Supplemental Table 1. Clinical Predictors of Response to Anti-PD-1/L1 Therapy in SCCHN

Supplemental Table 1. Clinical predictors of response to anti-PD-1/L1 therapy in SCCHN

Variable Total (N = 126) OR [95% CI] p-value Gender 0.41 0.05-3.45 0.41 Age at diagnosis 0.99 0.95-1.04 0.93 Smoking history 0.79 0.39-2.02 0.62 ECOG performance status 0.87 0.91-1.13 0.86 HPV status 0.95 0.28-3.22 0.94 Primary tumor subsite 1.43 0.98-2.09 0.06 Initial stage of disease 1.43 0.56-3.61 0.44 Prior chemotherapy exposure 0.07 0.01-0.54 0.01 Prior radiation exposure 1.27 0.48-3.37 0.62 OR = odds ratio, CI = confidence interval; logistic regression analysis was only performed if n ≥ 15 patients were available in each subgroup.

Supplemental Table 2. Clinical response and outcomes to anti-PD-1/L1 therapy in patients with SCCHN among correlative subgroups

Overall NGS available Flow cytometric p-value (N = 126) (N = 81) data available (N = 42)

Best response to therapy 0.17 CR 6 (5)A 5 (6) 4 (10) PR 11 (9) 7 (9) 4 (10) SD 32 (25) 20 (25) 13 (31) PD 67 (53) 39 (48) 11 (26) UnevaluableB 10 (8) 10 (12) 10 (24)

Clinical benefit rateC 49 (39) 32 (40) 21 (50) A (equals %); B treatment ongoing and no interval imaging available at the time of analysis; CR = complete response, PR = partial response, SD = stable disease, PD = progression of disease, C equals CR + PR + SD

Supplemental Table 3. Comprehensive clinical and treatment response data for SCCHN patients treated with anti-PD-1/L1 blockade Gen Tob Age Dx V S Tx R G B V F I Gen Tob Age Dx V S Tx R G B V F I 1 M F 52 NPC P 3 IC CR Y D 2 Y Y 64 M F 71 LAR N 4 S + CRT PD 2 M N 70 CUT N 3 CRT CR Y P 3 65 M F 60 OPC P 4 CRT PD Y R 2 Y Y 3 M F 58 OPC P 4 S + XRT CR Y R 2 Y Y 66 M F 69 OPC P 4 S + CRT PD Y D 2 Y Y 4 M N 71 CUT N 4 IC CR Y D 3 Y Y 67 M N 66 OPC P 4 CRT PD Y R 3 Y Y 5 M F 58 OPC P 4 S + CRT CR Y R 3 Y Y 68 M F 59 LAR N 4 CRT PD 6 M N 55 OPC P 4 S + XRT CR 69 M F 72 CUP N 4 S PD 7 M F 42 OPC P 4 CRT PR 70 M F 54 OPC P 4 S + CRT PD Y D 3 Y Y 8 M F 47 OPC P 4 CRT PR 71 M N 53 LAR P 4 S PD 9 M N 54 OPC P 4 S + XRT PR Y D 3 Y Y 72 M N 43 OC N 4 CRT PD 10 M C 47 LAR N 4 CRT PR Y R 2 73 F N 53 OC N 1 S + CRT PD 11 M F 62 CUP N 4 CRT PR Y D 3 74 M C 51 NPC N 3 CRT PD Y R 2 12 F F 57 LAR N 3 S PR 75 M F 54 CUT N 2 CRT PD Y D 2 Y Y 13 M N 55 OC N 4 S PR 76 M N 65 OPC N 4 IC PD Y P 3 14 M N 64 CUT N 4 CRT PR Y R 3 Y Y 77 M N 39 OC N 4 CRT PD 15 M F 65 LAR N 4 S + CRT PR Y R 3 Y Y 78 M F 61 OC N 3 S PD Y D 2 16 M N 64 OC N 4 S + CRT PR Y P 2 79 M N 51 OPC P 4 S PD Y P 2 17 M F 50 LAR N 4 S + CRT PR Y D 2 Y Y 80 M F 52 OPC P 4 CRT PD Y R 3 18 F F 64 OPC P 4 S + CRT SD Y D 2 Y Y 81 M F 69 OPC P 4 S + XRT PD 19 M N 59 OPC P 4 S + CRT SD 82 M N 46 OC N 2 IC PD Y D 2 Y Y 20 M N 62 OPC N 4 S + CRT SD 83 F N 20 OC N 1 S PD Y R 3 Y Y 21 M N 54 CUP N 4 CRT SD Y R 3 Y Y 84 F N 48 NPC P 3 CRT PD Y R 2 22 M F 67 OPC P 4 CRT SD 85 M F 63 OPC N 4 CRT PD 23 M C 65 LAR N 4 C SD 86 F N 52 OC N 4 CRT PD 24 M N 49 OPC N 4 CRT SD Y R 2 Y Y 87 M N 65 OPC P 4 CRT PD Y D 3 25 M N 59 OPC P 4 CRT SD Y R 3 Y Y 88 M N 47 OPC P 4 S + CRT PD 26 M N 64 OPC P 4 S + XRT SD 89 F F 64 OC N 4 S + XRT PD Y R 3 Y Y 27 M N 50 OPC P 4 CRT SD 90 F F 71 OPC N 2 CRT PD Y P 3 28 M N 33 OPC P 4 C SD Y D 2 Y Y 91 M F 64 CUT N 4 S + XRT PD Y R 2 Y Y 29 M F 62 OC N 4 CRT SD Y R 3 Y Y 92 F N 39 NPC N 3 CRT PD Y P 2 30 M N 72 OPC P 4 CRT SD 93 M F 65 OPC P 4 CRT PD Y P 2 31 M N 62 OPC P 4 CRT SD Y R 2 Y Y 94 M N 59 OC N 3 S PD Y P 2 32 M F 56 NPC N 2 CRT SD Y D 2 Y Y 95 M N 55 OC N 4 S + CRT PD Y R 3 Y Y 33 M F 54 LAR N 1 CRT SD Y D 3 Y Y 96 M F 63 LAR N 4 CRT PD Y P 2 34 M N 49 OPC P 4 CRT SD Y R 3 Y Y 97 F N 70 OC N 4 IC PD Y D 3 Y Y 35 F N 64 OPC P 4 IC SD 98 M F 55 OPC N 4 CRT PD Y R 2 36 M C 38 NPC N 3 CRT SD Y R 3 99 M F 86 CUT N 1 S PD Y P 2 37 F F 34 NPC N 4 IC SD Y P 3 100 M F 56 OPC P 4 C PD Y D 2 Y Y 38 M F 67 LAR N 3 CRT SD Y D 3 Y Y 101 M N 66 OPC P 4 S PD Y R 2 Y Y 39 F N 43 OC N 4 IC SD Y R 2 Y Y 102 M C 39 OPC P 4 S + CRT PD Y R 3 Y Y 40 M F 55 OPC P 4 C SD Y P 3 103 M N 55 OPC P 4 C PD Y P 2 41 F F 67 OC N 2 CRT SD Y D 3 Y Y 104 M F 74 CUT N 4 S PD Y R 2 42 M N 44 OPC P 4 S + XRT SD Y D 2 105 M N 46 OPC P 2 S PD Y R 2 Y Y 43 M N 27 OC N 4 CRT SD Y R 2 Y Y 106 M N 49 OPC P 4 S + XRT PD 44 M F 57 OPC P 3 S SD Y P 3 107 M C 74 LAR N 4 IC PD 45 F F 86 OC N 4 IC SD 108 M F 55 OPC N 4 CRT PD 46 M N 47 LAR N 3 CRT SD 109 M N 30 OC N 4 CRT PD 47 F N 71 OC N 2 S + CRT SD Y P 3 110 M F 73 CUT N 2 S + CRT PD 48 M C 55 OPC N 4 S + CRT SD Y D 3 111 M C 54 CUT N 2 S PD 49 M F 58 OC N 3 IC SD 112 M F 88 CUT N 2 CRT PD Y R 2 50 M F 38 NPC N 4 CRT PD 113 M C 65 CUP N 4 CRT PD Y P 2 51 M F 65 OPC P 4 C PD Y P 3 114 F N 64 OC N 4 CRT PD 52 F F 60 OC N 2 IC PD 115 M F 57 OPC P 4 S + XRT PD 53 M F 51 OPC P 4 CRT PD Y D 3 116 M F 58 OPC P 4 S PD Y P 3 54 M N 45 CUP P 4 CRT PD Y P 3 117 M N 65 OPC P 4 CRT UE 55 M N 59 OC N 4 S + CRT PD Y R 2 Y Y 118 M F 59 CUP N 4 S + CRT UE Y D 3 56 F N 57 OC N 4 C PD 119 M F 51 OPC P 4 CRT UE 57 M N 59 OPC N 4 CRT PD Y R 2 Y Y 120 F F 66 OC N 4 CRT UE Y P 2 58 F N 26 OPC N 4 S PD Y D 3 Y Y 121 M N 56 NPC N 4 CRT UE 59 M N 57 OC N 4 CRT PD 122 M F 54 OPC P 4 CRT UE Y R 2 60 M N 59 OPC P 4 CRT PD Y R 3 123 M F 56 CUP N 4 S UE Y P 3 61 M N 52 OPC P 4 IC PD Y P 2 124 M N 57 CUT N 1 S + CRT UE 62 M F 64 LAR N 4 S + CRT PD Y D 3 Y Y 125 M F 45 OC N 4 CRT UE 63 F N 89 CUT N 3 S PD Y R 3 Y Y 126 M N 57 OPC P 4 C UE Gen = gender, Tob = tobacco use (F = former smoker, N = never smoker, C = current smoker), Age at diagnosis, Dx = primary site of disease (NPC = nasopharynx, CUT = cutaneous, OPC = oropharynx, LAR = larynx/hypopharynx, OC = oral cavity, CUP = carcinoma of unknown primary), V = viral status (P = human papillomavirus positive, N = HPV negative), S = initial staging, Tx = initial treatment (S = surgery, XRT = radiation, C = chemotherapy, CRT = chemoradiation, IC = induction chemotherapy followed by chemoradiation), R = best overall response (CR = complete response, PR = partial response, SD = stable disease, PD = progressive disease, UE = unevaluable), G = targeted genomic sequencing available, B = biopsy source (P = primary tumor, R = locoregional recurrence site or D = distant site), V = genomic sequencing panel version (2 or 3), F = flow cytometry results for immunoprofiling available, I = immunohistochemistry for tumor PD-L1 available

Supplemental Table 4. Cancer genomic assay to detect somatic mutations, copy number variations and structural variants from tumor DNA

The Oncopanel assay surveys exonic DNA sequences of 447 cancer genes: ABCB11 CCND2 ERBB3 GLI2 MAPK1 OGG1 REL STAT6 ABL1 CCND3 ERBB4 GNA11 MAX PALB2 RELA STK11 ACVR1 CCNE1 ERCC1 GNAQ MBD4 PARK2 RET SUFU AKT1 CD274 ERCC2 GNAS MCL1 PAX5 RHBDF2 SUZ12 AKT2 CD79B ERCC3 GPC3 MCM8 PAXIP1 RHEB TAL1 AKT3 CDC73 ERCC4 GREM1 MDM2 PBRM1 RHOA TAL2 ALK CDH1 ERCC5 H19 MDM4 PDCD1LG2 RHOH TAZ APC CDH4 ERCC6 H3F3A MECOM PDGFRA RHOT1 TCEB1 AR CDK12 ERG H3F3B MED12 PDGFRB RICTOR TCF3 ARAF CDK4 ESR1 HABP2 MEF2B PHF6 RIF1 TCF7L2 ARHGAP35 CDK6 ETV1 HELQ MEN1 PHOX2B RINT1 TDG ARHGEF12 CDK8 ETV4 HFE MET PIK3C2B RIT1 TERC ARID1A CDKN1A ETV5 HIST1H3B MGA PIK3CA RMRP TERT ARID1B CDKN1B ETV6 HIST1H3C MITF PIK3R1 RNF43 TET1 ARID2 CDKN1C EWSR1 HMBS MLH1 PIM1 RNF8 TET2 ASXL1 CDKN2A EXO1 HNF1A MLH3 PML ROS1 TFE3 ATM CDKN2B EXT1 HOXB13 MPL PMS1 RPA1 TLX3 ATR CDKN2C EXT2 HRAS MRE11A PMS2 RPTOR TMEM127 ATRX CEBPA EZH2 ID3 MSH2 PNKP RSPO2 TMPRSS2 AURKA CHEK1 FAH ID4 MSH6 POLB RSPO3 TNFAIP3 AURKB CHEK2 FAM175A IDH1 MTA1 POLD1 RUNX1 TOPBP1 AXIN2 CIC FAM46C IDH2 MTAP POLE RUNX1T1 TP53 AXL CIITA FAN1 IGF1R MTOR POLH SBDS TP53BP1 B2M COL7A1 FANCA IGF2 MUS81 POLQ SDHA TRAF3 BABAM1 CREBBP FANCB IKZF1 MUTYH POT1 SDHAF2 TRAF7 BAP1 CRKL FANCC IL7R MYB PPARG SDHB TRIM37 BARD1 CRLF2 FANCD2 ITK MYBL1 PPM1D SDHC TSC1 BCL11B CRTC1 FANCE JAK1 MYC PPP2R1A SDHD TSC2 BCL2 CSF3R FANCF JAK2 MYCL1 PRDM1 SERPINA1 TSHR BCL2L1 CTCF FANCG JAK3 MYCN PRF1 SETBP1 U2AF1 BCL2L12 CTLA4 FANCI JAZF1 MYD88 PRKAR1A SETD2 UBE2T BCL6 CTNNA1 FANCL KAT6A NBN PRKCI SF3B1 UIMC1 BCOR CTNNB1 FANCM KAT6B NEIL1 PRKDC SH2B3 UROD BCORL1 CUX1 FAS KCNQ1 NEIL2 PRSS1 SH2D1A USP28 BLM CXCR4 FAT1 KDM5A NEIL3 PTCH1 SLC25A13 USP8 BMPR1A CYLD FBXW7 KDM5C NF1 PTEN SLC34A2 VEGFA BRAF DAXX FGFR1 KDM6A NF2 PTK2B SLX1A VHL BRCA1 DCLRE1C FGFR2 KDR NFE2L2 PTPN11 SLX1B WAS BRCA2 DDB1 FGFR3 KEAP1 NFKBIA PTPN14 SLX4 WHSC1 BRCC3 DDB2 FGFR4 KIF1B NFKBIE PVRL4 SMAD2 WHSC1L1 BRD3 DDR2 FH KIT NFKBIZ QKI SMAD4 WRN BRD4 DICER1 FLCN KLF2 NKX2-1 RAC1 SMARCA4 WT1 BRE DIS3 FLT1 KLF4 NKX3-1 RAD21 SMARCB1 XPA BRIP1 DIS3L2 FLT3 KLLN NOTCH1 RAD50 SMARCE1 XPC BUB1B DKC1 FLT4 KMT2A NOTCH2 RAD51 SMC3 XPO1 C17ORF70 DMC1 FOXA1 KMT2D NOTCH3 RAD51C SMO XRCC1 C19ORF40 DNMT3A FOXL2 KRAS NPM1 RAD51D SOCS1 XRCC2 C1ORF86 DOCK8 FUS LIG4 NR0B1 RAD52 SOS1 XRCC3 CALR EGFR GALNT12 LMO1 NRAS RAD54B SOX2 XRCC4 CARD11 EGLN1 GATA2 LMO2 NRG1 RAF1 SOX9 XRCC5 CASP8 ELANE GATA3 MAF NSD1 RARA SPOP XRCC6 CBFA2T3 EME1 GATA4 MAFB NT5C2 RASA1 SRSF2 YAP1 CBFB ENG GATA6 MAP2K1 NTHL1 RB1 SRY ZNF217 CBL EP300 GBA MAP2K2 NTRK1 RBBP8 SS18 ZNRF3 CBLB EPCAM GEN1 MAP2K4 NTRK2 RBM10 STAG2 ZRSR2 CCND1 ERBB2 GLI1 MAP3K1 NTRK3 RECQL4 STAT3 It also surveys 191 regions across 60 genes for rearrangement detection: ABL1 CRTC1 EWSR1 KMT2A NRG1 PDGFRA RET TMPRSS2 ALK CRTC3 FGFR1 MET NTRK1 PDGFRB ROS1 TP53 BCL6 EGFR FGFR2 MYB NTRK2 PHF1 RSPO2 WWTR1 BIRC3 (API2) ERG FGFR3 MYBL1 NTRK3 PML RSPO3 YAP1 BRAF ESR1 FIP1L1 NAB2 NUP214 PPARG RUNX1 YWHAE CBFB ETV4 FOXO1 NCOA2 (CAN) RAF1 SLC34A2 CIC ETV5 FUS NPM1 NUTM1 RARA SS18 CIITA ETV6 JAK2 NR4A3 PDGFB RELA SUZ12 4

S u p p le m e n ta l F ig u re 1 . F o re s t p lo t o f m o rta lity ris k a c c o rd in g to in d e p e n d e n t c lin ic a l fe a tu re s a n d g e n o m ic o r im m u n e m e tric s a m o n g S C C H N p a tie n ts tre a te d w ith a n ti-P D -1 /L 1 th e ra p y

A b u n d a n c e o f C D 8 + T IL s * T u m o r P D -L 1 + g e n o m ic & * im m u n o lo g ic T IC

T M B * L o c a tio n o f re c u rre n c e

T re a tm e n t re g im e n

In itia l s ta g e o f d is e a s e

T u m o r v ira l s ta tu s * P rim a ry s ite o f d is e a s e c lin ic al P e rfo rm a n c e s ta tu s

S m o k in g h is to ry * * G e n d e r

A g e a t d ia g n o s is

.5 .0 .0 0 1 5

C o x p ro p o rtio n a l h a rz a rd s m o d e lin g d e p ic tin g u n s tra tifie d h a z a rd ra tio s o f d e a th a c c o rd in g to in d e p e n d e n t c lin ic o p a th o lo g ic fe a tu re s a n d g e n o m ic a n d im m u n e m e tric s a m o n g S C C H N p a tie n ts tre a te d w ith im m u n o th e ra p y . T IL s = tu m o r-in filtra tin g ly m p h o c y te s (q u a n tita tiv e ly s c o re d b y flo w c y to m e try ), P D -L 1 = p ro g ra m m e d c e ll d e a th p ro te in -1 lig a n d (s c o re d u s in g im m u n o h is to c h e m ic a l [IH C ] e x p re s s io n in te n s ity ). (* ) p < 0 .0 5 , (* * ) p < 0 .0 1 .

S u p p le m e n ta l F ig u re 2 . G e n o m ic la n d s c a p e a m o n g a n ti-P D -1 /L 1 n o n -re s p o n d e rs w ith p ro g re s s iv e d is e a s e in S C C H N

P D

T P 5 3 SR S S S S 39% K M T 2 D SD 24% P IK 3 C A 22% E P 3 0 0 22% C D K N 2 A S A 22% P R K D C 16% C Y L D S S S S 16% N O T C H 1 14% A P C 12% B R C A 2 12%

N O T C H 2 12% F A T 1 12% T E R T 12% A T M 10% B R D 4 SR 10% C R E B B P SR 10%

F L T 4 SR 10% A S X L 1 8% D O C K 8 8% F B X W 7 8% N F E 2 L 2 8% N S D 1 8% P IK 3 C 2 B 8% R E T 8% S M A R C A 4 8% T O P B P 1 8% T P 5 3 B P 1 8% A L K 8% A R ID 1 A 8% K M T 2 A SD 8% M T O R 8% P D G F R A SR 8%

1 2 3 4 5 6 7 8 9 1 0 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 2 0 2 1 2 2 2 3 2 4 2 5 2 6 2 7 2 8 2 9 3 0 3 1 3 2 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 0 4 1 4 2 4 3 4 4 4 5 4 6 4 7 4 8 4 9

M u ta tio n a l p lo t s h o w in g s o m a tic a lte ra tio n s in o rd e r o f fre q u e n c y (h ig h e s t o n to p ). S o m a tic m u ta tio n k e y : b lu e (m is s e n s e ), p u rp le (n o n s e n s e ), o ra n g e (in -fra m e o r fra m e s h ift), re d (p ro m o te r), lig h t b lu e (in tro n ). S S = s p lic e s ite , S R = s p lic e re g io n , S D = s p lic e d o m a in , S A = s p lic e a c c e p to r. O n ly th o s e a lte ra tio n s o c c u rrin g in  4 tu m o r s a m p le s a re in c lu d e d in th e g rid .

S u p p le m e n ta l F ig u re 3 . C o p y -n u m b e r a lte ra tio n e v e n ts a m o n g a n ti-P D -1 /L 1 n o n -re s p o n d e rs w ith p ro g re s s iv e d is e a s e in S C C H N

L o c u s G e n e

3 p 1 3 M I T F 4 3 % 3 p 2 1 B A P 1 4 3 % 3 p 2 1 S E T D 2 4 1 % 3 p 2 1 M L H 1 4 1 % 3 p 2 2 C T N N B 1 4 1 % 3 p 2 2 M Y D 8 8 3 9 % 3 q 2 6 S O X 2 3 9 % 3 q 2 6 P IK 3 C A 3 9 % 3 q 2 6 M E C O M 3 9 % 3 q 2 6 P R K C I 3 9 % 3 q 2 6 T E R C 3 5 % 3 q 2 7 B C L 6 3 5 % 4 p 1 6 F G F R 3 3 3 % 8 p 1 2 W R N 3 3 % 8 p 2 3 G A T A 4 3 3 % 8 q 1 3 M Y B L 1 3 1 % 8 q 2 1 N B N 2 9 % 8 q 2 4 M Y C 2 9 % 8 q 2 4 R E C Q L 4 2 9 % 8 q 2 4 E X T 1 2 9 % 9 p 2 1 C D K N 2 A 2 9 % 9 p 2 1 C D K N 2 B 2 9 % 9 p 2 4 J A K 2 2 9 % 9 p 2 4 P D C D 1 L G 2 2 9 % 1 1 q 2 2 A T M 2 9 % 1 1 q 2 3 K M T 2 A 2 7 % 1 1 q 2 3 S D H D 2 4 % 1 1 q 2 3 C B L 2 4 % 1 3 q 1 4 R B 1 2 4 % 1 3 q 2 1 D IS 3 2 4 % 1 4 q 1 3 N F K B IA 2 2 % 1 4 q 1 3 N K X 2 - 1 2 2 % 1 4 q 3 2 A K T 1 2 2 % 1 6 q 2 2 C D H 1 2 0 % 1 7 p 1 3 A U R K B 2 0 %

1 2 3 4 5 6 7 8 9 1 0 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 2 0 2 1 2 2 2 3 2 4 2 5 2 6 2 7 2 8 2 9 3 0 3 1 3 2 3 3 3 4 3 5 3 6 3 7 3 8 3 9 4 0 4 1 4 2 4 3 4 4 4 5 4 6 4 7 4 8 4 9

C o p y -n u m b e r v a ria tio n (C N V ) p lo t s h o w in g lo s s e s a n d g a in s in o rd e r o f g e n e lo c i a m o n g th o s e g e n e s w ith th e g re a te s t fre q u e n c y o f a lte ra tio n a m o n g th e c o h o rt ( 1 0 e v e n ts ). C N V k e y : lig h t b lu e (s in g le c o p y lo s s ), d a rk b lu e (h o m o z y g o u s d e le tio n ), p in k (lo w c o p y g a in ), re d (a m p lific a tio n ).