. 2019 Apr 26;2(4):e192906. doi: 10.1001/jamanetworkopen.2019.2906

Table. Summary of the Molecular Profiling of 62 Patients.

Patient No.	Cancer Type	Tissue Type and Source	Mean Coverage, X		RNA, Million Reads	Potentially Actionable Somatic Alteration	Potentially Actionable Germline Alteration	Category of Potentially Actionable Findings
Patient No.	Cancer Type	Tissue Type and Source	WES, Normal	WES, Tumoral	RNA, Million Reads	Potentially Actionable Somatic Alteration	Potentially Actionable Germline Alteration	Category of Potentially Actionable Findings
2	ETP-ALL	Bone marrow	61	76	98	MLLT10-PICALM fusion; KMT2E-ASNS fusion	NA	Targeted therapy, MRD/biomarker, diagnostic
2	ETP-ALL	Bone marrow	61	76	98	del(5q)	NA	Targeted therapy
5	Ewing sarcoma	Left femur biopsy	257	233	NA	ERCC2 F332V	NA	No effect
5	Ewing sarcoma	Left femur biopsy	257	233	NA		SDHD G12S	Genetic counseling
10	Rhabdomyosarcoma	Thigh biopsy	196	194	NA	PAX7-FOXO1 fusion	NA	MRD/biomarker, diagnostic
10	Rhabdomyosarcoma	Thigh biopsy	196	194	NA	MDM2 amplification; CDKN2A A102V	NA	Targeted therapy
11	Pilocytic astrocytoma	CNS needle biopsy	191	289	NA	BRAF 507insVLR	NA	Targeted therapy
12	Malignant rhabdoid tumor	Intra-abdominal biopsy	124	455	947	No potentially actionable findings	NA	No effect
13	Medulloblastoma	Cerebellum biopsy	128	383	75	PTCH1 T1195S and PTCH1 copy loss (LOH), GLI2 amplification	NA	Targeted therapy
13	Medulloblastoma	Cerebellum biopsy	128	383	75	TP53K132N and TP53 copy loss (LOH)		No effect
14	AML-M7	Bone marrow	88	507	115	NUP98-KDM5A fusion	NA	MRD/biomarker
14	AML-M7	Bone marrow	88	507	115	RB1 copy loss	NA	No effect
15	B-ALL	Bone marrow	120	424	362	CDKN2A/B homozygous deletion	NA	Targeted therapy
						DDX5-KLF2 fusion	NA	MRD/biomarker
						TP53 R248Q and TP53 copy loss (LOH)	NA	No effect
19	B-ALL	Bone marrow (diagnosis)	115	355	172	PAX5-JAK2 fusion	NA	Targeted therapy, MRD/biomarker, risk stratification
						CDKN2A homozygous deletion	NA	Targeted therapy
						PAX5 A322T and PAX5 copy loss (LOH)	NA	No effect
20	Adrenal gland carcinoma	Adrenal gland biopsy	98	248	178	AKT1 amplification (4 copies)	NA	Targeted therapy
						JAK1 copy gain
						DPYD I543V and DPYD copy loss (LOH)
						TP53 R181H and TP53 copy loss (LOH)	NA	No effect
21	Osteosarcoma	Left femur biopsy	105	282	168	MDM2 (6 copies) and FRS2 (12 copies) amplifications, AURKA copy gain	NA	Targeted therapy
21	Osteosarcoma	Left femur biopsy	105	282	168	PMP22-TP53 fusion	NA	MRD/biomarker
22	ETP-ALL	Bone marrow	88	265	131	JAK3 L857P, PHF6 R225X, MED12 S672fs	NA	Targeted therapy
						KMT2E-ASNS fusion	NA	Targeted therapy, MRD/biomarker
						PICALM-MLLT10 fusion	NA	Targeted therapy, MRD/biomarker, diagnostic
24	B-ALL	Bone marrow	107	406	137	BRAF A320V, KRAS G12V, JAK2 R683G	NA	Targeted therapy
25	Hepatoblastoma	Liver biopsy (FFPE sample)	72	230	122	PRKCA copy gain, ABL2 and DDR2 copy gain and high expression, NOTCH1 G1196D, NCSTN A572G, TLR8 N515H	NA	Targeted therapy
26	Osteosarcoma	Right femur biopsy	145	390	66	MYC amplification (5 copies)	NA	Targeted therapy
26	Osteosarcoma	Right femur biopsy	145	390	66	TP53 copy loss, RB1 copy loss	NA	No effect
29	Adrenal gland carcinoma	Adrenal gland biopsy	87	261	164	PTK2 copy gain, JAK3 copy gain, AKT2 copy gain, ABL1 A34V, TOP2A A1515S, G1386D (LOH)	NA	Targeted therapy
29	Adrenal gland carcinoma	Adrenal gland biopsy	87	261	164	NA	TP53p. R337H	Diagnostic, genetic counseling
31	Neuroblastoma	Mediastinum biopsy	100	226	102	Trisomy 7 (BRAF), CHEK1 copy loss, PRKCA copy gain, PHOX2B 270-272del frameshift, XPC S346P (LOH), APC D917Y	NA	Targeted therapy
32	AML-M5	Bone marrow	90	252	149	CBFB-MYH11 and ICAM2-STX7 fusion	NA	MRD/biomarker
						TP53 (indel) mutation and copy loss (LOH)	NA	No effect
						Trisomy 8 (MYC), NF1 S2309fs and NF1 copy loss (LOH)	NA	Targeted therapy
33	Paraganglioma	Adrenal gland biopsy	111	308	134	SDHB copy loss, DDB2 copy loss, MUTYH Q338H	NA	Targeted therapy
34	Aggressive fibromatosis	Mandible/gums biopsy	60	178	193	CTNNB1 T41A	NA	Targeted therapy
37	B-ALL	Bone marrow	70	206	131	KMT2A-MLLT1 fusion	NA	MRD/biomarker
39	Ewing sarcoma	Rib needle biopsy	138	372	254	CDKN2A copy loss, trisomy 8 (MYC and FGFR1), BRCA1 mutations (LOH), STAG2 R1012X	NA	Targeted therapy
						TP53 R273H	NA	No effect
						EWSR1/FLI1 fusion	NA	MRD/biomarker, diagnostic
						NA	SDHD G12S	Genetic counseling
40	Wilms tumor	Kidney needle biopsy	122	381	238	DDR2 and ABL2 copy gain, DNMT3A P904L	NA	Targeted therapy
47	T-ALL	Bone marrow	90	256	133	CDKN2A homozygous deletion, NOTCH1 I1718T and S2467fs, STAT5B N642H, NT5C2 R367Q	NA	Targeted therapy
48	Myeloproliferative neoplasm	Bone marrow	75	179	132	No findings	NA	No effect
49	Rhabdomyosarcoma	Left fornix biopsy	100	252	127	FGFR4 G388R (LOH)	NA	Targeted therapy
49	Rhabdomyosarcoma	Left fornix biopsy	100	252	127	TP53 copy loss (LOH)	TP53 p.R273C	Diagnostic, genetic counseling
50	Pilocytic astrocytoma	Brain, third ventricle biopsy	73	380	217	FGFR1 656EL, NF1 N1465S, PTPN11 G503A	NA	Targeted therapy
51	Osteosarcoma	Left femur biopsy	134	411	202	TP53 copy loss (LOH)	TP53 p.G245S (mosaicism)	Genetic counseling
51	Osteosarcoma	Left femur biopsy	134	411	202	CDKN2A homozygous deletion, VEGF-A amplification (>4 copies), MYC amplification (>10 copies), JAK2 G996R, CSF1R H362R (LOH), PTK2 exon17:c.1332 + 2T>C (splicing)	NA	Targeted therapy
54	Pilocytic astrocytoma	Optic chiasm–hypothalamus biopsy	142	383	183	KIAA1549-BRAF fusion	NA	Targeted therapy, MRD/biomarker
55	Osteosarcoma	Right tibia biopsy	89	285	112	TEK N452D, KIT S590I, MYC amplification (10 copies)	NA	Targeted therapy
55	Osteosarcoma	Right tibia biopsy	89	285	112	TP53 homozygous del	NA	No effect
57	Neuroblastoma	Abdomen biopsy	125	419	54	PRKCA amplification (5 copies), BRAF amplification (4 copies), AKT2 copy gain, HSP90B1 I66T, CSF1R N648S	NA	Targeted therapy
59	Osteosarcoma	Left femur biopsy	135	408	202	VEGF-A amplification (4 copies) and highly expressed	NA	Targeted therapy
59	Osteosarcoma	Left femur biopsy	135	408	202	TP53-RAB44 fusion	NA	MRD/biomarker
60	T-Cell lymphoblastic lymphoma	Lymph node	135	404	157	MAP2K2 P128L, NOTCH1 S1674F and Q2503insX, MTOR F1888L, CDKN2A R80X, STAT5B N713insKGKGGG	NA	Targeted therapy
60	T-Cell lymphoblastic lymphoma	Lymph node	135	404	157	KLHL33-TEP1 fusion	NA	MRD/biomarker
61	Osteosarcoma	Left humerus biopsy	128	453	178	CDKN2A copy loss, MYC copy gain, DDR2 copy gain and highly expressed, MTOR G1954R	NA	Targeted therapy
62	Sinus carcinoma	Sinus biopsy	111	289	163	PTK2 copy gain, MYC copy gain, ABL2 and DDR2 copy gain, ALK G159fs, NOTCH1 S1674P	NA	Targeted therapy
62	Sinus carcinoma	Sinus biopsy	111	289	163	TP53 copy loss	NA	No effect
67	Epithelial tumor (NOS)	Abdomen biopsy	138	430	51	CREM-FUS fusion	NA	MRD/biomarker
68	T-ALL	Bone marrow	59	203	65	ABL1 copy gain, DDR2 R742W	NA	Targeted therapy
68	T-ALL	Bone marrow	59	203	65	KMT2A-MLLT4 fusion	NA	Targeted therapy, MRD/biomarker
69	Grey zone lymphoma	Lymph node	64	246	70	NA	TP53 p.R213Q	Diagnostic, genetic counseling
70	Leiomyoma	Clavicle biopsy	67	236	55	No potentially actionable findings	NA	No effect
71	Hepatoblastoma	Liver biopsy	62	237	64	No findings	NA	No effect
72	Hepatocarcinoma	Liver biopsy	119	346	120	DNAJB1-PRKACA fusion	NA	MRD/biomarker, diagnostic
73	Pleuropulmonary blastoma	Right lung biopsy	113	311	92	MYC and FGFR1 copy gain and highly expressed, CHEK1 copy loss, CTNNB1 copy gain and very highly expressed, MET Q1276L, DICER1 E1813D	NA	Targeted therapy
73	Pleuropulmonary blastoma	Right lung biopsy	113	311	92	NA	DICER p.Y1225X	Diagnostic, genetic counseling
74	NUT-midline carcinoma	Left fibula needle biopsy	115	354	149	BRD4-NUTM1 fusion	NA	MRD/biomarker, diagnostic
76	Neuroblastoma	Abdominal needle biopsy	103	318	109	CDKN2A homozygous deletion, MET amplification (4 copies) and highly expressed, PHOX2B copy loss, CHEK1 copy loss, ALK F1245I	NA	Targeted therapy
77	Round cell sarcoma	Soft-tissue left ankle biopsy	109	272	67	BCORexon16 ITD, DDR2 copy gain	NA	Diagnostic, targeted therapy
78	Rhabdomyosarcoma	Right calf biopsy	113	393	147	MYCN amplification (5 copies) and highly expressed, KDM1A G703R (LOH)	NA	Targeted therapy
78	Rhabdomyosarcoma	Right calf biopsy	113	393	147	PAX7-FOXO1 fusion	NA	MRD/biomarker, diagnostic
79	Osteosarcoma	Left tibia biopsy (FFPE)	121	367	190	SMO A374E, FBXW7 R465H	NA	Targeted therapy
81	B-ALL	Bone marrow	123	298	143	NRAS G12D, SETD2 E1265fs	NA	Targeted therapy
82	B-ALL	Bone marrow	113	311	215	IKZF1 deletion, FLT3 Y589D	NA	Targeted therapy
82	B-ALL	Bone marrow	113	311	215	ZEB2-CXCR4 fusion and CXCR4 very highly expressed, SEMA6A-FEM1C fusion	NA	MRD/biomarker
86	Metastatic Wilms tumor	Right kidney biopsy	106	287	143	CDC73 M1V, CSF3R G751A, FLT4 A992fs, NTRK1 G607V and H598Y and copy loss (LOH)	NA	Targeted therapy
87	Gastric NET	Celiac lymph node biopsy	99	256	38	CHEK1 copy loss	NA	No effect
88	Burkitt lymphoma	Abdomen biopsy	115	364	38	B2M M1R, HDAC1 Y303H, PIK3C2A splicing mutation, CCND3 R256fs, PTEN copy loss	NA	Targeted therapy
						IGH-MYC fusion	NA	MRD/biomarker
						TP53 G302fs	NA	No effect
89	B-ALL	Bone marrow	56	134	111	CDKN2A homozygous deletion, AURKA copy loss, NRAS G12D	NA	Targeted therapy
91	Teratoma malignant (NOS)	Brain, left ventricle biopsy	103	261	107	No findings	NA	No effect
92	AML	Bone marrow	61	179	134	NRAS G12D	NA	Targeted therapy
92	AML	Bone marrow	61	179	134	KMT2A-MLLT3 fusion	NA	MRD/biomarker
93	Ganglioneuroblastoma nodular	Retroperitoneal biopsy	142	340	80	MET K324M, High ALK expression	NA	Targeted therapy
94	Lymphoma	Mediastinum biopsy (FFPE)	66	246	NA	CDKN2A homozygous deletion,	NA	Targeted therapy
94	Lymphoma	Mediastinum biopsy (FFPE)	66	246	NA	PTEN L182fs and copy-neutral LOH	NA	Targeted therapy
99	AML	Bone marrow	76	248	109	HDAC2 E455fs	NA	Targeted therapy
99	AML	Bone marrow	76	248	109	KHDRBS3-ANGPT1 fusion		Targeted therapy, MRD/biomarker
100	Ovarian tumor	Ovary biopsy	82	268	72	CD74 P98S	NA	Targeted therapy
102	Melanotic neuroectodermal tumor of infancy	Periostium skull lesion biopsy (FFPE)	83	170	NA	No potentially actionable findings	NA	No effect
104	Alveolar rhabdomyosarcoma	Right foot biopsy	359	160	77	PAX3-FOXO1 fusion	NA	MRD/biomarker, diagnostic
104	Alveolar rhabdomyosarcoma	Right foot biopsy	359	160	77	RB1 F650S and copy loss (LOH)	NA	No effect
106	Neuroblastoma	Right adrenal biopsy	131	352	64	MYCN amplification (10 copies)	NA	Targeted therapy
106	Neuroblastoma	Right adrenal biopsy	131	352	64	MYCN amplification (10 copies)	SDHB S163P	Genetic counseling

Abbreviations: AML, acute myeloid leukemia; B-ALL, B-cell acute lymphoblastic leukemia; CNS, central nervous system; ETP-ALL, early T-cell precursor acute lymphoblastic leukemia; FFPE, formalin-fixed, paraffin embedded; LOH, loss of heterozygosity; MRD, minimal residual disease; NA, not applicable; NET, neuroendocrine tumors; NOS, not otherwise specified; NUT, nuclear protein of the testis; T-ALL, T-cell acute lymphoblastic leukemia; VEGF-A, vascular endothelial growth factor A; WES, whole-exome sequencing.