Supplementary material J Clin Pathol Supplementary table 1 : Genetic alterations identified in the four tumors analyzed. Genetic alterations Tumor Gene Chromosome Coordinate Variant HGVSc HGVSp ADAM29 4 175899088 G>G/T NM_014269.4:c.2412G>T NP_055084.3:p.Arg804Ser ANKRD36 2 97833499 G>G/C NM_001164315.1:c.1628G>C NP_001157787.1:p.Gly543Ala CBX2 17 77757739 G>G/A NM_005189.2:c.497G>A NP_005180.1:p.Arg166Gln CDH1 16 68846080 C>C/T NM_004360.3:c.1051C>T NP_004351.1:p.Gln351Ter CDRT15 17 14139702 G>G/A NM_001007530.1:c.308C>T NP_001007531.1:p.Ala103Val CNIH3 1 224927032 A>A/T NM_152495.1:c.457A>T NP_689708.1:p.Met153Leu CTBP2 10 126686682 A>A/T NM_022802.2:c.2036T>A NP_073713.2:p.Ile679Asn CTBP2 10 126686692 C>C/T NM_022802.2:c.2026G>A NP_073713.2:p.Asp676Asn CX3CR1 3 39307802 C>C/T NM_001171174.1:c.295G>A NP_001164645.1:p.Asp99Asn FAM8A1 6 17601058 G>G/A NM_016255.2:c.418G>A NP_057339.1:p.Ala140Thr FOXC1 6 1611802 G>G/GGGC NM_001453.2:c.1139_1141dupGCG NP_001444.2:p.Gly380dup GBE1 3 81698058 C>C/T NM_000158.3:c.640G>A NP_000149.3:p.Ala214Thr HAUS4 14 23421618 A>A/C NM_017815.2:c.249T>G NP_060285.2:p.Ile83Met HES4 1 935076 T>T/A NM_001142467.1:c.278A>T NP_001135939.1:p.Lys93Ile HOMEZ 14 23745840 C>C/G NM_020834.2:c.597G>C NP_065885.2:p.Gln199His ICAM5 19 10404565 G>G/A NM_003259.3:c.1657G>A NP_003250.3:p.Glu553Lys IL32 16 3119297 C>C/CG NM_004221.4:c.514dupG NP_004212.4:p.Asp172GlyfsTer12 IQSEC2 X 53264161 G>G/A NM_001111125.2:c.3707C>T NP_001104595.1:p.Ser1236Phe IVL 1 152883493 T>T/A NM_005547.2:c.1220T>A NP_005538.2:p.Val407Glu KIR2DL1 19 55284986 C>C/G NM_014218.2:c.272C>G NP_055033.2:p.Thr91Arg KMT2C 7 151962265 C>C/T NM_170606.2:c.1042G>A NP_733751.2:p.Asp348Asn KRT8 12 53298648 G>G/A NM_001256282.1:c.202C>T NP_001243211.1:p.Arg68Ter KRT8 12 53298675 A>A/C NM_001256282.1:c.175T>G NP_001243211.1:p.Ser59Ala MAGED2 X 54836575 G>G/C NM_177433.1:c.466G>C NP_803182.1:p.Glu156Gln MST1L 1 17085006 C>C/T NM_001271733.1:c.1469G>A NP_001258662.1:p.Gly490Glu MST1L 1 17087541 GGTGCT>GGTGCT/G NM_001271733.1:c.119_123delAGCAC NP_001258662.1:p.Gln40ProfsTer18 MTCH2 11 47660294 C>C/T NM_014342.3:c.236G>A NP_055157.1:p.Cys79Tyr MUC12 7 100634922 G>G/A NM_001164462.1:c.1078G>A NP_001157934.1:p.Ala360Thr NFKBIZ 3 101568542 G>G/A NM_031419.3:c.70G>A NP_113607.1:p.Gly24Ser Primary breast Bergeron A, et al. J Clin Pathol 2020;0:1–5. doi: 10.1136/jclinpath-2019-205783 Supplementary material J Clin Pathol Primary breast OR2T35 1 248801778 A>T/T NM_001001827.1:c.782T>A NP_001001827.1:p.Leu261Gln tumor PDZD8 10 119134498 T>T/G NM_173791.3:c.241A>C NP_776152.1:p.Thr81Pro PFKM 12 48527121 A>A/G NM_001166686.1:c.664A>G NP_001160158.1:p.Thr222Ala PFKM 12 48534616 G>G/A NM_001166686.1:c.1516G>A NP_001160158.1:p.Val506Ile PHRF1 11 610711 G>G/A NM_020901.2:c.4624G>A NP_065952.2:p.Glu1542Lys PIK3R6 17 8726721 G>G/C NM_001010855.2:c.1609C>G NP_001010855.1:p.Gln537Glu PRB1 12 11506856 G>G/A NM_005039.3:c.181C>T NP_005030.2:p.Pro61Ser PRSS3,UBE2R2-AS1 9 33798529 C>C/G NM_007343.3:c.671C>G NP_031369.2:p.Thr224Ser PRUNE2 9 79324135 A>A/ATGACTGTTGCAGM_015225.2:c.3043_3054dupCTGCAACAGTCANP_056040.2:p.Leu1015_Ser1018dup RHOA 3 49405978 C>C/T NM_001664.2:c.160G>A NP_001655.1:p.Glu54Lys ROBO2 3 75986750 C>C/T NM_001128929.2:c.106C>T NP_001122401.1:p.Gln36Ter SIPA1L2 1 232650316 C>C/T NM_020808.3:c.770G>A NP_065859.3:p.Arg257His SLC23A2 20 4893567 G>G/T NM_203327.1:c.166C>A NP_976072.1:p.Leu56Ile SPHKAP 2 228882558 C>C/G NM_001142644.1:c.3012G>C NP_001136116.1:p.Lys1004Asn SRR 17 2218895 A>A/G NM_021947.1:c.41A>G NP_068766.1:p.Lys14Arg SSBP4 19 18542496 A>A/C NM_032627.4:c.475A>C NP_116016.1:p.Thr159Pro TBC1D29 17 28890301 G>G/A NM_015594.2:c.311G>A NP_056409.1:p.Ser104Asn TIGD6 5 149375086 C>C/T NM_030953.3:c.826G>A NP_112215.1:p.Glu276Lys TPRX1 19 48305819 C>C/G NM_198479.2:c.449G>C NP_940881.2:p.Arg150Pro TRIM6,TRIM6-TRIM34 11 5632482 C>C/G NM_001003818.2:c.1461C>G NP_001003818.1:p.Phe487Leu TYW1B 7 72081809 T>T/C NM_001145440.1:c.1634A>G NP_001138912.1:p.Gln545Arg USP5 12 6972416 G>G/C NM_001098536.1:c.1829G>C NP_001092006.1:p.Gly610Ala ZAN 7 100350330 C>C/A NM_003386.1:c.2602C>A NP_003377.1:p.Pro868Thr ZKSCAN1 7 99627887 G>G/T NM_003439.1:c.688G>T NP_003430.1:p.Glu230Ter ZNF260 19 37004920 C>C/G NM_001012756.2:c.1221G>C NP_001012774.1:p.Gln407His ZNF3 7 99669169 G>G/T NM_001278284.1:c.938C>A NP_001265213.1:p.Ala313Asp ZNF493 19 21607406 C>C/A NM_001076678.2:c.1945C>A NP_001070146.1:p.Gln649Lys ZNF595 4 86022 C>A/A NM_182524.2:c.627C>A NP_872330.1:p.Tyr209Ter ZNF717 3 75786035 G>G/GA NM_001128223.1:c.2738dupT NP_001121695.1:p.Ter915LeufsTer? ZNF92 7 64864361 G>G/T NM_152626.2:c.1334G>T NP_689839.1:p.Arg445Ile ADGRG4 X 135431135 A>A/C NM_153834.3:c.5270A>C NP_722576.3:p.Asp1757Ala AKNA 9 117124731 G>G/A NM_030767.4:c.1871C>T NP_110394.3:p.Pro624Leu ALG10B 12 38714929 A>G/G NM_001013620.3:c.1336A>G NP_001013642.1:p.Ile446Val Bergeron A, et al. J Clin Pathol 2020;0:1–5. doi: 10.1136/jclinpath-2019-205783 Supplementary material J Clin Pathol ANKRD44 2 197990689 G>G/A NM_001195144.1:c.334C>T NP_001182073.1:p.His112Tyr ARMC4 10 28250610 C>C/A NM_018076.2:c.1273G>T NP_060546.2:p.Asp425Tyr BCL6B 17 6928019 C>C/CCAG NM_181844.3:c.729_731dupCAG NP_862827.1:p.Ser244dup BPIFB4 20 31673898 C>C/T NM_182519.2:c.854C>T NP_872325.2:p.Thr285Met C12ORF29 12 88440676 G>C/C NM_001009894.2:c.712G>C NP_001009894.2:p.Val238Leu C4ORF22 4 81529518 T>C/C NM_001206997.1:c.365T>C NP_001193926.1:p.Ile122Thr CBX2 17 77757739 G>G/A NM_005189.2:c.497G>A NP_005180.1:p.Arg166Gln CDC27 17 45229253 T>T/G NM_001114091.1:c.1007A>C NP_001107563.1:p.Lys336Thr CDC27 17 45229254 T>T/G NM_001114091.1:c.1006A>C NP_001107563.1:p.Lys336Gln CDH1 16 68846080 C>C/T NM_004360.3:c.1051C>T NP_004351.1:p.Gln351Ter CDK11A 1 1638961 C>C/T NM_024011.2:c.1132G>A NP_076916.2:p.Glu378Lys CEP128 14 80963847 G>G/C NM_152446.3:c.3260C>G NP_689659.2:p.Pro1087Arg CEP44 4 175225452 G>A/A NM_001145314.1:c.439G>A NP_001138786.1:p.Gly147Ser CSMD3 8 113657433 C>C/T NM_198123.1:c.3215G>A NP_937756.1:p.Arg1072Lys CTDSP2 12 58217736 AGG>AGG/A NM_005730.3:c.639_640delCC NP_005721.3:p.Leu214HisfsTer24 CX3CR1 3 39307802 C>C/T NM_001171174.1:c.295G>A NP_001164645.1:p.Asp99Asn ESD 13 47354101 C>T/T NM_001984.1:c.569G>A NP_001975.1:p.Gly190Glu FER1L6,FER1L6-AS1 8 125015458 C>C/T NM_001039112.2:c.1571C>T NP_001034201.2:p.Ser524Leu FGD6 12 95604290 T>C/C NM_018351.3:c.770A>G NP_060821.3:p.Gln257Arg FGL1 8 17731961 G>A/A NM_004467.3:c.314C>T NP_004458.3:p.Pro105Leu GBP2 1 89575909 T>T/A NM_004120.4:c.1403A>T NP_004111.2:p.Asp468Val GRIN3B 19 1004740 T>T/C NM_138690.1:c.1240T>C NP_619635.1:p.Trp414Arg HAUS4 14 23421618 A>A/C NM_017815.2:c.249T>G NP_060285.2:p.Ile83Met HEYL 1 40092267 G>G/T NM_014571.3:c.899C>A NP_055386.1:p.Ser300Ter HLA-DRB5 6 32489939 T>C/C NM_002125.3:c.113A>G NP_002116.2:p.Gln38Arg HOMEZ 14 23745840 C>C/G NM_020834.2:c.597G>C NP_065885.2:p.Gln199His IL13RA2 X 114248386 GA>GA/G NM_000640.2:c.466delT NP_000631.1:p.Ser156LeufsTer6 KCNJ12 17 21319650 CGAG>CGAG/C NM_021012.4:c.1000_1002delGAG NP_066292.2:p.Glu334del KCNJ12 17 21319767 C>C/G NM_021012.4:c.1113C>G NP_066292.2:p.Ser371Arg KIR3DL2 19 55370581 T>T/A NM_006737.3:c.997T>A NP_006728.2:p.Ser333Thr KMT2D 12 49426460 A>G/G NM_003482.3:c.12028T>C NP_003473.3:p.Ser4010Pro KRT19 17 39684321 G>G/C NM_002276.4:c.179C>G NP_002267.2:p.Ala60Gly KRTAP4-7 17 39240661 C>G/G NM_033061.3:c.203C>G NP_149050.3:p.Thr68Ser Bergeron A, et al. J Clin Pathol 2020;0:1–5. doi: 10.1136/jclinpath-2019-205783 Supplementary material J Clin Pathol LRIT3 4 110790911 A>T/T NM_198506.4:c.1006A>T NP_940908.3:p.Met336Leu LYPD2 8 143833856 C>T/T NM_205545.1:c.14G>A NP_991108.1:p.Arg5Gln MAGED2 X 54836575 G>G/C NM_177433.1:c.466G>C NP_803182.1:p.Glu156Gln mars-08 10 45953767 A>G/G NM_145021.4:c.796T>C NP_659458.2:p.Tyr266His MUC16 19 9015382 C>C/T NM_024690.2:c.38206G>A NP_078966.2:p.Gly12736Ser MUC20 3 195452799 C>T/T NM_152673.2:c.812C>T NP_689886.2:p.Thr271Ile Bone MYO9A 15 72270565 A>A/C NM_006901.3:c.1791T>G NP_008832.2:p.Asn597Lys metastasis N/A 1 233518183 G>G/A NM_032435.2:c.2837G>A NP_115811.2:p.Arg946His NOTCH4 6 32191658 TAGC>TAGC/T NM_004557.3:c.45_47delGCT NP_004548.3:p.Leu16del NTN4 12 96131895 A>G/G NM_021229.3:c.613T>C NP_067052.2:p.Tyr205His OR2T35 1 248801592 C>C/T NM_001001827.1:c.968G>A NP_001001827.1:p.Gly323Asp OR9K2 12 55523586 AT>A/A NM_001005243.1:c.38delT NP_001005243.1:p.Leu13CysfsTer22 OTC X 38226617 G>G/A NM_000531.5:c.151G>A NP_000522.3:p.Glu51Lys OTOP3 17 72937851 G>A/A NM_178233.2:c.437G>A NP_839947.1:p.Arg146Gln PFKM 12 48534616 G>G/A NM_001166686.1:c.1516G>A NP_001160158.1:p.Val506Ile PFKM 12 48534652 C>A/A NM_001166686.1:c.1552C>A NP_001160158.1:p.Gln518Lys PGLYRP2 19 15582863 C>T/T NM_052890.3:c.1181G>A NP_443122.3:p.Arg394Gln PIK3CB 3 138417865 C>C/T NM_006219.2:c.1654G>A NP_006210.1:p.Glu552Lys PKD1L2 16 81161473G>G/GTACTGCCAAGCCTGGGGAAA2892.3:c.6241_6242insGCTTTCCCCAGGCTTGGCA NP_443124.3:p.Thr2081SerfsTer? PLD2 17 4720469 C>T/T NM_002663.4:c.1730C>T NP_002654.3:p.Thr577Ile PRR21 2 240982116 C>A/A NM_001080835.1:c.284G>T NP_001074304.1:p.Arg95Leu PRSS3 9 33797928 G>G/GCC NM_007343.3:c.473_474insCC NP_031369.2:p.Arg158SerfsTer11 PRSS3 9 33797930 GAC>GAC/G NM_007343.3:c.478_479delAC NP_031369.2:p.Thr160SerfsTer4 PTEN 10 89720804 ACTTT>ACTTT/A NM_000314.4:c.956_959delCTTT NP_000305.3:p.Thr319LysfsTer24 REPS1 6 139242207 T>T/C NM_031922.3:c.1393A>G NP_114128.3:p.Met465Val RFPL4B 6 112671015 C>C/G NM_001013734.2:c.105C>G NP_001013756.2:p.Ile35Met RHOA 3 49405978 C>C/T NM_001664.2:c.160G>A NP_001655.1:p.Glu54Lys ROBO2 3 75986750 C>C/T NM_001128929.2:c.106C>T NP_001122401.1:p.Gln36Ter SLC39A11 17 70645032 G>A/A NM_001159770.1:c.860C>T NP_001153242.1:p.Ala287Val SPHKAP 2 228882558 C>C/G NM_001142644.1:c.3012G>C NP_001136116.1:p.Lys1004Asn SPTA1 1 158631146 C>C/G NM_003126.2:c.2518G>C NP_003117.2:p.Glu840Gln SRR 17 2218895 A>A/G NM_021947.1:c.41A>G NP_068766.1:p.Lys14Arg TACC3 4 1729988 G>A/A NM_006342.2:c.859G>A NP_006333.1:p.Gly287Ser Bergeron A, et al.