Supplementary Table 2 - Gene variations in GAGA samples Single nucleotide variants - nonsynonymous GAGA1 Gene Symbol Chr Pos Ref Cons AA Change GAGA1-pri MYO18B chr22 26286832 A M Q1475P GAGA1 SC-xenograft ZCCHC16 chrX 111698639 C S S228X GAGA1-pri, GAGA1 SC-xenograft ABCC8 chr11 17485061 C Y R168H GAGA1-pri, GAGA1 SC-xenograft ADNP chr20 49510190 T Y N354S GAGA1-pri, GAGA1 SC-xenograft ALDH1A3 chr15 101427836 G T W88C GAGA1-pri, GAGA1 SC-xenograft ALPK3 chr15 85382286 A M E329A GAGA1-pri, GAGA1 SC-xenograft ARF5 chr7 127231099 A M E138A GAGA1-pri, GAGA1 SC-xenograft C1QL3 chr10 16556645 A R V217A GAGA1-pri, GAGA1 SC-xenograft CDH10 chr5 24487971 A R L723P GAGA1-pri, GAGA1 SC-xenograft CHRNA6 chr8 42612179 A W I89N GAGA1-pri, GAGA1 SC-xenograft CIT chr12 120128017 T C D2042G GAGA1-pri, GAGA1 SC-xenograft CPB1 chr3 148558692 A M E135A GAGA1-pri, GAGA1 SC-xenograft CRELD2 chr22 50316956 A G T304A GAGA1-pri, GAGA1 SC-xenograft CSMD2 chr1 34254282 C M V488F GAGA1-pri, GAGA1 SC-xenograft DDX58 chr9 32488143 C M V338F GAGA1-pri, GAGA1 SC-xenograft FAM180B chr11 47609771 C Y L131F GAGA1-pri, GAGA1 SC-xenograft FLNA chrX 153582802 A R L1788P GAGA1-pri, GAGA1 SC-xenograft FPR1 chr19 52250091 A M F53V GAGA1-pri, GAGA1 SC-xenograft GFM1 chr3 158369910 C S P239A GAGA1-pri, GAGA1 SC-xenograft GIN1 chr5 102433384 T K K247N GAGA1-pri, GAGA1 SC-xenograft GNPTAB chr12 102158500 T K K732T GAGA1-pri, GAGA1 SC-xenograft GPR112 chrX 135430205 A W E1447V GAGA1-pri, GAGA1 SC-xenograft GRIN2B chr12 13724768 A R V714A GAGA1-pri, GAGA1 SC-xenograft GYPA chr4 145039876 A R S88P GAGA1-pri, GAGA1 SC-xenograft HMGB4 chr1 34330171 A R T127A GAGA1-pri, GAGA1 SC-xenograft IL1RAP chr3 190373907 G K K525N GAGA1-pri, GAGA1 SC-xenograft JAKMIP1 chr4 6083373 T W E355V GAGA1-pri, GAGA1 SC-xenograft KIF2B chr17 51900539 A W I49F GAGA1-pri, GAGA1 SC-xenograft MARCH7 chr2 160605039 C S P413R GAGA1-pri, GAGA1 SC-xenograft MAST4 chr5 66461677 G S G2224R GAGA1-pri, GAGA1 SC-xenograft OLFM4 chr13 53624842 T K L490R GAGA1-pri, GAGA1 SC-xenograft OR2L13 chr1 248263489 A R K271R GAGA1-pri, GAGA1 SC-xenograft OR56A3 chr11 5968596 A R D7G GAGA1-pri, GAGA1 SC-xenograft OR8H2 chr11 55873269 T W F251I GAGA1-pri, GAGA1 SC-xenograft PCDH11X chrX 91090687 C S Q62E GAGA1-pri, GAGA1 SC-xenograft PDZD8 chr10 119042971 C Y M1091I GAGA1-pri, GAGA1 SC-xenograft PNPLA1 chr6 36260842 T Y L148P GAGA1-pri, GAGA1 SC-xenograft POGLUT1 chr3 119199006 G R E189K GAGA1-pri, GAGA1 SC-xenograft POLH chr6 43550073 A W D6V GAGA1-pri, GAGA1 SC-xenograft PROL1 chr4 71275389 G A G115E GAGA1-pri, GAGA1 SC-xenograft RPS6KA6 chrX 83359515 A M C536G GAGA1-pri, GAGA1 SC-xenograft SFMBT2 chr10 7247860 A M V454G GAGA1-pri, GAGA1 SC-xenograft SIL1 chr5 138282864 T W E443V GAGA1-pri, GAGA1 SC-xenograft SLC17A9 chr20 61595640 T K F295V GAGA1-pri, GAGA1 SC-xenograft SLC1A6 chr19 15064947 C Y S455N GAGA1-pri, GAGA1 SC-xenograft SMAD3 chr15 67477148 A T N319Y GAGA1-pri, GAGA1 SC-xenograft SMARCA2 chr9 2097430 A W R1013X GAGA1-pri, GAGA1 SC-xenograft SPRR4 chr1 152944518 A M K51T GAGA1-pri, GAGA1 SC-xenograft STAC3 chr12 57640682 C Y A170T GAGA1-pri, GAGA1 SC-xenograft TENM4 chr11 78419444 G R R1391W GAGA1-pri, GAGA1 SC-xenograft THSD7B chr2 138163225 T Y M817T GAGA1-pri, GAGA1 SC-xenograft TMF1 chr3 69077107 T W K901X GAGA1-pri, GAGA1 SC-xenograft TNPO3 chr7 128610260 G T P847H GAGA1-pri, GAGA1 SC-xenograft TRDMT1 chr10 17199620 T W E236V GAGA1-pri, GAGA1 SC-xenograft TTN chr2 179544746 A R V9908A GAGA1-pri, GAGA1 SC-xenograft UHRF1BP1L chr12 100482777 A W F313I GAGA1-pri, GAGA1 SC-xenograft USP31 chr16 23160144 C G E150Q GAGA1-pri, GAGA1 SC-xenograft VCAN chr5 82816692 T W L856H GAGA1-pri, GAGA1 SC-xenograft WFDC3 chr20 44418583 G K A11E GAGA1-pri, GAGA1 SC-xenograft WT1 chr11 32450142 C Y G156R GAGA1-pri, GAGA1 SC-xenograft ZNF526 chr19 42729057 G R V168I GAGA1-pri, GAGA1 SC-xenograft ZNF530 chr19 58118590 A R K566R

Insertions/deletions (Indels) Genes Chr Start End Type GAGA1-pri, GAGA1 sc-xenograft SH2D4B chr10 82331241 82331242 -A GAGA1-pri, GAGA1 sc-xenograft PHLDB2 chr3 111680997 1.12E+08 -TG

Copy Number Variants (CNVs) Genes KDM6A SMAD2 FGFR2 MYC KRAS CDKN2A (exon 27-29) GAGA1-pri HD - - amplified HD HD GAGA1-pri, GAGA1 SC-xenograft HD - - amplified HD HD

Single nucleotide variants - nonsynonymous GAGA2 Gene Symbol Chr Pos Ref Cons AA Change GAGA2 primary ASB10 chr7 150884559 C Y R84H GAGA2 primary C6orf170 chr6 121624769 C M K358N GAGA2 primary CDH10 chr5 24509843 C M G363V GAGA2 primary CELF3 chr1 151681771 C Y V111I GAGA2 primary CNTN5 chr11 100169966 G K G820C GAGA2 primary COL23A1 chr5 177669107 C Y R506Q GAGA2 primary COL5A1 chr9 137701059 C T R1133X GAGA2 primary COL6A3 chr2 238257270 G R R2306C GAGA2 primary DCAF8L1 chrX 27997690 C Y E588K GAGA2 primary DNAJC28 chr21 34861220 G R R161C GAGA2 primary GPR148 chr2 131487412 C M L230I GAGA2 primary HS3ST4 chr16 25704231 A R S165G GAGA2 primary KCNJ11 chr11 17409491 G R R50W GAGA2 primary KL chr13 33638070 G R R929H GAGA2 primary LCE6A chr1 152816180 C Y R62C GAGA2 primary NTRK1 chr1 156849903 T Y I720T GAGA2 primary PRDM16 chr1 3321424 C Y R336C GAGA2 primary PRPF6 chr20 62614510 A R K61R GAGA2 primary PRRT4 chr7 127991302 C Y G770R GAGA2 primary SLC22A3 chr6 160858039 G R A362T GAGA2 primary SRCAP chr16 30750244 C M N2961K GAGA2 primary TAF1 chrX 70627422 A W 3' splice site GAGA2 primary TLL2 chr10 98192647 C Y R146Q GAGA2 primary TP53 chr17 7577094 G A R282W GAGA2 primary TRIM37 chr17 57119222 A M L569V GAGA2 primary WDR73 chr15 85189556 T K I126L GAGA2 primary ZFP1 chr16 75200754 G K M34I GAGA2 primary ZHX3 chr20 39831239 G R A773V

Copy Number Variants (CNVs) Genes FGFR2 MYC KRAS GAGA2 primary amplified - -

Single nucleotide variants - nonsynonymous GAGA3 Gene Symbol Chr Pos Ref Cons AA Change GAGA3-primary C14orf104 chr14 50100537 G R A444V GAGA3-pri, IP-xenograft, SC-xenograft ABTB2 chr11 34192538 C Y R307H GAGA3-pri, IP-xenograft, SC-xenograft AC135724.1 chr17 29708969 G R G63R GAGA3-pri, IP-xenograft, SC-xenograft ANK2 chr4 114244917 G R R947H GAGA3-pri, IP-xenograft, SC-xenograft AOX1 chr2 201531429 T Y V1188A GAGA3-pri, IP-xenograft, SC-xenograft ARHGEF17 chr11 73020890 G R D403N GAGA3-pri, IP-xenograft, SC-xenograft BAP1 chr3 52436336 G A R720C GAGA3-pri, IP-xenograft, SC-xenograft BAP1 chr3 52438566 G A R385X GAGA3-pri, IP-xenograft, SC-xenograft C16orf62 chr16 19710947 G R G924S GAGA3-pri, IP-xenograft, SC-xenograft C1orf125 chr1 179437770 C Y S664F GAGA3-pri, IP-xenograft, SC-xenograft CBLB chr3 105572318 C T R120Q GAGA3-pri, IP-xenograft, SC-xenograft CCDC8 chr19 46915167 C M D301Y GAGA3-pri, IP-xenograft, SC-xenograft CEP152 chr15 49054726 C M E808D GAGA3-pri, IP-xenograft, SC-xenograft CHPF chr2 220408100 C Y G54D GAGA3-pri, IP-xenograft, SC-xenograft CHRNA4 chr20 61981907 T Y T286A GAGA3-pri, IP-xenograft, SC-xenograft DOCK10 chr2 225672675 T Y K1180E GAGA3-pri, IP-xenograft, SC-xenograft ELF3 chr1 201983060 C A F303L GAGA3-pri, IP-xenograft, SC-xenograft EML5 chr14 89171869 T Y D630G GAGA3-pri, IP-xenograft, SC-xenograft ESPNL chr2 239025586 C Y R300W GAGA3-pri, IP-xenograft, SC-xenograft GALNT13 chr2 155102432 G R R265H GAGA3-pri, IP-xenograft, SC-xenograft IKZF3 chr17 37922642 C Y A311T GAGA3-pri, IP-xenograft, SC-xenograft JPH2 chr20 42815327 C Y D7N GAGA3-pri, IP-xenograft, SC-xenograft KCTD17 chr22 37457593 C Y P250S GAGA3-pri, IP-xenograft, SC-xenograft KLHL1 chr13 70549861 C Y A191T GAGA3-pri, IP-xenograft, SC-xenograft LDHBP2 chrX 75555581 C Y D187N GAGA3-pri, IP-xenograft, SC-xenograft MAGEA6 chrX 151869975 G S W222S GAGA3-pri, IP-xenograft, SC-xenograft MED12 chrX 70360552 G R V2038I GAGA3-pri, IP-xenograft, SC-xenograft MIA2 chr14 39716763 T W L329I GAGA3-pri, IP-xenograft, SC-xenograft MSH6 chr2 48027958 G K E946X GAGA3-pri, IP-xenograft, SC-xenograft NEGR1 chr1 72241942 C Y V150I GAGA3-pri, IP-xenograft, SC-xenograft NKAP chrX 119072768 A W L131X GAGA3-pri, IP-xenograft, SC-xenograft NRK chrX 105167275 G K A926S GAGA3-pri, IP-xenograft, SC-xenograft OR4A5 chr11 51411635 A R I254T GAGA3-pri, IP-xenograft, SC-xenograft PCDH17 chr13 58208370 G S E564Q GAGA3-pri, IP-xenograft, SC-xenograft PCDH19 chrX 99663057 G R T180M GAGA3-pri, IP-xenograft, SC-xenograft PCDHB3 chr5 140480967 C Y P245L GAGA3-pri, IP-xenograft, SC-xenograft PODXL2 chr3 127379998 C Y T376M GAGA3-pri, IP-xenograft, SC-xenograft PTPRC chr1 198721859 G T G1154V GAGA3-pri, IP-xenograft, SC-xenograft PXDN chr2 1680705 C Y R281Q GAGA3-pri, IP-xenograft, SC-xenograft RECQL4 chr8 145739012 G R R715W GAGA3-pri, IP-xenograft, SC-xenograft RHOA chr3 49412946 C T S26N GAGA3-pri, IP-xenograft, SC-xenograft RNF213 chr17 78280995 G R R832Q GAGA3-pri, IP-xenograft, SC-xenograft SCFD1 chr14 31091564 C Y A7V GAGA3-pri, IP-xenograft, SC-xenograft SERPINA9 chr14 94936170 G K S21Y GAGA3-pri, IP-xenograft, SC-xenograft SETX chr9 135202894 C M R1364I GAGA3-pri, IP-xenograft, SC-xenograft SIPA1 chr11 65413940 C Y R479C GAGA3-pri, IP-xenograft, SC-xenograft SLC24A3 chr20 19673903 C M S442X GAGA3-pri, IP-xenograft, SC-xenograft SNX15 chr11 64802562 C Y S135F GAGA3-pri, IP-xenograft, SC-xenograft SSPO chr7 149484875 G K A1233S GAGA3-pri, IP-xenograft, SC-xenograft TMEM2 chr9 74345045 G S T633S GAGA3-pri, IP-xenograft, SC-xenograft TRIM5 chr11 5686046 C Y S492N GAGA3-pri, IP-xenograft, SC-xenograft YME1L1 chr10 27408224 C M M579I GAGA3-pri, IP-xenograft, SC-xenograft ZACN chr17 74078558 G R V355I GAGA3-pri, IP-xenograft ACSBG1 chr15 78471961 G R A472V GAGA3-pri, IP-xenograft AHNAK chr11 62289721 C Y W4056X GAGA3-pri, IP-xenograft ALDH1A1 chr9 75520939 G K C456X GAGA3-pri, IP-xenograft AMOT chrX 112065681 G R P225L GAGA3-pri, IP-xenograft AMPD1 chr1 115221126 G R A340V GAGA3-pri, IP-xenograft ANKRD50 chr4 125592133 G K L767I GAGA3-pri, IP-xenograft ANXA5 chr4 122607473 C S E22Q GAGA3-pri, IP-xenograft B4GALT4 chr3 118942904 C M 5' splice site GAGA3-pri, IP-xenograft CHGA chr14 93393924 C S Q73E GAGA3-pri, IP-xenograft CNOT1 chr16 58616986 C Y G303R GAGA3-pri, IP-xenograft CRYBB1 chr22 27012103 C M 5' splice site GAGA3-pri, IP-xenograft CSMD3 chr8 113418828 C M G1912X GAGA3-pri, IP-xenograft CTCFL chr20 56098718 C M 5' splice site GAGA3-pri, IP-xenograft CXorf30 chrX 36319196 T K F70L GAGA3-pri, IP-xenograft E2F8 chr11 19256485 C M G191V GAGA3-pri, IP-xenograft EED chr11 85977143 G S E249Q GAGA3-pri, IP-xenograft EFR3A chr8 132988307 G K R398M GAGA3-pri, IP-xenograft FAM161A chr2 62067153 G K A329E GAGA3-pri, IP-xenograft FAM75E1 chr9 90500319 T Y L306P GAGA3-pri, IP-xenograft FAT3 chr11 92532098 A M K1973N GAGA3-pri, IP-xenograft FBRSL1 chr12 133146795 C M S325R GAGA3-pri, IP-xenograft FHAD1 chr1 15616150 G R V186I GAGA3-pri, IP-xenograft FOXD3 chr1 63788883 G K E52X GAGA3-pri, IP-xenograft GCOM1 chr15 57931658 C M A345E GAGA3-pri, IP-xenograft HIVEP2 chr6 143091989 T K K1296T GAGA3-pri, IP-xenograft HMCN1 chr1 186008104 G S A1999P GAGA3-pri, IP-xenograft HOXD1 chr2 177054176 A M K216T GAGA3-pri, IP-xenograft IKBKAP chr9 111693336 C M G31W GAGA3-pri, IP-xenograft IMP4 chr2 131103272 G R V147M GAGA3-pri, IP-xenograft IRX1 chr5 3596431 C Y A71V GAGA3-pri, IP-xenograft ITM2C chr2 231740464 G R V131M GAGA3-pri, IP-xenograft KLHDC4 chr16 87760444 G R T229I GAGA3-pri, IP-xenograft LHX9 chr1 197890771 A W I239F GAGA3-pri, IP-xenograft LPHN2 chr1 82456305 C M P1230T GAGA3-pri, IP-xenograft LRRK2 chr12 40699653 A W R1282X GAGA3-pri, IP-xenograft LRRK2 chr12 40699654 G K R1282I GAGA3-pri, IP-xenograft MARCH9 chr12 58152490 C S P284R GAGA3-pri, IP-xenograft MUC16 chr19 9048719 G K T10971K GAGA3-pri, IP-xenograft NPVF chr7 25266510 A W F92I GAGA3-pri, IP-xenograft OCA2 chr15 28202821 C Y R566H GAGA3-pri, IP-xenograft OR6C4 chr12 55945468 C Y A153V GAGA3-pri, IP-xenograft OSBP chr11 59344157 C Y E773K GAGA3-pri, IP-xenograft PEX13 chr2 61275678 A W N329Y GAGA3-pri, IP-xenograft PML chr15 74315338 C S H258D GAGA3-pri, IP-xenograft PPP1R3F chrX 49143457 G K V769F GAGA3-pri, IP-xenograft PYHIN1 chr1 158906810 C M P37Q GAGA3-pri, IP-xenograft RARA chr17 38510644 G R A300T GAGA3-pri, IP-xenograft RBM46 chr4 155720191 G K G293X GAGA3-pri, IP-xenograft SFRP2 chr4 154709927 A R S21P GAGA3-pri, IP-xenograft SHROOM2 chrX 9863410 G R A488T GAGA3-pri, IP-xenograft SNAI2 chr8 49831441 T K K244N GAGA3-pri, IP-xenograft SPEF2 chr5 35659223 G K V361F GAGA3-pri, IP-xenograft SPOPL chr2 139310249 G S E160Q GAGA3-pri, IP-xenograft TMEM145 chr19 42819163 G R E147K GAGA3-pri, IP-xenograft TOP1 chr20 39728847 G R R376Q GAGA3-pri, IP-xenograft TRIM10 chr6 30124770 G R R281W GAGA3-pri, IP-xenograft TRIML2 chr4 189012645 G K A349D GAGA3-pri, IP-xenograft TRIP12 chr2 230724195 T K K65T GAGA3-pri, IP-xenograft TTN chr2 179507038 C M G10927V GAGA3-pri, IP-xenograft TTN chr2 179507039 C M G10927X GAGA3-pri, IP-xenograft UFL1 chr6 96985286 C Y A280V GAGA3-pri, IP-xenograft USH2A chr1 216595645 A M F12V GAGA3-pri, IP-xenograft WASF1 chr6 110428317 T W D168V GAGA3-pri, IP-xenograft WASF1 chr6 110428318 C M D168Y GAGA3-pri, IP-xenograft WFS1 chr4 6303952 C M F810L GAGA3-pri, IP-xenograft ZEB1 chr10 31810035 A M N592T GAGA3-pri, IP-xenograft ZFHX4 chr8 77617688 C M H455Q GAGA3-pri, IP-xenograft ZFP62 chr5 180277476 T W D340V GAGA3-pri, IP-xenograft ZKSCAN1 chr7 99621890 C S F180L GAGA3-pri, IP-xenograft ZNF251 chr8 145947856 G R R397W GAGA3-pri, IP-xenograft ZSCAN12 chr6 28359411 T K K219T GAGA3-pri, SC-xenograft AMPD2 chr1 110167943 G K G91V GAGA3-pri, SC-xenograft ANKRD28 chr3 15737654 A W L519Q GAGA3-pri, SC-xenograft ATPBD4 chr15 35747021 C M E105X GAGA3-pri, SC-xenograft CSMD1 chr8 2830822 C M 3' splice site GAGA3-pri, SC-xenograft CSMD1 chr8 2830823 T Y 3' splice site GAGA3-pri, SC-xenograft CUX1 chr7 101840283 G K G542V GAGA3-pri, SC-xenograft DUS1L chr17 80017823 C Y 5' splice site GAGA3-pri, SC-xenograft EPHA6 chr3 96962857 A W E444D GAGA3-pri, SC-xenograft ERCC5 chr13 103514613 A R R372G GAGA3-pri, SC-xenograft FAM160A2 chr11 6239021 G R P613S GAGA3-pri, SC-xenograft FAM83A chr8 124195455 G K S120I GAGA3-pri, SC-xenograft FSIP2 chr2 186669461 A R K5232R GAGA3-pri, SC-xenograft GPRASP2 chrX 101969845 G S K16N GAGA3-pri, SC-xenograft HECTD1 chr14 31675028 C S D39H GAGA3-pri, SC-xenograft HIST1H4D chr6 26189147 T Y E53G GAGA3-pri, SC-xenograft IGSF10 chr3 151155483 C Y R2289K GAGA3-pri, SC-xenograft ITGBL1 chr13 102235688 T Y S284P GAGA3-pri, SC-xenograft KDM6A chrX 44935965 C Y S909F GAGA3-pri, SC-xenograft NOX1 chrX 100117484 T K T190P GAGA3-pri, SC-xenograft NSRP1 chr17 28512508 C Y A498V GAGA3-pri, SC-xenograft NTRK3 chr15 88483897 T Y Y558C GAGA3-pri, SC-xenograft OR10A5 chr11 6867723 G K E270D GAGA3-pri, SC-xenograft PLOD2 chr3 145790350 G K H616N GAGA3-pri, SC-xenograft PVRL3 chr3 110791306 C S P14A GAGA3-pri, SC-xenograft RBL2 chr16 53500968 A W 3' splice site GAGA3-pri, SC-xenograft SACS chr13 23906896 G R L3707F GAGA3-pri, SC-xenograft SCGB1D2 chr11 62010895 A W R64X GAGA3-pri, SC-xenograft SFRP4 chr7 37956057 C Y R28H GAGA3-pri, SC-xenograft SFXN5 chr2 73285693 C M L45F GAGA3-pri, SC-xenograft SLC5A9 chr1 48713146 A W R684S GAGA3-pri, SC-xenograft SNCAIP chr5 121787094 A R N851S GAGA3-pri, SC-xenograft SOX11 chr2 5832960 A R E36G GAGA3-pri, SC-xenograft SSPO chr7 149522435 G R D4688N GAGA3-pri, SC-xenograft TRIM64C chr11 49077932 T W D247V GAGA3-pri, SC-xenograft ZNF256 chr19 58453608 G S H190D GAGA3-pri, SC-xenograft ZNF445 chr3 44491089 T W I283F GAGA3 IP-xenograft, SC-xenograft RIMBP2 chr12 130935748 C S E149Q GAGA3 IP-xenograft ABCA6 chr17 67080605 C M V1410L GAGA3 IP-xenograft ABCB7 chrX 74293780 G S C290W GAGA3 IP-xenograft CARD6 chr5 40854039 C Y Q869X GAGA3 IP-xenograft CD207 chr2 71061153 T Y 3' splice site GAGA3 IP-xenograft GLT1D1 chr12 129391462 A W Q118L GAGA3 IP-xenograft GLT1D1 chr12 129391463 G K Q118H GAGA3 IP-xenograft HERC2 chr15 28389255 G R S3756L GAGA3 IP-xenograft LRTM2 chr12 1940180 C M S49R GAGA3 IP-xenograft NOL6 chr9 33462669 G R T1145I GAGA3 IP-xenograft NRG1 chr8 32611949 C M L259I GAGA3 IP-xenograft PDE1C chr7 31855570 G R A654V GAGA3 IP-xenograft PIPOX chr17 27382837 C M P325T GAGA3 IP-xenograft RAB3IP chr12 70206619 A R S414G GAGA3 IP-xenograft SLIT2 chr4 20620607 G R C1522Y GAGA3 IP-xenograft TMEM246 chr9 104238338 C Y R346Q GAGA3 IP-xenograft ZDHHC4 chr7 6628488 C S Q328E GAGA3 SC-xenograft AGPAT4 chr6 161570274 G R P238S GAGA3 SC-xenograft AKAP11 chr13 42866577 A W E36D GAGA3 SC-xenograft ANKHD1-EIF4EBP3 chr5 139908094 C Y H1855Y GAGA3 SC-xenograft ARFGAP3 chr22 43203133 T K S453R GAGA3 SC-xenograft BCL2L10 chr15 52402095 A W S189T GAGA3 SC-xenograft C17orf51 chr17 21438578 A R S217P GAGA3 SC-xenograft C1orf123 chr1 53683867 T K S80R GAGA3 SC-xenograft CFH chr1 196711016 C Y L990F GAGA3 SC-xenograft CNDP1 chr18 72245489 T Y I365T GAGA3 SC-xenograft CNTNAP4 chr16 76587236 T Y C1094R GAGA3 SC-xenograft COG2 chr1 230798918 G K R111L GAGA3 SC-xenograft COL6A6 chr3 130289763 T K L835V GAGA3 SC-xenograft CPN2 chr3 194063428 G R L2F GAGA3 SC-xenograft CRY1 chr12 107393823 G R A241V GAGA3 SC-xenograft CSPG4 chr15 75977739 A M F1365V GAGA3 SC-xenograft DAAM1 chr14 59819301 G R E750K GAGA3 SC-xenograft DIP2C chr10 486840 T Y Q122R GAGA3 SC-xenograft EFR3A chr8 132982864 T W V378E GAGA3 SC-xenograft EPPK1 chr8 144946320 C Y D368N GAGA3 SC-xenograft ETAA1 chr2 67630989 T Y F392S GAGA3 SC-xenograft GIGYF1 chr7 100279486 C Y 5' splice site GAGA3 SC-xenograft GRM3 chr7 86416158 G S W350C GAGA3 SC-xenograft GUCY1A2 chr11 106680788 T K Q541H GAGA3 SC-xenograft HEATR5A chr14 31762803 G K A1950D GAGA3 SC-xenograft IL22RA1 chr1 24447480 G R Q514X GAGA3 SC-xenograft KATNAL1 chr13 30784460 C M V423F GAGA3 SC-xenograft KCNK2 chr1 215408432 G K G409C GAGA3 SC-xenograft KIF3C chr2 26204071 A R V239A GAGA3 SC-xenograft LATS1 chr6 150023260 C Y M1I GAGA3 SC-xenograft LIN7A chr12 81283099 T K E44D GAGA3 SC-xenograft MAGI2 chr7 78636484 A M L114V GAGA3 SC-xenograft MLL chr11 118343697 G R R608Q GAGA3 SC-xenograft MLL chr11 118350897 A M K1193T GAGA3 SC-xenograft MUC16 chr19 9061532 T W K8638N GAGA3 SC-xenograft MXRA5 chrX 3241045 T K K894T GAGA3 SC-xenograft NR3C1 chr5 142779575 T Y K277R GAGA3 SC-xenograft PAPPA2 chr1 176659471 A R K779R GAGA3 SC-xenograft PKIA chr8 79510659 T K S14A GAGA3 SC-xenograft PLCL1 chr2 198949196 T K L319V GAGA3 SC-xenograft RASGRF1 chr15 79272991 T W R1171S GAGA3 SC-xenograft RFX7 chr15 56395811 G S I153M GAGA3 SC-xenograft RNF146 chr6 127608509 C Y Q251X GAGA3 SC-xenograft SLC4A8 chr12 51888782 C M F941L GAGA3 SC-xenograft SSH2 chr17 27963065 G K A701D GAGA3 SC-xenograft SUZ12 chr17 30315348 C S P345A GAGA3 SC-xenograft TAS2R20 chr12 11150416 C Y G20E GAGA3 SC-xenograft TDRD6 chr6 46660897 C M P1678T GAGA3 SC-xenograft TEP1 chr14 20856091 C M S886I GAGA3 SC-xenograft TUBB7P chr4 190903910 G R P286L GAGA3 SC-xenograft ZNF667 chr19 56953574 G R Q264X

Insertions/deletions (Indels) Genes Chr Start End Type GAGA3-pri CACNA2D4 chr12 1919451 1919451 +A GAGA3-pri, IP-xenograft, SC-xenograft FAP chr2 163039943 1.63E+08 +T GAGA3-pri, IP-xenograft, SC-xenograft SLC28A2 chr15 45567619 45567622 -CTT GAGA3-pri, IP-xenograft, SC-xenograft TST chr22 37414479 37414479 +CAC GAGA3-pri, IP-xenograft CYP11B1 chr8 143961199 1.44E+08 -G GAGA3-pri, IP-xenograft DEFA5 chr8 6912992 6912993 -C GAGA3-pri, IP-xenograft KIAA1377 chr11 101857633 1.02E+08 -C GAGA3-pri, IP-xenograft RFX6 chr6 117252660 1.17E+08 -G GAGA3-pri, IP-xenograft TG chr8 133880379 1.34E+08 +A GAGA3-pri, IP-xenograft ZFHX4 chr8 77767089 77767090 -A GAGA3-pri, SC-xenograft CHL1 chr3 402023 402023 +A GAGA3-pri, SC-xenograft EYS chr6 66094366 66094366 +T GAGA3-pri, SC-xenograft KIF26B chr1 245861459 2.46E+08 +A GAGA3-pri, SC-xenograft RORB chr9 77277420 77277423 -TCC SC-xenograft AFF3 chr2 100199429 1E+08 +T SC-xenograft EPS8L3 chr1 110300579 1.1E+08 +T SC-xenograft HEATR5A chr14 31787477 31787477 +T

Copy Number Variants (CNVs) Genes FGFR2 MYC KRAS GAGA3-pri amplified amplified amplified GAGA3 IP-xenograft - amplified amplified GAGA3 SC-xenograft amplified - -

Single nucleotide variants - nonsynonymous GAGA6 Gene Symbol Chr Pos Ref Cons AA Change GAGA6 primary AGAP1 chr2 236579292 G S W183C GAGA6 primary AIM1L chr1 26671719 C Y R477Q GAGA6 primary ARID3A chr19 929686 G R R53Q GAGA6 primary CNTN6 chr3 1269641 A M T108P GAGA6 primary CRIPAK chr4 1388817 C S P173R GAGA6 primary EIF5B chr2 100011237 G K A1049S GAGA6 primary ELFN1 chr7 1786409 C Y P726L GAGA6 primary FCGR2B chr1 161645059 A R Y258C GAGA6 primary FIG4 chr6 110059539 A R I220V GAGA6 primary GLG1 chr16 74566050 G R P147L GAGA6 primary GOLGA6L1 chr15 22743086 C Y R491W GAGA6 primary GOLGA6L2 chr15 23685463 G C S720X GAGA6 primary GOLGA6L2 chr15 23685464 A T S720T GAGA6 primary GOLGA6L2 chr15 23685583 T Y E680G GAGA6 primary HOMER1 chr5 78671772 C Y V24I GAGA6 primary IQSEC3 chr12 176463 C A H139N GAGA6 primary KIAA0825 chr5 93805791 G R R583X GAGA6 primary KIF20B chr10 91492852 C S L862V GAGA6 primary LYST chr1 235901584 G R R5C GAGA6 primary MAFIP chr4 56462 A G M1T GAGA6 primary MEF2A chr15 100252741 A M Q422P GAGA6 primary MESP2 chr15 90320144 C S Q186E GAGA6 primary MOCS1 chr6 39895039 C M G41V GAGA6 primary MUC2 chr11 1093286 C S T1702S GAGA6 primary MUC2 chr11 1093430 C M T1750N GAGA6 primary MUC3A chr7 100608884 G R A655T GAGA6 primary MUC4 chr3 195507226 A R V3742A GAGA6 primary MUC6 chr11 1017069 G R T1911M GAGA6 primary PRR25 chr16 855468 C Y P9L GAGA6 primary SMC1B chr22 45790627 T G K425N GAGA6 primary THBS1 chr15 39882019 G R R647H GAGA6 primary TINAG chr6 54219325 C Y R381C GAGA6 primary TRBV6-5 chr7 142180737 T W Q55L GAGA6-pri, GAGA6 SC-xenograft ABCA5 chr17 67247973 G A R1484W GAGA6-pri, GAGA6 SC-xenograft ABCG1 chr21 43639380 G R C3Y GAGA6-pri, GAGA6 SC-xenograft ABL2 chr1 179087846 C Y G367R GAGA6-pri, GAGA6 SC-xenograft ACSM1 chr16 20702429 G R R28C GAGA6-pri, GAGA6 SC-xenograft ACTR10 chr14 58675803 G R R107H GAGA6-pri, GAGA6 SC-xenograft ACTR1A chr10 104241913 C Y R257Q GAGA6-pri, GAGA6 SC-xenograft ADCY1 chr7 45726165 C Y R783C GAGA6-pri, GAGA6 SC-xenograft ADCY10 chr1 167791296 G K L1418I GAGA6-pri, GAGA6 SC-xenograft AGPHD1 chr15 78825664 C S S258R GAGA6-pri, GAGA6 SC-xenograft AHNAK chr11 62291412 C S D3493H GAGA6-pri, GAGA6 SC-xenograft AHNAK2 chr14 105411302 G C L3496V GAGA6-pri, GAGA6 SC-xenograft AMIGO3 chr3 49756438 T Y H154R GAGA6-pri, GAGA6 SC-xenograft ANKH chr5 14871373 G R R62X GAGA6-pri, GAGA6 SC-xenograft ANKRD11 chr16 89349575 G T D1125E GAGA6-pri, GAGA6 SC-xenograft ANKRD9 chr14 102973280 T C K316R GAGA6-pri, GAGA6 SC-xenograft AQP6 chr12 50369366 A W E254V GAGA6-pri, GAGA6 SC-xenograft ARHGEF1 chr19 42398593 G R A287T GAGA6-pri, GAGA6 SC-xenograft ARHGEF33 chr2 39158410 T Y Y135H GAGA6-pri, GAGA6 SC-xenograft ARHGEF37 chr5 149003590 G K V451F GAGA6-pri, GAGA6 SC-xenograft ARMC3 chr10 23290960 C M T513K GAGA6-pri, GAGA6 SC-xenograft ARMCX1 chrX 100808158 T C L82S GAGA6-pri, GAGA6 SC-xenograft ARRDC4 chr15 98504164 G S E25Q GAGA6-pri, GAGA6 SC-xenograft ASPM chr1 197072725 G R R1886C GAGA6-pri, GAGA6 SC-xenograft ASPSCR1 chr17 79941506 G A V79M GAGA6-pri, GAGA6 SC-xenograft ATAD3C chr1 1386065 T Y M1T GAGA6-pri, GAGA6 SC-xenograft ATF5 chr19 50436269 G R V257M GAGA6-pri, GAGA6 SC-xenograft ATP10B chr5 160033805 G R R1043X GAGA6-pri, GAGA6 SC-xenograft BARHL1 chr9 135458494 G R D104N GAGA6-pri, GAGA6 SC-xenograft BCAN chr1 156628886 C Y A899V GAGA6-pri, GAGA6 SC-xenograft BEND6 chr6 56882032 C Y R183C GAGA6-pri, GAGA6 SC-xenograft BIRC7 chr20 61867545 C Y R33C GAGA6-pri, GAGA6 SC-xenograft BLK chr8 11405617 G S K84N GAGA6-pri, GAGA6 SC-xenograft BLOC1S3 chr19 45682758 G K E68D GAGA6-pri, GAGA6 SC-xenograft BLOC1S3 chr19 45682759 C Y P69S GAGA6-pri, GAGA6 SC-xenograft C12orf5 chr12 4461796 C Y T251M GAGA6-pri, GAGA6 SC-xenograft C14orf132 chr14 96556480 G R R171H GAGA6-pri, GAGA6 SC-xenograft C16orf58 chr16 31504903 C Y G185R GAGA6-pri, GAGA6 SC-xenograft C19orf35 chr19 2276479 G R P208S GAGA6-pri, GAGA6 SC-xenograft C22orf46 chr22 42091080 G T S297I GAGA6-pri, GAGA6 SC-xenograft C5orf34 chr5 43492857 T Y N484D GAGA6-pri, GAGA6 SC-xenograft C5orf42 chr5 37108450 G R T3121M GAGA6-pri, GAGA6 SC-xenograft C6 chr5 41161887 C Y A456T GAGA6-pri, GAGA6 SC-xenograft C8A chr1 57378283 C S Q530E GAGA6-pri, GAGA6 SC-xenograft C8B chr1 57425206 G R S20F GAGA6-pri, GAGA6 SC-xenograft CACNA1G chr17 48653379 C T T539M GAGA6-pri, GAGA6 SC-xenograft CCDC168 chr13 103390575 C Y D4158N GAGA6-pri, GAGA6 SC-xenograft CCDC87 chr11 66360149 C Y R113Q GAGA6-pri, GAGA6 SC-xenograft CCDC88C chr14 91766317 C Y A1245T GAGA6-pri, GAGA6 SC-xenograft CD1D chr1 158152820 C M L254M GAGA6-pri, GAGA6 SC-xenograft CDH1 chr16 68855940 T G L583R GAGA6-pri, GAGA6 SC-xenograft CFHR3 chr1 196748349 G R R39H GAGA6-pri, GAGA6 SC-xenograft CFHR5 chr1 196963287 G R V170M GAGA6-pri, GAGA6 SC-xenograft CHD4 chr12 6688017 T Y D1659G GAGA6-pri, GAGA6 SC-xenograft CLCNKA chr1 16353068 A R Y179C GAGA6-pri, GAGA6 SC-xenograft CLEC2L chr7 139229366 C Y T19M GAGA6-pri, GAGA6 SC-xenograft CNNM2 chr10 104678571 A R N112D GAGA6-pri, GAGA6 SC-xenograft CNTD2 chr19 40729330 C Y G213R GAGA6-pri, GAGA6 SC-xenograft CNTROB chr17 7851580 G A R772Q GAGA6-pri, GAGA6 SC-xenograft COL20A1 chr20 61951688 G R D1041N GAGA6-pri, GAGA6 SC-xenograft COL20A1 chr20 61956683 G R R42Q GAGA6-pri, GAGA6 SC-xenograft COL6A6 chr3 130377568 G R D1928N GAGA6-pri, GAGA6 SC-xenograft CPAMD8 chr19 17108001 C Y V386M GAGA6-pri, GAGA6 SC-xenograft CREG2 chr2 101971724 A R M239T GAGA6-pri, GAGA6 SC-xenograft CRLF1 chr19 18709278 G R R221C GAGA6-pri, GAGA6 SC-xenograft CRY1 chr12 107391466 C Y R431H GAGA6-pri, GAGA6 SC-xenograft CTNNA3 chr10 68280456 G R R484C GAGA6-pri, GAGA6 SC-xenograft CUX2 chr12 111786041 G R R1458Q GAGA6-pri, GAGA6 SC-xenograft CYP2W1 chr7 1028238 G R A164T GAGA6-pri, GAGA6 SC-xenograft CYP8B1 chr3 42916798 G R R171C GAGA6-pri, GAGA6 SC-xenograft DBNDD1 chr16 90071719 T A T167S GAGA6-pri, GAGA6 SC-xenograft DCAF4 chr14 73423135 G K Q407H GAGA6-pri, GAGA6 SC-xenograft DCAF4 chr14 73423137 A W Y408F GAGA6-pri, GAGA6 SC-xenograft DCHS2 chr4 155412054 G R Q152X GAGA6-pri, GAGA6 SC-xenograft DENND1B chr1 197479654 A W M755K GAGA6-pri, GAGA6 SC-xenograft DGAT2 chr11 75480125 C Y P30L GAGA6-pri, GAGA6 SC-xenograft DLGAP3 chr1 35370137 G R P283L GAGA6-pri, GAGA6 SC-xenograft DNASE1 chr16 3711892 C S H32D GAGA6-pri, GAGA6 SC-xenograft DPP4 chr2 162903471 T Y N80S GAGA6-pri, GAGA6 SC-xenograft DUS4L chr7 107216830 A R R167G GAGA6-pri, GAGA6 SC-xenograft DVL1 chr1 1275118 C Y R15Q GAGA6-pri, GAGA6 SC-xenograft DYNC2H1 chr11 103048454 G R R2015Q GAGA6-pri, GAGA6 SC-xenograft E2F2 chr1 23848471 T Y S146G GAGA6-pri, GAGA6 SC-xenograft EBF4 chr20 2730512 T Y I300T GAGA6-pri, GAGA6 SC-xenograft ENDOD1 chr11 94862249 A R T337A GAGA6-pri, GAGA6 SC-xenograft EP400 chr12 132562138 A W S3098C GAGA6-pri, GAGA6 SC-xenograft ESYT2 chr7 158586362 A R I236T GAGA6-pri, GAGA6 SC-xenograft EXD3 chr9 140242561 T C M654V GAGA6-pri, GAGA6 SC-xenograft F5 chr1 169505766 G R A1650V GAGA6-pri, GAGA6 SC-xenograft FAM154B chr15 82575245 T W F347I GAGA6-pri, GAGA6 SC-xenograft FAM184A chr6 119338066 C Y R459K GAGA6-pri, GAGA6 SC-xenograft FAM186A chr12 50745783 T W Q1611L GAGA6-pri, GAGA6 SC-xenograft FAM45B chrX 129629208 G A V26I GAGA6-pri, GAGA6 SC-xenograft FAM5C chr1 190067720 C S G577R GAGA6-pri, GAGA6 SC-xenograft FARP2 chr2 242380917 C M P453T GAGA6-pri, GAGA6 SC-xenograft FASTKD3 chr5 7867920 T Y N93D GAGA6-pri, GAGA6 SC-xenograft FER1L5 chr2 97359690 G R V1200I GAGA6-pri, GAGA6 SC-xenograft FER1L6 chr8 125107273 G R M1563I GAGA6-pri, GAGA6 SC-xenograft FILIP1 chr6 76023519 G R L677F GAGA6-pri, GAGA6 SC-xenograft FLRT2 chr14 86088469 C S T204R GAGA6-pri, GAGA6 SC-xenograft FLT4 chr5 180048589 C Y R658Q GAGA6-pri, GAGA6 SC-xenograft FMO2 chr1 171178072 G R G466R GAGA6-pri, GAGA6 SC-xenograft FOXQ1 chr6 1313723 A M S262R GAGA6-pri, GAGA6 SC-xenograft FSIP2 chr2 186661731 T Y S3379P GAGA6-pri, GAGA6 SC-xenograft FTSJ1 chrX 48341132 T A F303I GAGA6-pri, GAGA6 SC-xenograft FUT7 chr9 139925446 C T G249S GAGA6-pri, GAGA6 SC-xenograft GAPDH chr12 6645742 A R I38V GAGA6-pri, GAGA6 SC-xenograft GCDH chr19 13007110 C Y R243W GAGA6-pri, GAGA6 SC-xenograft GLI2 chr2 121747758 A R N1423S GAGA6-pri, GAGA6 SC-xenograft GLI3 chr7 42004052 G R T1540M GAGA6-pri, GAGA6 SC-xenograft GNA14 chr9 80046295 G A R179X GAGA6-pri, GAGA6 SC-xenograft GOLGA2 chr9 131020818 A M D708E GAGA6-pri, GAGA6 SC-xenograft GOLGA6L2 chr15 23685517 C Y C702Y GAGA6-pri, GAGA6 SC-xenograft GOLGA6L2 chr15 23685728 C S D632H GAGA6-pri, GAGA6 SC-xenograft GPLD1 chr6 24448179 G R P535L GAGA6-pri, GAGA6 SC-xenograft GPNMB chr7 23293854 C Y A97V GAGA6-pri, GAGA6 SC-xenograft GPR111 chr6 47649593 C S S365X GAGA6-pri, GAGA6 SC-xenograft GPR116 chr6 46826114 C Y A1176T GAGA6-pri, GAGA6 SC-xenograft GPSM1 chr9 139252666 G A R93Q GAGA6-pri, GAGA6 SC-xenograft GREB1L chr18 19076621 G R R1118Q GAGA6-pri, GAGA6 SC-xenograft GRIK5 chr19 42566915 T K K113Q GAGA6-pri, GAGA6 SC-xenograft GRM8 chr7 126086158 G R P900L GAGA6-pri, GAGA6 SC-xenograft GTF2F2 chr13 45841492 A W D204V GAGA6-pri, GAGA6 SC-xenograft GTPBP2 chr6 43589190 G K L86I GAGA6-pri, GAGA6 SC-xenograft HEATR4 chr14 73965019 C Y E796K GAGA6-pri, GAGA6 SC-xenograft HERC5 chr4 89396999 C Y T467I GAGA6-pri, GAGA6 SC-xenograft HERC6 chr4 89318061 C Y P316S GAGA6-pri, GAGA6 SC-xenograft HEXDC chr17 80391622 C Y A124V GAGA6-pri, GAGA6 SC-xenograft HIVEP1 chr6 12123542 G R G1172R GAGA6-pri, GAGA6 SC-xenograft HOXC4 chr12 54448837 C M H215N GAGA6-pri, GAGA6 SC-xenograft HRCT1 chr9 35906477 G T G65C GAGA6-pri, GAGA6 SC-xenograft HRNR chr1 152191037 C Y S1023N GAGA6-pri, GAGA6 SC-xenograft HRNR chr1 152192865 C Y G414S GAGA6-pri, GAGA6 SC-xenograft HSD17B8 chr6 33173043 A W I106F GAGA6-pri, GAGA6 SC-xenograft ICAM3 chr19 10449451 T Y N84D GAGA6-pri, GAGA6 SC-xenograft IGFN1 chr1 201181220 C Y T2400M GAGA6-pri, GAGA6 SC-xenograft IMPG2 chr3 100964807 G S T461R GAGA6-pri, GAGA6 SC-xenograft INPPL1 chr11 71949350 C S P1244A GAGA6-pri, GAGA6 SC-xenograft ITGAD chr16 31435968 G A E65K GAGA6-pri, GAGA6 SC-xenograft ITGAV chr2 187533544 C S P830R GAGA6-pri, GAGA6 SC-xenograft ITPKC chr19 41245298 A W T629S GAGA6-pri, GAGA6 SC-xenograft KBTBD7 chr13 41767837 T Y H186R GAGA6-pri, GAGA6 SC-xenograft LAMA1 chr18 6949209 C T R2816Q GAGA6-pri, GAGA6 SC-xenograft LAMA1 chr18 7032076 C T G755S GAGA6-pri, GAGA6 SC-xenograft LASP1 chr17 37054949 C A Y178X GAGA6-pri, GAGA6 SC-xenograft LINC00176 chr20 62669697 G R R47Q GAGA6-pri, GAGA6 SC-xenograft LPHN1 chr19 14288464 C Y V55I GAGA6-pri, GAGA6 SC-xenograft LRRC16A chr6 25492219 T Y V396A GAGA6-pri, GAGA6 SC-xenograft LRRC7 chr1 70489001 A R T542A GAGA6-pri, GAGA6 SC-xenograft LRRIQ3 chr1 74507410 C Y R402Q GAGA6-pri, GAGA6 SC-xenograft LRRTM3 chr10 68687320 C S Q216E GAGA6-pri, GAGA6 SC-xenograft MAGI3 chr1 114226512 C S T1441S GAGA6-pri, GAGA6 SC-xenograft MAPKAPK3 chr3 50655078 C S P28A GAGA6-pri, GAGA6 SC-xenograft MAST2 chr1 46501014 T Y M1558T GAGA6-pri, GAGA6 SC-xenograft MCM4 chr8 48878894 T Y V327A GAGA6-pri, GAGA6 SC-xenograft MED23 chr6 131914198 C Y A1116T GAGA6-pri, GAGA6 SC-xenograft METTL13 chr1 171763595 A M M585L GAGA6-pri, GAGA6 SC-xenograft MFI2 chr3 196746600 G R A262V GAGA6-pri, GAGA6 SC-xenograft MFSD8 chr4 128865090 C Y G86S GAGA6-pri, GAGA6 SC-xenograft MIIP chr1 12091860 C Y P388S GAGA6-pri, GAGA6 SC-xenograft MMP11 chr22 24124066 C A T110N GAGA6-pri, GAGA6 SC-xenograft MR1 chr1 181019428 G R E189K GAGA6-pri, GAGA6 SC-xenograft MS4A15 chr11 60535024 G S G82R GAGA6-pri, GAGA6 SC-xenograft MSANTD2 chr11 124670392 T Y E51G GAGA6-pri, GAGA6 SC-xenograft MUC12 chr7 100643560 G R R3239H GAGA6-pri, GAGA6 SC-xenograft MUC4 chr3 195512107 T A D2115V GAGA6-pri, GAGA6 SC-xenograft MUC4 chr3 195512186 T C I2089V GAGA6-pri, GAGA6 SC-xenograft MUC5AC chr11 1212902 C S T39S GAGA6-pri, GAGA6 SC-xenograft MX2 chr21 42735623 G R R22Q GAGA6-pri, GAGA6 SC-xenograft MYB chr6 135518157 C Y S421L GAGA6-pri, GAGA6 SC-xenograft MYH2 chr17 10451186 G R R18X GAGA6-pri, GAGA6 SC-xenograft NBEAL1 chr2 204000893 T W F1407Y GAGA6-pri, GAGA6 SC-xenograft NCKAP5L chr12 50190501 C S W381S GAGA6-pri, GAGA6 SC-xenograft NDRG1 chr8 134249753 C S L169F GAGA6-pri, GAGA6 SC-xenograft NDUFAF1 chr15 41679733 A R I298T GAGA6-pri, GAGA6 SC-xenograft NDUFS7 chr19 1394588 G S G73R GAGA6-pri, GAGA6 SC-xenograft NDUFS7 chr19 1394589 G K G73V GAGA6-pri, GAGA6 SC-xenograft NOS1 chr12 117768538 C M G113C GAGA6-pri, GAGA6 SC-xenograft NUP210 chr3 13383282 C M G1065V GAGA6-pri, GAGA6 SC-xenograft OBSCN chr1 228462377 G R V1930M GAGA6-pri, GAGA6 SC-xenograft OR13C4 chr9 107289157 A T C112S GAGA6-pri, GAGA6 SC-xenograft OR1A1 chr17 3119840 C T S309L GAGA6-pri, GAGA6 SC-xenograft OR2B11 chr1 247614827 C Y W153X GAGA6-pri, GAGA6 SC-xenograft OR2T2 chr1 248616432 G R E112K GAGA6-pri, GAGA6 SC-xenograft OS9 chr12 58090107 A R N177S GAGA6-pri, GAGA6 SC-xenograft OTP chr5 76932978 C Y G39R GAGA6-pri, GAGA6 SC-xenograft PABPC5 chrX 90690734 C Y P53L GAGA6-pri, GAGA6 SC-xenograft PCDHGB2 chr5 140739785 C S A28G GAGA6-pri, GAGA6 SC-xenograft PCNT chr21 47783504 T K M755R GAGA6-pri, GAGA6 SC-xenograft PCSK4 chr19 1487249 G R P249L GAGA6-pri, GAGA6 SC-xenograft PDE6A chr5 149323780 C Y V153I GAGA6-pri, GAGA6 SC-xenograft PHF20 chr20 34535440 T Y L977P GAGA6-pri, GAGA6 SC-xenograft PHF7 chr3 52443683 G R G6E GAGA6-pri, GAGA6 SC-xenograft PHYHD1 chr9 131684610 G C C3S GAGA6-pri, GAGA6 SC-xenograft PI4KA chr22 21065707 G A P276L GAGA6-pri, GAGA6 SC-xenograft PIGO chr9 35091966 G A R640C GAGA6-pri, GAGA6 SC-xenograft PINX1 chr8 10691269 G R A51V GAGA6-pri, GAGA6 SC-xenograft PINX1 chr8 10692106 A R S67P GAGA6-pri, GAGA6 SC-xenograft PLCB4 chr20 9319602 G R R96Q GAGA6-pri, GAGA6 SC-xenograft PLCH2 chr1 2411235 C Y P112S GAGA6-pri, GAGA6 SC-xenograft PLEK chr2 68613758 T K S199R GAGA6-pri, GAGA6 SC-xenograft PLOD3 chr7 100850890 G R T635I GAGA6-pri, GAGA6 SC-xenograft PNKP chr19 50365832 C M G300V GAGA6-pri, GAGA6 SC-xenograft PNMA1 chr14 74179836 G S I169M GAGA6-pri, GAGA6 SC-xenograft PODN chr1 53535832 C S S150C GAGA6-pri, GAGA6 SC-xenograft PPP1R13B chr14 104260916 C Y R81Q GAGA6-pri, GAGA6 SC-xenograft PPP1R36 chr14 65054060 A R E287G GAGA6-pri, GAGA6 SC-xenograft PRAMEF4 chr1 12943094 A R L41P GAGA6-pri, GAGA6 SC-xenograft PRB3 chr12 11420369 A R S230P GAGA6-pri, GAGA6 SC-xenograft PREPL chr2 44548854 T Y Y37C GAGA6-pri, GAGA6 SC-xenograft PRF1 chr10 72358223 C S E418D GAGA6-pri, GAGA6 SC-xenograft PRPF40A chr2 153532977 T Y S325G GAGA6-pri, GAGA6 SC-xenograft PRPF4B chr6 4032245 C Y S165L GAGA6-pri, GAGA6 SC-xenograft PRPF6 chr20 62641560 G K E398D GAGA6-pri, GAGA6 SC-xenograft PRRC2A chr6 31593807 C Y R284C GAGA6-pri, GAGA6 SC-xenograft PTGER2 chr14 52781969 G R G235R GAGA6-pri, GAGA6 SC-xenograft PTPN18 chr2 131127735 G S G221R GAGA6-pri, GAGA6 SC-xenograft PTPRCAP chr11 67203434 C Y E131K GAGA6-pri, GAGA6 SC-xenograft R3HCC1 chr8 23147548 C T P180S GAGA6-pri, GAGA6 SC-xenograft RAB18 chr10 27793348 G S S17T GAGA6-pri, GAGA6 SC-xenograft RAB3D chr19 11436133 C Y G201R GAGA6-pri, GAGA6 SC-xenograft RALY chr20 32664910 T Y V26A GAGA6-pri, GAGA6 SC-xenograft RASGEF1B chr4 82377621 T Y K208E GAGA6-pri, GAGA6 SC-xenograft RFX6 chr6 117248606 A R N768D GAGA6-pri, GAGA6 SC-xenograft RRM1 chr11 4133277 G R R212H GAGA6-pri, GAGA6 SC-xenograft RRNAD1 chr1 156702121 G R V54M GAGA6-pri, GAGA6 SC-xenograft RYR1 chr19 38996454 G K E2803D GAGA6-pri, GAGA6 SC-xenograft SEC31A chr4 83788076 G R T361I GAGA6-pri, GAGA6 SC-xenograft SEMA6C chr1 151105195 G S P885R GAGA6-pri, GAGA6 SC-xenograft SERPINB10 chr18 61597350 T C Y188H GAGA6-pri, GAGA6 SC-xenograft SGMS2 chr4 108816573 C Y S11F GAGA6-pri, GAGA6 SC-xenograft SIRT6 chr19 4174678 C Y R335Q GAGA6-pri, GAGA6 SC-xenograft SIX3 chr2 45171742 G S R281P GAGA6-pri, GAGA6 SC-xenograft SKIDA1 chr10 21805036 G S N572K GAGA6-pri, GAGA6 SC-xenograft SLC16A1 chr1 113456734 C Y V428I GAGA6-pri, GAGA6 SC-xenograft SLC30A7 chr1 101431388 G R V333I GAGA6-pri, GAGA6 SC-xenograft SLC35A2 chrX 48769149 C A K2N GAGA6-pri, GAGA6 SC-xenograft SLC4A10 chr2 162661016 G R R63Q GAGA6-pri, GAGA6 SC-xenograft SLITRK3 chr3 164906580 C Y R680Q GAGA6-pri, GAGA6 SC-xenograft SLITRK4 chrX 142717696 C T S410N GAGA6-pri, GAGA6 SC-xenograft SNRNP48 chr6 7601707 T Y I182T GAGA6-pri, GAGA6 SC-xenograft SNTN chr3 63645496 A R I81V GAGA6-pri, GAGA6 SC-xenograft SOAT2 chr12 53516948 C M F440L GAGA6-pri, GAGA6 SC-xenograft SOGA2 chr18 8706304 C T P216S GAGA6-pri, GAGA6 SC-xenograft SOGA2 chr18 8785971 C T P590L GAGA6-pri, GAGA6 SC-xenograft SPTBN2 chr11 66478202 C S E308D GAGA6-pri, GAGA6 SC-xenograft SRRT chr7 100482597 C Y A45V GAGA6-pri, GAGA6 SC-xenograft SSPO chr7 149477401 A R Q491R GAGA6-pri, GAGA6 SC-xenograft SSPO chr7 149508031 G K C3142F GAGA6-pri, GAGA6 SC-xenograft SSR2 chr1 155982358 T Y R21G GAGA6-pri, GAGA6 SC-xenograft STAT3 chr17 40469213 T Y I711V GAGA6-pri, GAGA6 SC-xenograft STK16 chr2 220112237 C Y R181C GAGA6-pri, GAGA6 SC-xenograft STON2 chr14 81744630 G R S342F GAGA6-pri, GAGA6 SC-xenograft TCF3 chr19 1646369 G R Q44X GAGA6-pri, GAGA6 SC-xenograft TCHH chr1 152082301 C Y R1131K GAGA6-pri, GAGA6 SC-xenograft TFE3 chrX 48895835 C T A223T GAGA6-pri, GAGA6 SC-xenograft TFR2 chr7 100238475 C Y A103T GAGA6-pri, GAGA6 SC-xenograft TIAM1 chr21 32526717 G S R1007G GAGA6-pri, GAGA6 SC-xenograft TIGD2 chr4 90035324 T Y I400T GAGA6-pri, GAGA6 SC-xenograft TLR6 chr4 38829471 T K K542Q GAGA6-pri, GAGA6 SC-xenograft TMEM130 chr7 98460828 C Y R94H GAGA6-pri, GAGA6 SC-xenograft TMEM79 chr1 156255037 T Y L7P GAGA6-pri, GAGA6 SC-xenograft TNFAIP2 chr14 103593025 C M P36Q GAGA6-pri, GAGA6 SC-xenograft TNRC18 chr7 5427549 G R R636C GAGA6-pri, GAGA6 SC-xenograft TP53 chr17 7577094 G A R282W GAGA6-pri, GAGA6 SC-xenograft TRIP6 chr7 100466106 T K V59G GAGA6-pri, GAGA6 SC-xenograft TRIQK chr8 93898312 T Y T50A GAGA6-pri, GAGA6 SC-xenograft TRPS1 chr8 116426706 C Y V1144M GAGA6-pri, GAGA6 SC-xenograft TSEN34 chr19 54697206 A W S308C GAGA6-pri, GAGA6 SC-xenograft TSPAN17 chr5 176083899 T K F254V GAGA6-pri, GAGA6 SC-xenograft TTC40 chr10 134627684 C Y G2454R GAGA6-pri, GAGA6 SC-xenograft TTN chr2 179440812 C S E20781D GAGA6-pri, GAGA6 SC-xenograft UBAP2 chr9 33923243 C A G982V GAGA6-pri, GAGA6 SC-xenograft UNC13A chr19 17728645 G R A1475V GAGA6-pri, GAGA6 SC-xenograft UNKL chr16 1442906 C Y G334S GAGA6-pri, GAGA6 SC-xenograft URB1 chr21 33716904 A W M1411K GAGA6-pri, GAGA6 SC-xenograft USH2A chr1 216419934 A M C934W GAGA6-pri, GAGA6 SC-xenograft USP36 chr17 76810633 T C D342G GAGA6-pri, GAGA6 SC-xenograft VASN chr16 4431287 C Y R137C GAGA6-pri, GAGA6 SC-xenograft VEZF1 chr17 56060354 C T G145D GAGA6-pri, GAGA6 SC-xenograft VIPR2 chr7 158826926 C Y G317S GAGA6-pri, GAGA6 SC-xenograft VWA2 chr10 116048897 C Y R591W GAGA6-pri, GAGA6 SC-xenograft WDHD1 chr14 55458043 T Y N410S GAGA6-pri, GAGA6 SC-xenograft WIZ chr19 15547682 C Y R155H GAGA6-pri, GAGA6 SC-xenograft YTHDF1 chr20 61834548 C M M248I GAGA6-pri, GAGA6 SC-xenograft ZBTB17 chr1 16269713 C Y R2Q GAGA6-pri, GAGA6 SC-xenograft ZC3H7A chr16 11870376 T Y I160V GAGA6-pri, GAGA6 SC-xenograft ZDBF2 chr2 207174685 T W N1811K GAGA6-pri, GAGA6 SC-xenograft ZFHX2 chr14 23991437 G A P2485S GAGA6-pri, GAGA6 SC-xenograft ZKSCAN2 chr16 25255171 C Y S639N GAGA6-pri, GAGA6 SC-xenograft ZNF124 chr1 247322346 G K S60R GAGA6-pri, GAGA6 SC-xenograft ZNF248 chr10 38122023 T Y D87G GAGA6-pri, GAGA6 SC-xenograft ZNF595 chr4 86691 T C F201L GAGA6-pri, GAGA6 SC-xenograft ZNF646 chr16 31090322 C Y R893W GAGA6-pri, GAGA6 SC-xenograft ZNF710 chr15 90610784 C Y P139S GAGA6-pri, GAGA6 SC-xenograft ZNF727 chr7 63537720 T Y V98A GAGA6-pri, GAGA6 SC-xenograft ZSWIM6 chr5 60817237 A R N494S GAGA6-pri, GAGA6 SC-xenograft ZYG11A chr1 53329734 C Y R411C GAGA6 SC-xenograft AHNAK2 chr14 105411464 C T D3442N GAGA6 SC-xenograft ANKRD30A chr10 37486343 T C I828T GAGA6 SC-xenograft APP chr21 27372339 C Y G342S GAGA6 SC-xenograft ARHGAP5 chr14 32545794 G A R4K GAGA6 SC-xenograft COL11A1 chr1 103449740 A R L837P GAGA6 SC-xenograft COL18A1 chr21 46925120 G R E1161K GAGA6 SC-xenograft CYB5R4 chr6 84627748 C S T157R GAGA6 SC-xenograft DCC chr18 50832080 C S L682V GAGA6 SC-xenograft DZANK1 chr20 18435965 C Y V102I GAGA6 SC-xenograft ECT2 chr3 172501685 C Y H572Y GAGA6 SC-xenograft EFCAB3 chr17 60493456 G S L413F GAGA6 SC-xenograft EFCAB3 chr17 60493602 G R R462K GAGA6 SC-xenograft EHD3 chr2 31457653 G S D56H GAGA6 SC-xenograft FAM171A2 chr17 42437463 C M E52D GAGA6 SC-xenograft FREM1 chr9 14747015 A G L2015P GAGA6 SC-xenograft IFI27 chr14 94578291 C Y P88L GAGA6 SC-xenograft IGSF10 chr3 151155406 C M A2315S GAGA6 SC-xenograft IL6ST chr5 55260065 C M C47F GAGA6 SC-xenograft ITPK1 chr14 93581423 T W E29V GAGA6 SC-xenograft LYZL2 chr10 30918549 G S A29G GAGA6 SC-xenograft MPHOSPH8 chr13 20247247 T K F23C GAGA6 SC-xenograft MUC4 chr3 195507062 C Y D3797N GAGA6 SC-xenograft PCSK5 chr9 78790157 G C W671S GAGA6 SC-xenograft PDE4DIP chr1 145014096 G R A149V GAGA6 SC-xenograft PITPNM1 chr11 67263700 C Y V756M GAGA6 SC-xenograft PLXNB2 chr22 50720146 G R T1124M GAGA6 SC-xenograft PPP2R3B chrX 308441 G C P44R GAGA6 SC-xenograft PTPRD chr9 8486144 G K Y891X GAGA6 SC-xenograft SLITRK4 chrX 142718428 A R L166P GAGA6 SC-xenograft TENM2 chr5 167589708 G R G830R GAGA6 SC-xenograft THSD7B chr2 137988733 C Y Q584X GAGA6 SC-xenograft TSPAN4 chr11 865528 C Y Q116X GAGA6 SC-xenograft TXNDC2 chr18 9886551 T W Y16X GAGA6 SC-xenograft WFDC8 chr20 44184357 G R T143M GAGA6 SC-xenograft ZNF100 chr19 21909951 A M L388R GAGA6 SC-xenograft ZPLD1 chr3 102181200 C M Q236K

Copy Number Variants (CNVs) Genes FGFR2 MYC KRAS GAGA6 primary amplified amplified - GAGA6 SC-xenograft amplified amplified - SC-xenograft = subcutaneous HD = homozygous deleted Ref = reference IP-xenograft = intraperitoneal Chr = chromosome Cons = predicted consensus Pos = position based on UCSC hg19 AA change = amino acid change