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