Table S30. GISTIC 2.0 Significant Regions for All TNBC Cases Residual q values after removing Unique Name Descriptor Wide Peak Limits Peak Limits Region Limits q values segments shared with higher peaks Amplification Peak 1 1p31.1 chr1:76899465-81393021(probes 14145:15040) chr1:78201746-78349213(probes 14454:14457) chr1:77784763-80054162(probes 14353:14768) 1.11E-01 1.11E-01 Amplification Peak 2 1q23.3 chr1:163166677-164240150(probes 25446:25683) chr1:163174427-163502325(probes 25447:25537) chr1:157283480-173865585(probes 24065:27911) 3.57E-05 1.08E-03 Amplification Peak 3 1q31.2 chr1:187749448-192099776(probes 30222:30892) chr1:191836317-191928252(probes 30855:30871) chr1:183785175-200139349(probes 29601:32116) 4.42E-12 1.92E-10 Amplification Peak 4 1q41 chr1:216403500-216618219(probes 35668:35702) chr1:216454484-216613760(probes 35677:35701) chr1:214556083-223904594(probes 35275:37052) 7.77E-10 1.23E-07 Amplification Peak 5 1q43 chr1:238540227-239597344(probes 40367:40633) chr1:239336072-239341527(probes 40584:40586) chr1:223929087-249250621(probes 37063:42843) 2.34E-07 1.12E-05 Amplification Peak 6 2p16.3 chr2:50171659-53114774(probes 54212:55006) chr2:51345516-51479169(probes 54533:54554) chr2:49400347-53722594(probes 54040:55163) 3.29E-04 6.30E-04 Amplification Peak 7 2p12 chr2:76242646-84330302(probes 59548:61200) chr2:78870454-78927327(probes 60115:60119) chr2:75878655-84432299(probes 59477:61215) 2.77E-03 5.97E-03 Amplification Peak 8 2q32.1 chr2:184954001-189883165(probes 77451:78098) chr2:185188573-185459543(probes 77495:77550) chr2:184954426-189904673(probes 77452:78100) 5.56E-02 5.56E-02 Amplification Peak 9 3p26.3 chr3:1-3276427(probes 88315:89512) chr3:2472786-2480437(probes 89135:89135) chr3:1-3280818(probes 88315:89516) 3.16E-02 3.16E-02 Amplification Peak 10 3p11.1 chr3:89191310-89497081(probes 107054:107085) chr3:89309407-89379934(probes 107069:107075) chr3:87949734-95795275(probes 106896:107356) 2.20E-02 2.72E-02 Amplification Peak 11 3q24 chr3:144500133-146653362(probes 116188:116562) chr3:145583562-146091890(probes 116364:116450) chr3:142889136-183339095(probes 115777:123011) 2.44E-06 2.81E-03 Amplification Peak 12 3q26.1 chr3:165852208-166522846(probes 119878:119962) chr3:165858272-166202006(probes 119879:119921) chr3:142889136-183339095(probes 115777:123011) 8.75E-17 1.60E-12 Amplification Peak 13 3q26.31 chr3:175607877-175635149(probes 121774:121776) chr3:175619644-175630352(probes 121775:121775) chr3:142889136-183339095(probes 115777:123011) 9.48E-11 1.17E-06 Amplification Peak 14 4q28.3 chr4:131097851-138482972(probes 148571:149601) chr4:134439151-135741791(probes 149015:149169) chr4:131104360-138371814(probes 148572:149585) 7.29E-02 7.29E-02 Amplification Peak 15 5p14.3 chr5:22024388-23861063(probes 164332:164634) chr5:23065166-23164030(probes 164504:164521) chr5:17776870-31302287(probes 163711:165872) 3.26E-07 3.26E-07 Amplification Peak 16 6p24.3 chr6:8378610-9558459(probes 196058:196280) chr6:8410537-8717286(probes 196067:196109) chr6:8273874-10245759(probes 196033:196503) 1.61E-02 1.73E-01 Amplification Peak 17 6p22.3 chr6:20438662-20663334(probes 198930:199003) chr6:20481826-20625633(probes 198940:198984) chr6:17483876-23872684(probes 198273:199856) 2.91E-03 2.91E-02 Amplification Peak 18 6p21.1 chr6:44946464-45358322(probes 205387:205427) chr6:44953787-45349508(probes 205388:205424) chr6:44651736-51799901(probes 205339:206578) 1.49E-03 2.99E-02 Amplification Peak 19 6q12 chr6:62059208-66658512(probes 207867:208438) chr6:63452577-64024023(probes 208012:208060) chr6:57685663-71434295(probes 207799:209432) 2.92E-04 2.12E-03 Amplification Peak 20 6q16.1 chr6:93573897-93741419(probes 213599:213645) chr6:93574270-93741038(probes 213600:213644) chr6:91437527-98734647(probes 213161:214476) 2.59E-04 1.40E-03 Amplification Peak 21 6q22.31 chr6:122607311-122667157(probes 218782:218790) chr6:122609877-122663661(probes 218783:218789) chr6:119517984-136393804(probes 218281:221678) 1.85E-03 4.32E-02 Amplification Peak 22 6q23.3 chr6:135315399-135541168(probes 221513:221556) chr6:135325919-135526767(probes 221514:221555) chr6:119517984-136393804(probes 218281:221678) 4.12E-03 8.89E-02 Amplification Peak 23 7p21.2 chr7:8764366-16780008(probes 231806:234164) chr7:15864160-15891803(probes 233913:233917) chr7:8772151-16926860(probes 231807:234235) 1.85E-02 1.85E-02 Amplification Peak 24 7q21.11 chr7:79086120-86097012(probes 245810:247115) chr7:84752426-85077204(probes 246942:246986) chr7:77964668-88080420(probes 245453:247471) 1.25E-03 1.64E-03 Amplification Peak 25 7q31.31 chr7:108258672-126665051(probes 251094:253858) chr7:118928232-119186067(probes 252694:252710) chr7:118342829-119301785(probes 252635:252718) 1.15E-01 1.62E-01 Amplification Peak 26 8p11.22 chr8:39399058-39611991(probes 271865:271900) chr8:39405338-39609625(probes 271866:271899) chr8:35999592-40576178(probes 271471:272131) 3.29E-04 3.29E-04 Amplification Peak 27 8q21.13 chr8:83163528-83991230(probes 278861:279004) chr8:83815084-83985295(probes 278987:279003) chr8:68677338-146364022(probes 275963:291409) 1.04E-06 8.91E-05 Amplification Peak 28 8q23.3 chr8:113545257-116210887(probes 284044:284459) chr8:115084138-115532355(probes 284285:284341) chr8:68677338-146364022(probes 275963:291409) 1.95E-18 7.23E-18 Amplification Peak 29 9p23 chr9:12503843-12726961(probes 295855:295914) chr9:12510516-12712156(probes 295856:295911) chr9:1-16404540(probes 291410:297104) 5.14E-09 5.14E-09 Amplification Peak 30 10p14 chr10:8689004-10524805(probes 320867:321257) chr10:9210501-9878348(probes 320992:321115) chr10:1-10968632(probes 318044:321403) 1.12E-03 1.12E-03 Amplification Peak 31 10q21.1 chr10:53195392-59492515(probes 329378:330856) chr10:55199971-55391608(probes 329947:330003) chr10:53200277-59504546(probes 329382:330858) 4.65E-02 1.46E-01 Amplification Peak 32 10q21.3 chr10:66412920-69330131(probes 332172:332911) chr10:66785647-67227684(probes 332244:332345) chr10:66380567-69378277(probes 332165:332917) 2.60E-02 1.05E-01 Amplification Peak 33 10q23.1 chr10:82737124-84937492(probes 335802:336279) chr10:82914030-83416996(probes 335829:335923) chr10:82670627-85583242(probes 335777:336413) 9.60E-03 1.51E-02 Amplification Peak 34 10q26.13 chr10:123151323-123215088(probes 343901:343918) chr10:123151489-123208880(probes 343902:343917) chr10:123088200-123217599(probes 343876:343920) 1.28E-01 1.28E-01 Amplification Peak 35 11p14.3 chr11:23564844-25230779(probes 353294:353657) chr11:24494466-25229289(probes 353450:353656) chr11:21177160-31740264(probes 352715:354700) 6.60E-03 2.07E-02 Amplification Peak 36 11p12 chr11:37102464-39018278(probes 355939:356214) chr11:38041872-38477540(probes 356083:356146) chr11:36805998-42715835(probes 355873:356873) 7.18E-04 2.74E-03 Amplification Peak 37 11q13.3 chr11:69160994-70118488(probes 360122:360342) chr11:69377671-69814828(probes 360186:360251) chr11:68894992-70327304(probes 360074:360363) 2.02E-02 5.17E-02 Amplification Peak 38 11q14.1 chr11:77259436-77367541(probes 361532:361539) chr11:77268461-77350336(probes 361533:361538) chr11:76377820-81879092(probes 361392:362621) 4.71E-04 4.79E-03 Amplification Peak 39 11q22.1 chr11:97222584-98338007(probes 365677:365884) chr11:98105072-98333594(probes 365848:365883) chr11:96192005-101771432(probes 365513:366914) 4.83E-05 3.23E-04 Amplification Peak 40 12p13.2 chr12:10492983-10829002(probes 377109:377179) chr12:10496725-10553266(probes 377111:377121) chr12:7341344-12321180(probes 376480:377537) 7.49E-05 3.34E-04 Amplification Peak 41 12p12.1 chr12:17918926-24453452(probes 378764:380461) chr12:23985380-24006667(probes 380288:380291) chr12:14902094-27698750(probes 378200:381389) 1.50E-04 9.77E-04 Amplification Peak 42 12q11 chr12:34810204-38245751(probes 382920:382926) chr12:34819927-38242028(probes 382921:382925) chr12:33144338-38631078(probes 382742:382942) 1.30E-02 2.16E-02 Amplification Peak 43 13q31.2 chr13:82010206-91047346(probes 414991:416415) chr13:87658987-87971335(probes 415901:415933) chr13:81217492-95022283(probes 414871:417218) 2.48E-03 1.07E-02 Table S30. GISTIC 2.0 Significant Regions for All TNBC Cases Residual q values after removing Unique Name Descriptor Wide Peak Limits Peak Limits Region Limits q values segments shared with higher peaks Amplification Peak 44 13q33.3 chr13:104104377-109878778(probes 419862:421453) chr13:109081999-109452428(probes 421239:421340) chr13:101655224-115169878(probes 419025:422661) 2.84E-04 1.04E-03 Amplification Peak 45 14q12 chr14:27362942-29116115(probes 424575:424881) chr14:28421092-28799517(probes 424759:424825) chr14:27370460-29120381(probes 424576:424883) 3.79E-02 6.42E-02 Amplification Peak 46 14q21.3 chr14:47267653-47377201(probes 428312:428322) chr14:47285767-47367885(probes 428313:428321) chr14:47110306-47730953(probes 428294:428390) 3.61E-02 6.03E-02 Amplification Peak 47 15q26.2 chr15:94423125-100729705(probes 455457:457082) chr15:98084344-98442531(probes 456377:456465) chr15:95769034-98954956(probes 455845:456602) 9.10E-02 9.10E-02 Amplification Peak 48 17q22 chr17:52363380-52637910(probes 483212:483257) chr17:52371644-52433671(probes 483213:483217) chr17:49825434-53273909(probes 482760:483410) 2.74E-05 2.89E-04 Amplification Peak 49 17q24.3 chr17:69075360-69502650(probes 486140:486257) chr17:69142875-69336173(probes 486158:486202) chr17:63285156-70140484(probes 484952:486403) 1.31E-05 1.35E-04 Amplification Peak 50 19q12 chr19:30253999-30587595(probes 510025:510070) chr19:30255091-30458484(probes 510026:510058) chr19:30029437-31047268(probes 509959:510170) 1.48E-02 1.48E-02 Amplification Peak 51 21q21.2 chr21:24253086-25069438(probes