11971 EME1 0.00270741 -6.5093379 LY6H 0.0667492 5.10817 PRODH 0.128076 -6.5082380 OR14C36 0.112301 5.0827 C2orf71 0.00741665 -6.4968381 FHOD3 0.000974623 5.08169 RASD1 0.023998 -6.4947382 SNORA40 0.0679781 5.07546 NRCAM 0.0154409 -6.4914383 PION 0.00968957 5.04379 CDC6 0.110362 -6.4869384 C4orf19 0.0562559 5.03647 CORO6 0.0752159 -6.4822385 LRRIQ1 0.156587 5.03447 PDE4C 0.0834328 -6.4683386 EFHC2 0.0675668 5.02604 FAM184A 0.0118869 -6.4642387 NFATC4 0.00191619 5.01572 CCNE2 0.00293138 -6.4602388 HDC 0.0352356 5.01192 KCND3 0.00205165 -6.4382389 SLC5A1 0.0624499 4.99909 ONECUT2 0.0809525 -6.4368390 LTBP1 0.112807 4.96585 RELN 0.0920823 -6.4248391 DNAH10 0.0277313 4.9539 LHX3 0.00213916 -6.4157392 EPCAM 0.0970943 4.95128 LEFTY2 0.0260433 -6.4125393 DPYD 0.0719089 4.95125 PLA2G4D 0.00594028 -6.3969394 AGBL2 0.102439 4.95104 DLK2 0.010912 -6.3856395 KLHDC7B 0.075974 4.95054 ZSCAN12L1 0.0376529 -6.3854396 NOSTRIN 0.000152104 4.93964 ARC 0.00264494 -6.3806397 MAPK10 0.014785 4.93106 DOK7 0.00145439 -6.3754398 CACNA1G 0.0793988 4.92614 KCNJ8 0.112762 -6.3615399 OR2M1P 0.0087315 4.92351 SPOCK3 0.0248272 -6.3598400 CLCNKB 0.00564259 4.92086 LINGO4 0.0870525 -6.3505401 ODF4 0.112807 4.91916 C21orf62 0.0732518 -6.3434402 ATHL1 0.0102376 4.91551 HOXA9 0.043135 -6.3371403 CHL1 0.0298052 4.90811 FLVCR2 0.00242539 -6.2997

29


404 NNMT 0.0256364 4.89501 C10orf62 0.0267478 -6.277405 SLC8A1 0.10648 4.87052 GALNT9 0.179217 -6.2691406 FLJ37587 0.00563503 4.86282 C12orf34 0.0490729 -6.254407 C1RL 0.00702893 4.85621 NMU 0.100531 -6.2296408 MRVI1 0.000152943 4.85145 COBL 0.0095194 -6.2271409 TCTEX1D4 0.0624816 4.84395 MEGF10 0.00788579 -6.2013410 GLT25D2 0.0637296 4.84068 GADD45G 0.0680213 -6.1955411 ATP8B1 0.0668592 4.83824 NECAB1 0.0493691 -6.1939412 IRX6 0.02287 4.83633 TNFRSF13C 0.0709688 -6.1916413 SNORD96A 0.0456711 4.82669 CCDC21 0.0121995 -6.167414 BOC 0.00205125 4.8237 CELA2B 8.58E-05 -6.1602415 SCTR 0.0233387 4.81268 RXRG 0.123513 -6.1342416 NR2E1 0.0713921 4.80778 RRM2 0.164487 -6.1314417 C1orf173 0.0300102 4.80575 NDST4 0.0236641 -6.116418 FCER1A 0.112159 4.80402 SLC38A3 0.0142319 -6.089419 TCEAL2 0.314381 4.78042 TRIM63 0.0232808 -6.0763420 ALOX12B 0.270644 4.77987 CDC7 0.00557901 -6.0485421 CCDC85B 0.0251995 4.77618 CDCA2 0.0510223 -6.0116422 CDC42EP5 0.00128496 4.77178 RIMS3 0.0450341 -6.0083423 C10orf113 0.174688 4.76997 SLC25A18 0.0835462 -5.9963424 DLG4 0.0358006 4.76914 GRM8 0.0876058 -5.996425 PGPEP1 0.00279081 4.75728 CKB 0.0168016 -5.969426 CES1 0.129729 4.75444 FNDC5 0.0319335 -5.9647427 TCEAL6 0.119112 4.75168 HHIP 0.00462212 -5.96428 PLP1 0.067104 4.74991 APOC2 0.03908 -5.96429 PRDM16 0.0864496 4.74944 CACNG6 0.131848 -5.9546430 SLC13A5 0.336679 4.74342 CAMK2N2 0.084966 -5.9363431 SCARNA11 0.0298052 4.74183 HBQ1 0.100724 -5.9339432 EVPL 0.183446 4.74064 HOXA7 0.0243102 -5.9298433 BEST4 0.0712244 4.72603 GGNBP2 0.0453978 -5.9255434 CDH8 0.111037 4.72394 LOC650137 0.0147946 -5.9232435 C10orf107 0.0391305 4.7212 TMEM233 0.115836 -5.9231436 STK33 0.12292 4.71743 ASB2 0.000261274 -5.9149437 LOC389332 0.0519209 4.71078 ZNF560 0.0869303 -5.9076

30


438 NRG2 0.0453872 4.694 GPR37 0.035534 -5.903439 SLC7A8 0.000570005 4.6872 RNF186 0.00202498 -5.9006440 C6orf118 0.0675668 4.67307 POM121L10P 0.123648 -5.8985441 CRISPLD1 0.0553134 4.6638 SYNPO2L 0.084966 -5.8849442 OR2L13 0.0582283 4.66044 SLC7A7 0.00147047 -5.8835443 LRRC16 0.00246561 4.656 FAM71E1 0.0480543 -5.8786444 DCLK1 0.00588305 4.64374 BLCAP 0.0033334 -5.8777445 OSAP 0.00758612 4.62586 FLJ45537 0.0038127 -5.8752446 DBX1 0.0975984 4.62391 CASC5 0.0719674 -5.8551447 SLC16A11 0.0349543 4.61924 MAGEA10 0.419347 -5.8493448 VTRNA1-2 0.166968 4.61041 NKAIN2 0.0921923 -5.8398449 GALR1 0.189718 4.6074 LYG2 0.0399226 -5.7995450 TBX1 0.0658589 4.60156 XIRP2 0.504632 -5.7949451 BLID 0.0159079 4.60063 ASB5 0.29795 -5.782452 WDR16 0.00927404 4.58445 MKRN3 0.112955 -5.7811453 GALIG 0.00409421 4.5775 COX6A2 0.0703379 -5.7725454 CMAH 0.00216897 4.57446 TGM3 0.113232 -5.7707455 SNORD85 0.019388 4.56739 HMX2 0.00025498 -5.7619456 SNORA5A 0.0214956 4.56305 ZNF57 0.000974001 -5.7365457 AHR 0.00128513 4.5544 C19orf15 0.0609461 -5.7318458 C9orf135 0.0819869 4.5512 OMG 0.0718113 -5.7287459 PDE1B 0.000594862 4.55048 SLC24A4 0.00877386 -5.7187460 SAMD5 0.155863 4.54784 LGI2 0.0115107 -5.7049461 MIR1294 0.0960054 4.54405 E2F7 0.00374303 -5.7001462 MRC2 0.00847146 4.54377 POU3F2 0.129884 -5.6905463 ALDH3A1 0.199235 4.54215 DHTKD1 0.00555599 -5.685464 C9orf171 0.106943 4.53871 BYSL 0.047879 -5.6847465 ADAD2 0.0338579 4.53452 ESPL1 0.0456711 -5.6826466 SRD5A2 0.105082 4.53421 TNNI2 0.0665913 -5.6805467 LOC339535 0.251123 4.5282 ZNF233 0.00704223 -5.6697468 RNF39 0.289904 4.52099 DHRS7C 0.26704 -5.6656469 TRIM29 0.201074 4.50835 C20orf55 0.0221066 -5.6402470 SPRR3 0.573007 4.50551 PIF1 0.00732758 -5.6389471 SLFN13 0.0047299 4.50308 TMCC3 0.00557187 -5.6317

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472 MAS1 0.325267 4.50128 CDK5R1 0.000550018 -5.6101473 TMEM102 0.297871 4.49321 PALM2 0.00843566 -5.6067474 ADCY5 0.0985109 4.48842 LHX2 0.32279 -5.5977475 MICA 0.101872 4.4877 TTK 0.019226 -5.5906476 STAT4 0.0144535 4.48697 KIF15 0.105405 -5.5898477 MAGEA4 0.119112 4.48641 ZIM2 0.00377321 -5.5847478 MOV10L1 0.125773 4.48578 C8orf34 0.000555404 -5.5684479 VIPR1 0.0334895 4.48334 CNPY1 0.0137071 -5.5509480 PREX2 0.029584 4.48268 HIST1H3I 0.00360054 -5.5095481 SNORD98 0.0662961 4.47743 EXOC3L 0.00337135 -5.477482 MPL 0.0137071 4.4763 GRWD1 0.0758011 -5.455483 FAM154B 0.0361029 4.471 TRIP13 0.059414 -5.4539484 SFRP2 0.029058 4.46388 DAPL1 0.378948 -5.4538485 LYNX1 0.0590961 4.46201 LILRA3 0.0679781 -5.4496486 CCDC148 0.0802006 4.4614 UPB1 0.111901 -5.4469487 LAMA3 0.0475947 4.45761 MXD3 0.0440306 -5.4244488 SPTB 0.112498 4.45527 SEMA3D 0.0659801 -5.4112489 CTAG1A 0.0318557 4.45062 KRT86 0.159964 -5.4042490 GNAL 0.0468844 4.4464 MSTN 0.0662151 -5.3946491 OVOL2 0.261526 4.44585 RACGAP1 0.00433889 -5.3869492 WDR69 0.314984 4.44267 ENO3 0.00384629 -5.3766493 LMTK3 0.0794846 4.44102 PLK4 0.00564259 -5.3711494 TTC6 0.091815 4.43514 HAS1 0.216671 -5.3673495 MS4A8B 0.171886 4.43036 CCDC141 0.00216897 -5.3573496 FRMD6 0.00176701 4.42964 C4orf39 0.0344745 -5.3518497 PIB5PA 0.0356074 4.42742 CD300C 0.0562709 -5.3466498 CCDC78 0.0774392 4.42656 TFAP2D 0.195981 -5.3459499 FLT4 0.107647 4.42564 IGSF1 0.0215873 -5.3344500 LRRK2 0.00147047 4.42522 CORO7 0.0340917 -5.3292

Additional Genes of InterestEPHA4 0.0303776 3.88906 MYCN 0.012638 -5.1539NEBL 0.187722 2.20586 TNNT2 0.0147057 -4.9123PRKAR2B 0.317593 2.12501 FOXO1 0.0164641 -4.683GREM1 0.400277 2.04276 MYOD1 0.08786 -4.6427

32


MET 0.924026 1.08033 ABAT 0.00012864 -3.7726DAPK1 0.933258 1.06335 CHD7 0.00781324 -3.6329TCF7L2 0.302596 1.57388 MARCH3 0.00204379 -3.3516ZFP36L2 0.19946 1.39455 CLCN5 0.0403314 -2.972GADD45A 0.772934 1.27471 QDPR 0.0886048 -2.8394

NCOA1 0.000297 -2.6343KCNN3 0.13756 -2.4728SKP2 0.00167743 -2.3208IGFBP3 0.531206 -2.2881MCAM 0.110593 -2.2576IGF1R 0.544864 -1.6023INPP1 0.101749 -1.4356IL4R 0.515506 -1.4091MEG3 0.818222 -1.3225DUSP4 0.947934 -1.112TM4SF10 0.894294 -1.0884HEY1 0.930696 -1.0857

*genes of interest are in bold letters (see Supplementary ref. 25-28). ^based on 8 SNS and 3 ARMS (see Figure 2).

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Supplementary Table 5. Primer and Probe Sequences

Gene Primers Prime Sequence UPL Probe PCR Product SizePAX3 -ex7-forA 5’-TTTCCAGCTATACAGACAGCTTTG MAML3 -ex2-revA 5’-CTAGTCGGAGAAAAATTCCCATC PAX3 -ex7-forB 5’-AGACAGCTTTGTGCCTCCGTCG MAML3 -ex2-revB 5’-ACAAGCACCATTCTGCTGGTCTCCPAX3 -ex5-forA 5’-TTGAGAGAACTCATTACCCTGACA 559 bp, Type 1 and/or MAML3 -ex2-revA 5’-CTAGTCGGAGAAAAATTCCCATC 178 bp, Type 2PAX3 -ex5-forB 5’-CGAACCACCTTCACAGCAGAMAML3 -ex2-revA 5’-CTAGTCGGAGAAAAATTCCCATC MAML3 -ex1-for 5’-CAAACAGCAGCACCCGAGCAAACCPAX3 -ex8-rev 5’-GACACCGTGGTGGTAGGTTCCAGA PAX3 -ex7-forD 5’-CCAGCACCAGGCATGGATTTFOXO1 -ex2-rev 5’-ATGAACTTGCTGTGTAGGGACAGPAX3 -ex7-forB 5’-AGACAGCTTTGTGCCTCCGTCG MAML1 -ex2-revA 5’-TTCTGAGGGGAAGTGGCGCTGTPAX3 -ex7-forC 5’-TCCAACCCCATGAACCCCACCA MAML1 -ex2-revB 5’-AGGAAAGAGGTCCCCGTAGCCA PAX3 -ex7-forB 5’-AGACAGCTTTGTGCCTCCGTCGMAML2 -ex2-revA 5’-ATTGGGTCGCTTGCTGTTGGCA PAX3 -ex7-forC 5’-TCCAACCCCATGAACCCCACCA MAML2 -ex2-revB 5’-AGCCATTGGGTCGCTTGCTGTTPAX3 -ex7-forE 5’-TATACAGACAGCTTTGTGCCTCC NCOA1 -ex10-rev 5’-CACCATCCATCCTGTCTGTC PAX3 -ex6-for 5’-TCAACTGATGGCTTTCAACC NCOA1 -ex11-rev 5’-CATGGAATCTGATCGCCTGTTPAX3 -ex7-forF 5’-GCACCAGGCATGGATTTTCCNCOA2 -ex10-revA 5’-TGTCAACTGATCCAGCAGGGPAX3 -ex7-forG 5’-GACAGCAGCTCTGCCTACTG NCOA2 -ex10-revB 5’-TGTCTGGGAAAAGCTGTGGTPAX7 -ex7-for 5’-CAACCACATGAACCCGGTCAGCA MAML3 -ex2-revB 5’-ACAAGCACCATTCTGCTGGTCTCCGAPDH- for 5'-GGAGTCAACGGATTTGGTGAPDH- rev 5'-GTGATGGGATTTCCATTGATPGK1 -for 5'-CAGTTTGGAGCTCCTGGAAGPGK1 -rev 5'-CTGGCACTGCATCTCTTGGCCNTRK3 -for-qPCR 5’-ACAAGATGCTTGTGGCTGTGNTRK3 -rev-qPCR 5’-CCTCCCTCTGGAAATCCTTC MYOD1 -for-qPCR 5’-CACTACAGCGGCGACTCCMYOD1 -rev-qPCR 5’-TAGGCGCCTTCGTAGCAG MLANA -for-qPCR 5’-GCCCACAAGAAGGGTTTGMLANA- rev-qPCR 5’-ATAAGCAGGTGGAGCATTGG

MYOD1 # 70 116 bp

MLANA # 56 92 bp

PGK1 189 bp

NTRK3 # 71 72 bp

PAX7-MAML3 115 bp

GAPDH 206 bp

PAX3-NCOA1175 bp

189 bp

PAX3-NCOA2213 bp

208 bp

PAX3-MAML1126 bp

135 bp

PAX3-MAML2139 bp

115 bp

MAML3-PAX3 183 bp

PAX3-FOXO1 145 bp

PAX3-MAML3

184bp, Type 1

148 bp, Type 1

224bp ,Type 2

34


MYOG- for-qPCR 5’-GCTCAGCTCCCTCAACCAMYOG- rev-qPCR 5’-GCTGTGAGAGCTGCATTCGPGK1- for-qPCR 5’-GGAGAACCTCCGCTTTCATPGK1- rev-qPCR 5’-GCTGGCTCGGCTTTAACCPAX3 -cloning-for 5’-CGCGGATCCATGGACTACAAGGACGACGACGATAAGACCACGCTGGCCGGCGCTGTGMAML3 -cloning-rev 5’-ATAAATATGCGGCCGCTTAGGGGTTACCAAACAATTCATCWildtype PAX3 probe-EMSA 5′-TTCTGTGGTGTGTGACTAATGGAGTGCMutant PAX3 probe-EMSA 5′-TTCTGTGGTGACGTCTAAATGGAGTGC

UPL, Universal probe library (Roche); EMSA, electrophorectic mobility shift assay.

MYOG # 20 94 bp

PAX3 binding probe

PGK1 # 69 78 bp

PAX3-MAML3 full-length cDNA

35


supplementary information - nature research...5 department of orthopedic surgery, mayo clinic,...

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