Supplementary Table 7. 159 primary tumor samples with CNV, methylation, RNA-seq, SNP data, and clinical follow-up information. sample_name gender height os weight age histological_type os_status stage_T stage_N stage_M stage TCGA-VR-A8EW 1 164 247 48 57 Esophagus Squamous Cell Carcinoma 1 T3 N2 M0 Stage IIIB TCGA-VR-A8EU 1 174 557 51 51 Esophagus Squamous Cell Carcinoma 1 T1 N1 M1 Stage IV TCGA-L5-A8NH 1 183 393 96 54 Esophagus Adenocarcinoma, NOS 1 T1 N0 M1 Stage IV TCGA-VR-A8EQ 1 184 694 75 73 Esophagus Adenocarcinoma, NOS 1 T3 N1 M0 Stage III TCGA-LN-A49Y 1 168 379 57 77 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-2H-A9GH 1 183 951 91 44 Esophagus Adenocarcinoma, NOS 1 T1 N1 M0 Stage IIB TCGA-L5-A8NG 1 166 1094 81 77 Esophagus Adenocarcinoma, NOS 0 T3 N1 M0 Stage III TCGA-V5-A7RE 1 169 500 77 45 Esophagus Adenocarcinoma, NOS 0 T3 N1 M0 Stage IB TCGA-L5-A8NT 1 183 825 84 69 Esophagus Adenocarcinoma, NOS 0 T3 N0 M0 Stage IIB TCGA-L5-A43C 1 155 96 95 81 Esophagus Adenocarcinoma, NOS 0 T3 N1 MX Stage III TCGA-2H-A9GI 1 188 435 100 68 Esophagus Adenocarcinoma, NOS 1 T3 N1 M0 Stage III TCGA-L5-A8NK 0 161 412 67 84 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-V5-AASW 1 175 282 88 72 Esophagus Adenocarcinoma, NOS 0 T3 N1 M0 Stage IIIA TCGA-Z6-AAPN 1 165 81 74 57 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-L5-A4OE 1 Not Available 730 88 81 Esophagus Adenocarcinoma, NOS 1 T3 N2 Stage IIIB TCGA-ZR-A9CJ 1 Not Available 600 Not Available 65 Esophagus Adenocarcinoma, NOS 1 T3 N3 MX Stage IIIC TCGA-LN-A5U5 1 164 136 47 57 Esophagus Squamous Cell Carcinoma 1 T3 N1 M1 Stage IV TCGA-L5-A8NW 1 178 1402 103 55 Esophagus Adenocarcinoma, NOS 1 T2 N1 M0 TCGA-LN-A5U7 1 169 768 53 46 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-VR-A8EY 0 165 1025 70 44 Esophagus Squamous Cell Carcinoma 0 T3 NX M0 Stage IIA TCGA-LN-A7HV 1 174 320 72 58 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-L5-A4OI 1 173 608 83 79 Esophagus Adenocarcinoma, NOS 0 T3 N3 MX Stage IIIC TCGA-L5-A8NJ 1 173 501 81 77 Esophagus Adenocarcinoma, NOS 0 T3 N1 M0 Stage III TCGA-LN-A49P 1 175 375 62 71 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-LN-A49X 1 Not Available 384 Not Available 44 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-2H-A9GR 1 168 987 67 80 Esophagus Adenocarcinoma, NOS 1 T3 N0 M0 Stage IIA TCGA-LN-A7HZ 1 176 401 62 49 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-JY-A93F 0 165 731 73 58 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IB TCGA-LN-A9FO 1 170 4 65 42 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-KH-A6WC 1 165 191 72 82 Esophagus Squamous Cell Carcinoma 0 T1 N0 M0 Stage IA TCGA-L5-A8NE 1 170 1688 94 77 Esophagus Adenocarcinoma, NOS 0 T2 N1 M0 Stage IIB TCGA-L5-A43J 1 169 0 61 90 Esophagus Squamous Cell Carcinoma 1 T3 N0 MX Stage IIB TCGA-IG-A97I 1 174 370 62 58 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-JY-A939 1 180 660 89 77 Esophagus Adenocarcinoma, NOS 0 T1 N1 M0 Stage IIB TCGA-L5-A4OW 0 157 217 100 56 Esophagus Adenocarcinoma, NOS 1 T2 N1 M0 Stage IIB TCGA-2H-A9GK 1 180 232 80 43 Esophagus Adenocarcinoma, NOS 1 T3 N1 M0 Stage III TCGA-LN-A4A1 1 172 383 65 60 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-LN-A4A9 1 178 351 72 58 Esophagus Squamous Cell Carcinoma 1 T2 N0 M0 Stage IIA TCGA-R6-A8WC 1 180 70 89 56 Esophagus Adenocarcinoma, NOS 0 T3 N0 M0 Stage IIA TCGA-L5-A88W 1 182 764 80 67 Esophagus Squamous Cell Carcinoma 1 T3 N0 MX Stage IIA TCGA-LN-A49W 1 162 403 61 73 Esophagus Squamous Cell Carcinoma 0 T3 N1 M0 Stage III TCGA-2H-A9GQ 1 178 128 80 80 Esophagus Adenocarcinoma, NOS 1 T3 N1 M0 Stage III TCGA-L5-A4OX 1 183 226 110 60 Esophagus Adenocarcinoma, NOS 1 T2 N1 M0 Stage IIB TCGA-JY-A93C 1 169 705 62 47 Esophagus Adenocarcinoma, NOS 0 T3 N2 M0 Stage IIIB TCGA-2H-A9GJ 1 189 1781 70 57 Esophagus Adenocarcinoma, NOS 1 T1 N0 M0 Stage I TCGA-2H-A9GO 1 170 494 83 58 Esophagus Adenocarcinoma, NOS 1 T3 N1 M1a Stage IVA TCGA-XP-A8T6 1 Not Available 763 70 54 Esophagus Squamous Cell Carcinoma 1 T2 N1 M0 Stage IIB TCGA-R6-A8W8 1 171 88 91 72 Esophagus Adenocarcinoma, NOS 1 T3 N1 M0 Stage IIIA TCGA-XP-A8T8 1 Not Available 437 62 49 Esophagus Squamous Cell Carcinoma 0 T1 N1 M0 Stage IIB TCGA-LN-A7HW 1 176 365 69 59 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-L5-A893 0 150 92 67 71 Esophagus Adenocarcinoma, NOS 0 T1 N0 M0 Stage I TCGA-R6-A6L4 1 179 496 106 27 Esophagus Adenocarcinoma, NOS 1 T3 N1 M0 Stage IIIA TCGA-VR-A8Q7 1 170 1590 57 60 Esophagus Squamous Cell Carcinoma 0 T3 N1 M0 Stage IIIA TCGA-R6-A6DQ 0 168 231 56 74 Esophagus Adenocarcinoma, NOS 1 T3 N1 M0 Stage IIIA TCGA-Z6-A8JD 1 172 104 69 53 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIB TCGA-R6-A6KZ 1 180 154 71 42 Esophagus Adenocarcinoma, NOS 1 TX NX M1 Stage IV TCGA-R6-A6XQ 1 178 193 85 58 Esophagus Adenocarcinoma, NOS 1 T3 N1 M1b Stage IVB TCGA-L5-A8NR 0 157 265 60 81 Esophagus Adenocarcinoma, NOS 0 T3 N1 M0 Stage III TCGA-JY-A6FG 1 173 1263 110 50 Esophagus Squamous Cell Carcinoma 1 T3 N1 M0 Stage III TCGA-IG-A3YA 1 179 632 76 53 Esophagus Squamous Cell Carcinoma 0 T4 N0 M0 Stage IIIA TCGA-LN-A4A8 1 175 472 68 52 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-IC-A6RE 1 183 234 102 59 Esophagus Adenocarcinoma, NOS 0 T1 N1 M0 Stage IIB TCGA-2H-A9GL 1 173 180 85 74 Esophagus Adenocarcinoma, NOS 1 T3 N1 M0 Stage III TCGA-JY-A6FE 1 176 112 62 49 Esophagus Squamous Cell Carcinoma 1 T3 N1 M0 Stage III TCGA-V5-AASX 1 192 273 100 74 Esophagus Adenocarcinoma, NOS 0 T3 N2 M1 Stage IV TCGA-LN-A9FQ 1 172 391 63 62 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-IG-A6QS 1 176 303 70 54 Esophagus Squamous Cell Carcinoma 1 T2 N1 M0 Stage IIB TCGA-L5-A88S 1 183 471 77 84 Esophagus Squamous Cell Carcinoma 0 T3 N0 MX Stage IB TCGA-LN-A4A5 1 175 681 68 49 Esophagus Squamous Cell Carcinoma 1 T2 N0 M0 Stage IIA TCGA-L5-A4OP 0 150 218 71 67 Esophagus Adenocarcinoma, NOS 0 T1 N0 MX Stage IA TCGA-JY-A6FB 1 177 1837 95 77 Esophagus Adenocarcinoma, NOS 0 T1 N0 M0 Stage I TCGA-LN-A7HX 1 172 372 67 72 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-JY-A93D 1 197 960 52 51 Esophagus Adenocarcinoma, NOS 1 T2 N3 M0 Stage IIIC TCGA-JY-A6FD 0 152 2069 65 51 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-L5-A88T 1 174 694 80 86 Esophagus Adenocarcinoma, NOS 0 T2 N1 M0 Stage IIB TCGA-LN-A49M 1 168 385 57 62 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-VR-A8EO 1 179 785 63 49 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-L5-A4OO 1 178 101 77 75 Esophagus Adenocarcinoma, NOS 0 T3 N3 M0 Stage IIIC TCGA-2H-A9GN 1 185 272 82 70 Esophagus Adenocarcinoma, NOS 1 T3 N1 M0 Stage III TCGA-LN-A9FP 0 151 366 49 60 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-L5-A4OS 0 157 1271 59 86 Esophagus Adenocarcinoma, NOS 0 T2 N1 M0 Stage IIB TCGA-M9-A5M8 1 174 1007 51 58 Esophagus Adenocarcinoma, NOS 0 T3 N0 M0 Stage IIA TCGA-IG-A3YC 1 169 612 66 62 Esophagus Squamous Cell Carcinoma 0 T3 N1 M0 Stage IIIA TCGA-RE-A7BO 0 167 213 77 72 Esophagus Adenocarcinoma, NOS 1 T1 N1 M0 Stage IIB TCGA-L5-A43E 1 183 920 74 74 Esophagus Adenocarcinoma, NOS 0 T1 N0 M0 Stage I TCGA-V5-A7RB 1 172 161 133 59 Esophagus Adenocarcinoma, NOS 1 T2 N1 MX Stage IIB TCGA-L5-A8NF 1 173 81 89 57 Esophagus Adenocarcinoma, NOS 1 T1 N0 M1a Stage IVA TCGA-L5-A4OM 0 Not Available 1458 69 54 Esophagus Squamous Cell Carcinoma 1 T1 N0 Stage IA TCGA-L5-A88V 1 175 79 73 60 Esophagus Adenocarcinoma, NOS 0 T3 N1 MX Stage III TCGA-L5-A88Y 1 185 11 76 76 Esophagus Adenocarcinoma, NOS 0 T1 N0 MX TCGA-L5-A8NV 1 183 1599 82 75 Esophagus Adenocarcinoma, NOS 1 T3 N0 M0 Stage IIA TCGA-JY-A93E 1 173 767 73 61 Esophagus Adenocarcinoma, NOS 0 T3 N1 M0 Stage IIIA TCGA-R6-A6XG 1 192 1168 103 64 Esophagus Adenocarcinoma, NOS 0 T3 N1 M0 Stage IIIA TCGA-VR-AA4D 1 178 1405 82 53 Esophagus Adenocarcinoma, NOS 1 T1 NX M0 Stage IIB TCGA-JY-A938 1 165 1060 72 75 Esophagus Adenocarcinoma, NOS 0 T3 N0 M0 Stage IIB TCGA-Z6-A9VB 1 159 40 62 53 Esophagus Squamous Cell Carcinoma 0 T3 N1 M0 Stage IIIA TCGA-IG-A50L 1 162 16 61 58 Esophagus Squamous Cell Carcinoma 0 T3 N1 M0 Stage IIIA TCGA-L5-A4OG 0 163 143 67 79 Esophagus Adenocarcinoma, NOS 0 T1 N0 M0 Stage I TCGA-L5-A8NI 1 Not Available 410 89 79 Esophagus Adenocarcinoma, NOS 1 T3 N1 M0 Stage III TCGA-R6-A6Y0 1 173 1641 94 54 Esophagus Adenocarcinoma, NOS 0 T3 N1 M1a Stage IVA TCGA-IG-A4QS 1 172 118 78 71 Esophagus Adenocarcinoma, NOS 1 T3 N2 M0 Stage IIIB TCGA-IG-A5S3 0 179 712 69 69 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIB TCGA-VR-A8EX 1 171 855 60 63 Esophagus Squamous Cell Carcinoma 1 T1 N1 M1a Stage IVA TCGA-LN-A49S 1 173 400 63 59 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-LN-A49U 1 178 467 64 62 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-L5-A4ON 1 180 558 111 65 Esophagus Adenocarcinoma, NOS 1 T1 N1 Stage IIB TCGA-IG-A97H 1 170 441 59 36 Esophagus Squamous Cell Carcinoma 0 T3 NX M0 Stage IIA TCGA-IG-A3YB 1 178 80 80 61 Esophagus Squamous Cell Carcinoma 0 T3 N1 M0 Stage IIIA TCGA-L5-A8NL 1 158 402 80 56 Esophagus Adenocarcinoma, NOS 0 T3 N1 M0 Stage III TCGA-LN-A9FR 1 172 373 61 70 Esophagus Squamous Cell Carcinoma 0 T2 N1 M0 Stage IIB TCGA-JY-A6FH 1 180 1441 95 53 Esophagus Adenocarcinoma, NOS 0 T2 N1 M0 Stage IIB TCGA-L5-A4OH 1 175 992 127 71 Esophagus Adenocarcinoma, NOS 0 T1 N0 M0 Stage I TCGA-IG-A3I8 0 165 1012 48 51 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-S8-A6BV 1 180 609 90 76 Esophagus Adenocarcinoma, NOS 0 T2 N0 MX Stage IIIA TCGA-Z6-A8JE 1 168 64 61 57 Esophagus Squamous Cell Carcinoma 0 T3 N1 M0 Stage IIIA TCGA-VR-AA7I 1 171 484 56 70 Esophagus Squamous Cell Carcinoma 1 T4 N0 M0 Stage III TCGA-IG-A625 1 168 390 50 60 Esophagus Squamous Cell Carcinoma 1 T3 N2 M0 Stage IIIB TCGA-IG-A7DP 0 166 452 58 50 Esophagus Adenocarcinoma, NOS 0 T4a NX MX Stage IIIA TCGA-LN-A4A3 1 172 388 63 61 Esophagus Squamous Cell Carcinoma 0 T3 N1 M0 Stage III TCGA-VR-A8ET 1 160 47 66 64 Esophagus Squamous Cell Carcinoma 1 T2 NX M0 Stage IIA TCGA-LN-A4MQ 1 168 375 56 46 Esophagus Squamous Cell Carcinoma 0 T3 N1 M0 Stage III TCGA-IG-A4P3 1 182 567 86 48 Esophagus Squamous Cell Carcinoma 1 T2 N1 M0 Stage IIB TCGA-LN-A4A4 1 175 383 62 36 Esophagus Squamous Cell Carcinoma 0 T3 N1 M0 Stage III TCGA-L5-A8NS 1 180 408 88 76 Esophagus Adenocarcinoma, NOS 0 T3 N0 M0 Stage IIB TCGA-VR-A8EP 1 173 824 59 51 Esophagus Squamous Cell Carcinoma 0 T3 NX M0 Stage IIIB TCGA-VR-A8EZ 1 167 553 69 47 Esophagus Squamous Cell Carcinoma 1 T3 NX M0 Stage IIIC TCGA-L5-A8NU 1 Not Available 2134 97 84 Esophagus Adenocarcinoma, NOS 1 T2 N0 M0 Stage IIA TCGA-L5-A4OU 1 175 882 82 81 Esophagus Adenocarcinoma, NOS 0 T3 N0 M0 Stage IIA TCGA-L5-A8NM 0 Not Available 236 60 84 Esophagus Adenocarcinoma, NOS 1 T2 N1 M0 Stage IIB TCGA-VR-AA4G 0 159 549 69 51 Esophagus Squamous Cell Carcinoma 0 T2 N2 M0 Stage IIIA TCGA-LN-A5U6 1 172 375 60 54 Esophagus Squamous Cell Carcinoma 0 T2 N1 M0 Stage IIB TCGA-VR-A8ER 1 164 378 46 54 Esophagus Squamous Cell Carcinoma 1 T4 N1 M0 Stage III TCGA-LN-A8HZ 1 175 375 63 56 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-IG-A5B8 1 170 24 64 72 Esophagus Squamous Cell Carcinoma 1 T3 N0 M0 Stage IB TCGA-LN-A8I0 1 171 407 65 52 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-LN-A7HY 1 176 366 65 50 Esophagus Squamous Cell Carcinoma 0 T3 N1 M0 Stage III TCGA-LN-A8I1 0 152 401 61 67 Esophagus Squamous Cell Carcinoma 0 T2 N0 M0 Stage IIA TCGA-2H-A9GF 1 183 784 95 67 Esophagus Adenocarcinoma, NOS 1 T3 N1 M0 Stage III TCGA-S8-A6BW 1 177 620 76 51 Esophagus Squamous Cell Carcinoma 0 T2 N0 MX Stage IB TCGA-IC-A6RF 0 170 477 100 69 Esophagus Squamous Cell Carcinoma 0 T1 N1 M0 Stage IA TCGA-L7-A56G 1 170 330 91 65 Esophagus Squamous Cell Carcinoma 1 T2 NX M0 TCGA-L5-A8NQ 1 178 650 87 71 Esophagus Squamous Cell Carcinoma 1 T2 N0 M0 Stage IIA TCGA-JY-A6FA 1 174 1361 64 51 Esophagus Squamous Cell Carcinoma 1 T2 N1 M0 Stage IIB TCGA-L5-A4OJ 0 164 639 114 70 Esophagus Adenocarcinoma, NOS 0 T1 N0 M0 Stage I TCGA-V5-A7RC 1 171 104 76 55 Esophagus Squamous Cell Carcinoma 1 T4 NX M1 Stage IV TCGA-LN-A49O 1 158 408 57 47 Esophagus Squamous Cell Carcinoma 0 T3 N0 M0 Stage IIA TCGA-IG-A51D 1 178 518 63 63 Esophagus Squamous Cell Carcinoma 0 T2 NX M1 Stage IIB TCGA-L5-A8NN 1 170 167 60 81 Esophagus Adenocarcinoma, NOS 0 T3 N1 M0 Stage III TCGA-R6-A8W5 1 177 480 77 60 Esophagus Adenocarcinoma, NOS 1 T3 N1 M1a Stage IVA TCGA-L5-A891 1 183 114 81 51 Esophagus Adenocarcinoma, NOS 0 T3 N1 M0 TCGA-Q9-A6FW 1 170 238 79 61 Esophagus Adenocarcinoma, NOS 0 T3 N2 M0 Stage IIIB TCGA-R6-A8WG 1 174 386 76 60 Esophagus Adenocarcinoma, NOS 1 T3 N0 M0 Stage IIA TCGA-L5-A4OT 1 178 149 98 77 Esophagus Adenocarcinoma, NOS 1 T3 N1 M1a Stage IV TCGA-2H-A9GM 1 179 424 77 53 Esophagus Adenocarcinoma, NOS 1 T1 N1 M0 Stage IIB TCGA-R6-A6DN 1 175 243 98 58 Esophagus Adenocarcinoma, NOS 1 TX NX M1 Stage IV TCGA-IG-A8O2 1 166 142 53 62 Esophagus Squamous Cell Carcinoma 1 T3 N2 M0 Stage IIIB TCGA-L5-A88Z 0 163 225 66 70 Esophagus Squamous Cell Carcinoma 0 T1 N1 M0 Stage IIA TCGA-V5-AASV 1 165 467 55 67 Esophagus Squamous Cell Carcinoma 0 T3 N0 MX Stage IIB TCGA-L7-A6VZ 1 185 315 111 62 Esophagus Adenocarcinoma, NOS 0 T3 N3 MX Stage IIIC