Supplemental Table 1: Targeted Genes for Next-Generation Sequencing and the Associated

Supplemental Table 1: Targeted genes for next-generation sequencing and the associated transcripts used for annotation.

Gene / Reference / Gene / Reference / Gene / Reference / Gene / Reference / Gene / Reference
ABL1* / NM_005157 / CDKN2C / NM_001262 / FLT4 / NM_002020 / MYC* / NM_002467 / RPL26 / NM_000987
AKT1 / NM_005163 / CEBPA / NM_004364 / FUS* / NM_004960 / MYCL1 / NM_001033082 / RUNX1 / NM_001001890
AKT2 / NM_001626 / CHEK2 / NM_007194 / GATA3 / NM_002051 / MYCN / NM_005378 / SBDS / NM_016038
AKT3* / NM_005465 / CIITA* / NM_000246 / GATA4 / NM_002052 / MYD88 / NM_002468 / SDHAF2 / NM_017841
ALK* / NM_004304 / CREBBP / NM_004380 / GATA6 / NM_005257 / NBN / NM_002485 / SDHB / NM_003000
ALOX12B / NM_001139 / CRKL / NM_005207 / GLI1 / NM_005269 / NF1 / NM_001042492 / SDHC / NM_003001
APC / NM_001127511 / CRLF2 / NM_022148 / GLI2 / NM_005270 / NF2 / NM_000268 / SDHD / NM_003002
AR / NM_000044 / CRTC1 / NM_015321 / GLI3 / NM_000168 / NFE2L2 / NM_006164 / SETBP1 / NM_015559
ARAF / NM_001654 / CRTC2 / NM_181715 / GNA11 / NM_002067 / NFKBIA / NM_020529 / SETD2 / NM_014159
ARID1A / NM_006015 / CTNNB1 / NM_001904 / GNAQ / NM_002072 / NFKBIZ / NM_031419 / SF1 / NM_004630
ARID1B / NM_017519 / CUX1 / NM_181552 / GNAS / NM_080425 / NKX2-1 / NM_003317 / SF3B1 / NM_012433
ARID2 / NM_152641 / CYLD / NM_015247 / GPC3 / NM_004484 / NOTCH1 / NM_017617 / SH2B3 / NM_005475
ASXL1 / NM_015338 / DDB2 / NM_000107 / GSTM5 / NM_000851 / NOTCH2 / NM_024408 / SMAD2 / NM_005901
ATM / NM_000051 / DDR2 / NM_001014796 / H3F3A / NM_005324 / NPM1* / NM_002520 / SMAD4 / NM_005359
ATRX / NM_000489 / DICER1 / NM_030621 / HNF1A / NM_000545 / NRAS / NM_002524 / SMARCA4 / NM_003072
AURKA / NM_198433 / DIS3 / NM_014953 / HRAS / NM_005343 / NTRK1 / NM_002529 / SMARCB1 / NM_003073
AURKB / NM_004217 / DMD / NM_004006 / ID3 / NM_002167 / NTRK2 / NM_001018064 / SMC1A / NM_006306
AXL / NM_021913 / DNMT3A / NM_022552 / IDH1 / NM_005896 / NTRK3 / NM_001012338 / SMC3 / NM_005445
B2M / NM_004048 / EGFR* / NM_005228 / IDH2 / NM_002168 / PALB2 / NM_024675 / SMO / NM_005631
BAP1 / NM_004656 / EP300 / NM_001429 / IGF1R / NM_000875 / PARK2 / NM_004562 / SOCS1 / NM_003745
BCL2* / NM_000633 / EPHA3 / NM_005233 / IgH* / PAX5* / NM_016734 / SOX2 / NM_003106
BCL2L1 / NM_138578 / EPHA5 / NM_004439 / IgK* / PDCD1LG2 / NM_025239 / SOX9 / NM_000346
BCL2L12 / NM_138639 / EPHA7 / NM_004440 / IgL* / PDGFRA* / NM_006206 / SRC / NM_005417
BCL6* / NM_001130845 / ERBB2 / NM_004448 / IKZF1 / NM_006060 / PDGFRB* / NM_002609 / SRSF2 / NM_003016
BCOR / NM_001123385 / ERBB3 / NM_001982 / IKZF3 / NM_012481 / PHF6 / NM_001015877 / STAG1 / NM_005862
BCORL1 / NM_021946 / ERBB4 / NM_005235 / JAK2* / NM_004972 / PHOX2B / NM_003924 / STAG2 / NM_006603
BLM / NM_000057 / ERCC2 / NM_000400 / JAK3 / NM_000215 / PIK3C2B / NM_002646 / STAT3 / NM_139276
BMPR1A / NM_004329 / ERCC3 / NM_000122 / KDM6A / NM_021140 / PIK3CA / NM_006218 / STAT6 / NM_003153
BRAF* / NM_004333 / ERCC4 / NM_005236 / KDM6B / NM_001080424 / PIK3R1 / NM_181523 / STK11 / NM_000455
BRCA1 / NM_007294 / ERCC5 / NM_000123 / KDR / NM_002253 / PIM1 / NM_002648 / SUFU / NM_016169
BRCA2 / NM_000059 / ESR1 / NM_001122742 / KIT / NM_000222 / PMS1 / NM_000534 / SUZ12 / NM_015355
BRD4 / NM_058243 / ETV1* / NM_004956 / KRAS / NM_033360 / PMS2 / NM_000535 / SYK / NM_003177
BRIP1 / NM_032043 / ETV4 / NM_001986 / LMO1 / NM_002315 / PNRC1 / NM_006813 / TCF3 / NM_003200
BUB1B / NM_001211 / ETV5 / NM_004454 / LMO2 / NM_001142316 / PRAME / NM_206956 / TCF7L1 / NM_031283
CARD11 / NM_032415 / ETV6 / NM_001987 / LMO3 / NM_018640 / PRDM1 / NM_001198 / TCF7L2 / NM_001146274
CBL / NM_005188 / EWSR1* / NM_005243 / MAP2K1 / NM_002755 / PRF1 / NM_001083116 / TERT / NM_198253
CBLB / NM_170662 / EXT1 / NM_000127 / MAP2K4 / NM_003010 / PRKAR1A / NM_212471 / TET2 / NM_001127208
CCND1 / NM_053056 / EXT2 / NM_207122 / MAP3K1 / NM_005921 / PRKCI / NM_002740 / TNFAIP3 / NM_006290
CCND2 / NM_001759 / EZH2 / NM_004456 / MAPK1 / NM_002745 / PRKCZ / NM_002744 / TP53 / NM_001126112
CCND3 / NM_001760 / FAM46C / NM_017709 / MCL1 / NM_021960 / PRKDC / NM_006904 / TRA*
CCNE1 / NM_001238 / FANCA / NM_000135 / MDM2 / NM_002392 / PRPF40B / NM_001031698 / TRB*
CD274 / NM_014143 / FANCC / NM_000136 / MDM4 / NM_002393 / PRPF8 / NM_006445 / TRG*
CD58 / NM_001779 / FANCD2 / NM_033084 / MECOM / NM_005241 / PSMD13 / NM_002817 / TSC1 / NM_000368
CD79B / NM_000626 / FANCE / NM_021922 / MEF2B / NM_001145785 / PTCH1 / NM_000264 / TSC2 / NM_000548
CDC73 / NM_024529 / FANCF / NM_022725 / MEN1 / NM_130800 / PTEN / NM_000314 / U2AF1 / NM_001025203
CDH1 / NM_004360 / FANCG / NM_004629 / MET / NM_000245 / PTK2 / NM_153831 / VHL / NM_000551
CDK1 / NM_001786 / FAS / NM_000043 / MITF / NM_198159 / PTPN11 / NM_002834 / WRN / NM_000553
CDK2 / NM_001798 / FBXW7 / NM_033632 / MLH1 / NM_000249 / RAD21 / NM_006265 / WT1 / NM_024426
CDK4 / NM_000075 / FGFR1* / NM_023110 / MLL* / NM_005933 / RAF1* / NM_002880 / XPA / NM_000380
CDK5 / NM_004935 / FGFR2 / NM_000141 / MLL2 / NM_003482 / RARA* / NM_000964 / XPC / NM_004628
CDK6 / NM_001259 / FGFR3* / NM_000142 / MPL / NM_005373 / RB1 / NM_000321 / XPO1 / NM_003400
CDK9 / NM_001261 / FGFR4 / NM_002011 / MSH2 / NM_000251 / RBL2 / NM_005611 / ZNF217 / NM_006526
CDKN1A / NM_000389 / FH / NM_000143 / MSH6 / NM_000179 / REL / NM_002908 / ZNF708 / NM_021269
CDKN1B / NM_004064 / FKBP9 / NM_007270 / MTOR / NM_004958 / RET* / NM_020975 / ZRSR2 / NM_005089
CDKN1C / NM_000076 / FLCN / NM_144997 / MUTYH / NM_012222 / RFWD2 / NM_022457
CDKN2A / NM_000077 / FLT1 / NM_002019 / MYB / NM_005375 / RHPN2 / NM_033103
CDKN2B / NM_004936 / FLT3 / NM_004119 / MYBL1 / NM_001080416 / ROS1* / NM_002944

*Hybrid capture includes enrichment of select introns in these genes.

Supplemental Table 2: Immunohistochemical markers.

Antibody / Source / Clone / Dilution / Pretreatment
TTF-1 / Dako, Inc. / 8G6G3/1 / 1:300 / Citrate buffer, pressure cooker
Napsin A / Novocastra / IP64 / 1:400 / Citrate buffer, pressure cooker
CK7 / Dako, Inc. / OV-TL 12/30 / 1:100 / 10' protease digestion
CK20 / Dako, Inc. / Ks20.8 / 1:50 / 10' protease digestion
CDX-2 / BioGenex / CDX2-88 / 1:200 / Citrate buffer, pressure cooker
MUC5AC / Invitrogen / 45M1 / 1:100 / Citrate buffer, pressure cooker
MUC6 / Leica Biosystems / CLH5 / 1:300 / Citrate buffer, pressure cooker

All antibodies use the Dako EnVision+ detection system.