Supplemental Material s24

1 Supplemental Material 2 3 4

5 Supplemental Methods

7 1)Sequencing:

8 Hybridization-based capture of 3320 exons from 182 cancer-related genes and 37

9 introns of 14 genes commonly rearranged in cancer (previous version of the test performed

10 for nine patients) and 3769 exons from 236 cancer-related genes and 47 introns of 19

11 genes commonly rearranged in cancer (performed for 338 patients) was applied to ≥ 50 ng

12 of DNA extracted from 347 tumor specimens and sequenced to high, uniform coverage

13 with a mean sequencing depth of 714× as previously described35. Consistent median

14 sequencing depth was achieved by processing specimens according to optimized, locked

15 down, standard operating procedures (SOP) on automated liquid handlers in a Clinical

16 Laboratory Improvement Act (CLIA)-certified laboratory as previously described35. Genomic

17 alterations (base substitutions, small indels, rearrangements, copy number alterations)

18 were determined and then reported for these patient samples. Six or seven copy numbers

19 are reported as equivocal and > 8 are definitive; for ERBB2, equivocal amplification was 5

20 to 7 copies; all (equivocal or definitely amplified) were designated as positive for

21 amplification for this study).

1 23 182 gene panel list:

2 27 236 gene panel list:

ABL1 BTK CTNNB1 FGF23 IL7R MLH1 PDGFRA SMO AKT1 CARD11 DAXX FGF3 INHBA MLL PDGFRB SOCS1 AKT2 CBFB DDR2 FGF4 IRF4 MLL2 PDK1 SOX10 AKT3 CBL DNMT3A FGF6 IRS2 MPL PIK3CA SOX2 ALK CCND1 DOT1L FGFR1 JAK1 MRE11A PIK3CG SPEN APC CCND2 EGFR FGFR2 JAK2 MSH2 PIK3R1 SPOP AR CCND3 EMSY FGFR3 JAK3 MSH6 PIK3R2 SRC (C11orf30) ARAF CCNE1 EP300 FGFR4 JUN MTOR PPP2R1A STAG2 ARFRP1 CD79A EPHA3 FLT1 KAT6A MUTYH PRDM1 STAT4 (MYST3) ARID1A CD79B EPHA5 FLT3 KDM5A MYC PRKAR1A STK11 ARID2 CDC73 EPHB1 FLT4 KDM5C MYCL1 PRKDC SUFU ASXL1 CDH1 ERBB2 FOXL2 KDM6A MYCN PTCH1 TET2 ATM CDK12 ERBB3 GATA1 KDR MYD88 PTEN TGFBR2 ATR CDK4 ERBB4 GATA2 KEAP1 NF1 PTPN11 TNFAIP3 ATRX CDK6 ERG GATA3 KIT NF2 RAD50 TNFRSF14 AURKA CDK8 ESR1 GID4(C1 KLHL6 NFE2L2 RAD51 TOP1 7orf39) AURKB CDKN1B EZH2 GNA11 KRAS NFKBIA RAF1 TP53 AXL CDKN2A FAM123B GNA13 LRP1B NKX2-1 RARA TSC1 (WTX) BAP1 CDKN2B FAM46C GNAQ MAP2K1 NOTCH1 RB1 TSC2 BARD1 CDKN2C FANCA GNAS MAP2K2 NOTCH2 RET TSHR BCL2 CEBPA FANCC GPR124 MAP2K4 NPM1 RICTOR VHL BCL2L2 CHEK1 FANCD2 GRIN2A MAP3K1 NRAS RNF43 WISP3 BCL6 CHEK2 FANCE GSK3B MCL1 NTRK1 RPTOR WT1 BCOR CIC FANCF HGF MDM2 NTRK2 RUNX1 XPO1 BCORL1 CREBBP FANCG HRAS MDM4 NTRK3 SETD2 ZNF217 BLM CRKL FANCL IDH1 MED12 NUP93 SF3B1 ZNF703 BRAF CRLF2 FBXW7 IDH2 MEF2B PAK3 SMAD2 BRCA1 CSF1R FGF10 IGF1R MEN1 PALB2 SMAD4 BRCA2 CTCF FGF14 IKBKE MET PAX5 SMARCA4 BRIP1 CTNNA1 FGF19 IKZF1 MITF PBRM1 SMARCB1 SELECT REARRANGEMENTS ALK BCR BCL2 BRAF EGFR ETV1 ETV4 ETV5 ETV6 EWSR1 MLL MYC NTRK1 PDGFRA RAF1 RARA RET ROS1 TMPRSS2 28

37 2)Therapy 3 38 Treatment was considered “matched” if at least one agent in the treatment regimen 39 targeted at least one aberration or pathway component harbored in a patient’s molecular 40 profile or a functionally active protein preferentially expressed in the tumor (e.g. estrogen 41 receptor (ER) or HER2, assessed by standard of care testing other than NGS) with a half

42 inhibitory concentration (IC50) in the low nM range. Examples of matched therapy included, 43 but were not limited to: anti-EGFR drugs in the presence of EGFR anomalies, mTOR 44 inhibitors for alterations in the PTEN/PIK3CA/Akt/mTOR pathway, BRAF or MEK inhibitors 45 for RAF or RAS aberrations. More specifically, we defined “matched-direct” if at least one 46 drug directly impacted the gene product of the molecular alteration or a differentially 47 expressed protein [e.g. an EGFR inhibitor in a patient with an EGFR alteration (direct effect 48 on the molecular aberration) or hormonal manipulation in patients with over-expressed 49 estrogen or androgen receptors (proteins preferentially expressed on tumor cells were 50 targeted)]. “Matched-indirect” was the term used for a drug that affects a target removed 51 from the molecular aberration (e.g. mTOR inhibitor administered to patient with a PIK3CA 52 mutation). Matched-direct therapy would include small molecule inhibitors with an IC50 ≤ 53 100 nM for the target, as well as antibodies whose primary target was the aberrant protein 54 or a differentially expressed protein. Small molecule inhibitors that directly impacted a 55 target, but had an 100 nM < IC50 ≤ 250 nM for that target were considered matched- 56 indirect treatments. Matching designation was confirmed by the senior investigator (RK), 57 who was blinded at the time of designation to the outcomes.

58 3)Matching Score 59 It is now well known that advanced tumors have multiple aberrations and that 60 combination therapy is likely to be better than monotherapy. Therefore, an exploratory 61 scoring system (“Matching Score”) was developed that divided the number of matched 62 drugs by the number of aberrations. Under this system, the higher the Matching Score, the 63 better the match. The score for each match (direct or indirect) was assigned a 1; no match 64 was a zero. If a drug directly impacted two targets present in the tumor, a 2 was given 65 (example, a multikinase inhibitor with potent activity against more than one target present 66 in a tumor); if two drugs each impacted a target directly in a patient, a 2 was also given. If 67 two drugs were given that impacted directly (or indirectly) the same target in a patient, the 68 number 2 was still given. The Matching Score was calculated by dividing the number 69 derived from the direct and indirect matches in each tumor (numerator) by the number of 70 aberrations (denominator). For instance, if a patient who tumor harbored six genomic 71 aberrations received two drugs, the Matching Score would be 2/6 or 0.33. The cut-off of 0.2 72 for the OS analysis was chosen according to the minimum p-value criteria (Mazumdar and 73 Glassman21).

74 4)Statistical Analysis 75 1. Patient’s characteristics 76 Patient characteristics were summarized using descriptive statistics. A diagram 77 displays the data availability for the matched and unmatched patients; patients who were 78 lost to follow up or were still on prior therapy or on observation were considered 79 unevaluable (see Figure 1). 80 2. Study endpoints and definitions 81 The following clinical endpoints were considered: (i) rate of [stable disease (SD)≥6 82 months/partial response (PR)/complete response (CR)]; (ii) progression-free survival (PFS) 4 83 of the first line of therapy given after molecular profile results (PFS2); (iii) PFS2 versus 84 PFS1 (immediate prior line of therapy), i.e., using patients as their own controls22,23; (iv) 85 percent of patients with a PFS2/PFS1 ratio ≥ 1.322; and (v) overall survival (OS). SD, PR, or 86 CR was determined per the assessment of the treating physician. PFS was defined as the 87 time from the beginning of therapy to progression or the time to last follow up for patients 88 that were progression-free (patients that were progression-free on the date of last follow up 89 were censored on that date). OS was defined as the time from the beginning of therapy to 90 death or last follow-up date for patients who were alive (the latter were censored on that 91 date). The cut-off date for the analysis was April 1st 2015; all patients that were 92 progression-free (for PFS) or alive (for OS) as of date of analysis were censored on that 93 date unless their date of last follow up was earlier, in which case that was the date of 94 censoring. 95 3. Analyses performed 96 Whenever appropriate, Chi-Square tests were used to compare categorical 97 variables and the non-parametric Mann Whitney-U test to compare two groups on one 98 continuous variable. Binary logistic regressions were performed for categorical endpoints. 99 PFS and OS were analyzed by the Kaplan-Meier method24 and the log-rank test was used 100 to compare variables. Cox regression models were used as multivariable analysis, when 101 appropriate for survival endpoints. The importance of a prognostic factor was assessed by 102 the Chi-Square and Wald-type test statistics (for the log-rank test and logistic 103 regression/Cox regression models, respectively). The higher the Chi-square or Wald, the 104 stronger the association. 105 3.1 Variables assessed 106 The main variables analyzed in this study were “matched versus unmatched”, the 107 primary diagnosis, the number of prior therapy lines (in advanced/metastatic setting), if the 108 therapy was single agent or a combination, the total number of alterations, the presence of 109 metastasis at diagnosis, the presence of metastasis at biopsy date (of tissue used for 110 molecular testing). 111 3.2 Propensity score for being matched vs. not 112 Given the retrospective nature of our study, and to account for imbalances between 113 patients who were “matched” versus not, the “propensity” to receive a matched therapy for 114 each patient was determined by using a multivariable logistic regression with “matched or 115 not” as the outcome26–28. Variables included in the final propensity score model were 116 “breast or not” cancers, “gastrointestinal or not” cancers, “skin/melanoma or not” cancers, 117 “first line of treatment or not”, and “number of alterations”. This propensity score was used 118 as a covariate in multivariable models or in the inverse probability of matched treatment 119 weighting method. In the latter method, “matched” patients were given [1/Propensity score] 120 as weight and “unmatched” patients were given [1/(1-Propensity score)] as weight. 121 P-values were two-sided and considered significant if ≤0.05. Statistical analysis were 122 performed by author MS with SPSS version 22.0.

124 Supplemental Table 1. Patient characteristics

Total patients, Characteristics N=347

5 Age at diagnosis (years) 54 (52-55) (Median, CI 95%) Gender Women 204 (59%) Men 143 (41%) Race Caucasian 247 (71.2%) Other 46 (13.3%) 26 (7.5%)

Asian 13 (3.7%) African American 9 (2.6%) Unknown 6 (1.7%) Hispanic Type of cancer Gastro-intestinal 94 (27.1%) Breast 82 (23.7%) 36 (10.4%)

Brain 34 (9.8%) Genitourinary 33 (9.5%) Head and neck 28 (8%) Lung 26 (7.5%) Melanoma 14 (4%) Othera 125 aEwing sarcoma, carcinoid tumor, sarcomatoid tumor, peripheral nerve 126 sheath tumor, pleiomorphic sarcoma (n=2), soft tissue 127 rhabdomyosarcoma, leiomyosarcoma, and unknown origin (n=6). 128

6 130 Supplemental Table 2. List of alterations and matched drugs 131

Matched drug # Tumor type Alterations (alteration(s) targeted SD ≥ 6 months/PR/CR bolded)

1 Lung PTEN splice site 493-1 G>A everolimus YES EGFR amplification, CCND1 amplification, CDKN2A/B loss, 2 Breast lapatinib YES FGFR1 amplification, MYC amplification, TP53 P151A 3 Breast ESR1a Y537S tamoxifen YES PTEN I67K, CDKN2A/B loss, 4 Head and neck CTNNB1 T257I, MCL1 everolimus NO amplification ERBB2 amplification, FGFR4 amplification, NF1 loss, PIK3CA 5 Head and neck E545K, CCNE1 amplification, everolimus + lapatinib NO MYC amplification, TP53 D228fs*1 FGFR2 amplification, CDKN2A loss, MYC amplification, APC 6 GI ponatinib NO I1307K, ARID1A P2139fs*62, TP53 F113C APC S1421fs*52, APC 7 GI bevacizumab NO A571fs*18, TP53 Y163C 8 Brain EGFR amplification, CDKN2A loss lapatinib NO 9 Breast ERBB2 amplification trastuzumab + lapatinib NO 10 Breast RET C634R, GATA3 P436fs*11+ sorafenib NO AKT3 amplification, MYC 11 Breast amplification, MYCL1 everolimus NO amplification, TP53 R248Q ERBB2 amplification, MYC 12 Breast amplification, CDK6 trastuzumab YES amplification, TP53 R213*

7 KRAS G13D, MYCL1 13 GI amplification, ATM R337C, bevacizumab YES DNMT3A R882H, TP53 G266R BRAF V600E, MYC amplification, 14 Skin/Melanoma dabrafenib NO MSH6 R1068 ERBB2 amplification, PIK3CA H1047L, AURKA amplification, trastuzumab + lapatinib + 15 Breast YES TP53 R342P, CREBBP P858S, everolimus ZNF217 amplification MCL1 amplification, ESR1a 16 Breast letrozole NO D538G FBXW7 E113D, MCL1 17 GU bevacizumab YES amplification, TP53 S241F AURKA amplification, CCND2 amplification, KRAS G12V, MYC A59V, RICTOR amplification, 18 GI bevacizumab YES TP53 R248Q, FGF23 amplification, ZNF217 amplification ERBB2 V777L, ERBB2 S1050*, FGFR1 amplification, PIK3CA 19 Breast trastuzumab + everolimus YES E545K, TET2 S714*, TP53 W53*, ZNF703 amplification NF1 Q1315*, NF1 Q2528fs*20, PTEN G44D, BRCA2 W993*, MLL R2204Q, TP53 G244S, TP53 20 GU everolimus NO S215G, KDM5C splice, MLH1 splice site 1558+1G>A, PBRM1 splice, SPEN splice STK11 loss, TP53 R248W, MYC amplification, SMAD4 21 Breast dasatinib NO D415fs*14, GATA3 splice, MYST3 amplification PTEN N329fs*3, TP53 splice site 22 Breast everolimus NO 994-2A>G

8 PIK3CA E545K, PTEN loss, MYC amplification, TP53 truncation 23 Breast intron 6, DNMT3A R882C, ASXL1 everolimus NO G181R, MAP3K1 C667fs*4, MAP3K1 H1058fs*24 PIK3CA H1047R, CCND1 amplification, ESR1a Y537S, 24 Breast KDM5C S717L, FGF19 everolimus + exemestane NO amplification, FGF3 amplification, FGF4 amplification PIK3CA H1047R, ERBB2 25 Breast amplification, TP53 Q317*, MYC T-DM1 YES amplification 26 Head and neck vemurafenib NO BRAF V600E, PIK3CA Q546K NF1 E2608*, PTEN H272fs*4, 27 Brain everolimus YES CDKN2A/B loss PIK3CA N345K, PTEN loss, CCND1 amplification, ARID1A 28 Breast F1728fs*4, NUP93 E14K, FGF19 everolimus YES amplification, FGF3 amplification, FGF4 amplification PTCH1 Q853*, CDKN2A R80*, 29 Head and neck MDM2 amplification, TP53 vismodegib NO R248Q, NOTCH1 E424K PIK3CA H1047R, MCL1 amplification,TP53 R156P, 30 Breast everolimus NO NFKBIA amplification, SF3B1 K700E 31 Breast ERBB2 amplification, FGFR1 trastuzumab + YES amplification, FGFR2 pertuzumab amplification, PIK3CA H1047R, MCL1 amplification, MYC amplification, TP53 K132R, FANCA D1325fs*38, ZNF703

9 amplification 32 Skin/Melanoma AKT1 E17K, FLT1 V395I sorafenib YES PTEN loss, CCND1 amplification, FGF19 amplification, FGF3 amplification, FGF4 33 Breast everolimus NO amplification, GATA3 H435fs*9+, MEN1 R465*, ZNF703 amplification EGFR E746_A750del, AKT2 amplification, CDK6 amplification, TP53 K120fs*26, CCND1 amplification, CCNE1 amplification, CDKN2A/B loss, 34 Lung erlotinib YES SMAD4 Y133fs*8, FGF19 amplification, FGF4 amplification, FGF3 amplification, AXL amplification, PBRM1 K416fs*3 ERBB2 amplification, TP53 35 Breast trastuzumab + lapatinib YES R248Q NF1 loss, PIK3CA E542K, CCND1 amplification, MCL1 amplification, TP53 splice site 36 Breast everolimus NO 993+1G>A, CDH1 P744fs*24, FGF19 amplification, FGF3 amplification, FGF4 amplification RET KIF5B-RET fusion, MDM2 37 Lung cabozantinib NO amplification AKT1 E17K, NF1 Q2373*, KRAS 38 Breast everolimus YES A146V EGFR G719A, EGFR L861Q, 39 Lung MDM2 amplification, CDK4 erlotinib YES amplification, GRIN2A R1022C 10 40 Breast PIK3CA E726K, PIK3CA H1047R everolimus YES NF2 L117fs*6, RET V804M, 41 Brain everolimus NO CDKN2A/B loss, CDKN2C loss ERBB2 amplification, FGFR1 amplification, TP53 I195T, NOTCH1 truncation exon 3, 42 Breast trastuzumab YES ARID1A A40fs*11, MAP3K1 Q390*, MYST3 amplification, ZNF703 amplification ERBB2 amplification, MDM2 43 Breast amplification, RUNX1 trastuzumab NO Y403fs*80+, EP300 P925T ERBB2 amplification, SRC amplification, ARID1A E1019*, 44 Breast ARID1A E1108*, ZNF217 T-DM1 + pertuzumab NO amplification, SPEN Q256*, GATA3 G335fs*16 HRAS G13V, CDKN2A P114L, RICTOR amplification –

equivocal⌘, TP53 P278R, FGF10 45 Head and neck trametinib NO

amplification – equivocal⌘

46 Head and neck vandetanib YES RET CCDC6-RET ALK EML4-ALK fusion, ARID2 47 Lung crizotinib NO A88fs*5 48 GU JAK2 amplification ruxolitinib NO

11 EGFR amplification, EGFR vIII, IRS2 amplification, CDKN2A/B 49 Brain erlotinib NO loss, CDKN2C L122fs*2, FANCA T1161M AKT1 E17K, CCND1 amplification-equivocal, ESR1a D538G, FGF3 amplification- 50 Breast everolimus + exemestane NO equivocal, FGF4 amplification- equivocal, FGF19 amplification- equivocal ERBB2 amplification –

equivocal⌘, TSC1 truncation

exon 7, PTPN11 E76K – 51 Breast trastuzumab + everolimus YES

subclonal⌘, TP53 R175H, BRIP1

duplication exons 15-17, BRIP1 amplification EGFR amplification, CDKN2A/B 52 Brain erlotinib NO loss, MLL2 R4238C FBXW7 R465H, PIK3CA V344G, 53 GU CCNE1 amplification, MYC bevacizumab NO amplification, TP53 R248W RAF1 amplification, MYC 54 Breast pazopanib YES amplification, TP53 E286G 55 GU PIK3CA amplification, ERBB4 MEK 162/BYL 719 trial YES (NCT01449058)

amplification – equivocal⌘,

12 SOX2 amplification, MCL1

TP53 E258G, BRCA2 2417fs*4 ERBB2 amplification, AKT3 amplification, JAK2 amplification

– equivocal⌘, ATM R337H,

56 Breast TP53 R273L, MYC amplification, lapatinib NO CDKN2A loss, ESR1 amplification

– equivocal⌘, CDKN1B

S56fs*15, CDK12 truncation NF1 S821fs*5, TP53 S166*, MYC 57 GU amplification, FANCC truncation bevacizumab YES exon 8 KRAS G12D, PTEN R130G, ATR F1134fs*6, BRCA2 T3033fs*29, CTNNB1 D32N, NOTCH1 MSC2363318A, a Dual 58 GU V1578del, ARID1A Q177fs*223, p70S6K/Akt Inhibitor trial NO ARID1A D1850fs*33, AXL (NCT01971515) V289M, CTCF T204fs*18, LRP1B splice 59 Breast IKBKE amplification everolimus NO BRAF V600E, CDKN2A/B loss, 60 Brain vemurafenib YES CTNNA1 R731* 61 Brain TP53 P278S, TP53 R249T, IDH1 bevacizumab NO

13 R132S, ATRX N1232fs*15 KRAS G13D, FBXW7 R13*, APC S1465fs*3, APC S559fs*2, MSH2 62 GI everolimus NO rearrangement exon 14, MAP2K4 loss PIK3CA N345K, MYCN amplification, TP53 C277*, 63 Breast everolimus NO ARFRP1 amplification, ZNF217 amplification EGFR splice site 3272-1G>A, MET L903F, KRAS G12A, CCNE1 amplification, TP53 G154V, NFKBIA amplification – 64 Lung bevacizumab NO

equivocal⌘

65 Brain bevacizumab NO

KDR amplification – equivocal⌘,

PDGFRA amplification –

equivocal⌘, KIT amplification –

equivocal⌘, JAK1 T593M,

CDKN2A A36fs*17, TP53 R158H, TP53 R273H, NOTCH1 Q1049fs*130, NOTCH Q1687*,

14 MSH2 Q395*, MSH6 K1358fs*2, SETD2 D2064fs*84, SPEN T3244fs*40, ATRX K358fs*2 66 GI EGFR amplification – bevacizumab YES

equivocal⌘, GNAS amplification

– equivocal⌘, PIK3CA E545K,

AURKA amplification –

equivocal⌘, CDK6

amplification, MYC amplification, TP53 R282W, CCND1 amplification, SMAD4 loss, FGF3 amplification, FGF4 amplification, FGF19 amplification, ZNF217

ARFRP1 amplification –

15 equivocal⌘

67 GU TP53 R273C bevacizumab NO EGFR amplification, TP53 C176Y, cetuximab and 68 GI NO APC R1435fs*38 bevacizumab CCND1 amplification, MDM2 amplification, FGF3 69 Breast amplification, FGF4 palbociclib NO amplification, FGF19 amplification, GATA3 D336fs*17 KRAS G12V, CDKN2A E88*, 70 GU trametinib NO MSH3 A60_A62del ERBB2 V777L, ERBB3 E928G, 71 GI lapatinib + trastuzumab NO SMAD4 R361C FGFR1 amplification –

equivocal⌘, NF1 Q1218*, TP53

R267G, ERBB2 I767M, MLL2 72 GU pazopanib NO P3668fs*5, MLL2 splice site 177- 1G>T, ZNF703 amplification –

equivocal⌘

NF1 E318fs*11, PIK3CA R38H, 73 Brain PTEN loss, CDKN2A/B loss, TP53 bevacizumab NO E171fs*3, TP53 L194H, TP53 loss

16 EGFR amplification –

equivocal⌘, EGFR

E746_A750del, EGFR T790M, AKT2 amplification –

equivocal⌘, FGFR4

EGFR inhibitor (clinical 74 Lung NO amplification, GNAS trial)

CCNE1 amplification, MCL1

TP53 E258K PIK3CA amplification, SOX2 75 Breast amplification, TP53 G302fs*42, faslodex for ER+ NO FLT3 L260* 76 Breast AKT1 (E17K) casodex for AR+ NO 77 Breast GATA3 *445fs*2+ tamoxifen for ER+ NO CCND1 amplification, MCL1 78 Breast faslodex for ER+ YES amplification, CDH1 P127fs*89 MYC amplification, ARID1A 79 Breast R1461*, PALB2 G808fs*43, estradiol for ER+ NO PALB2 Y1183*

17 TOP1 amplification, MYC amplification, AURKA amplification, TP53 R196P, 80 Breast exemestane for ER+ NO MYST3 amplification, ZNF217 amplification, ZNF703 amplification FGFR1 amplification, CCND1 amplification, FGF19 amplification, FGF3 81 Breast amplification, FGF4 faslodex for ER+ YES amplification, MYST3 amplification, ZNF703 amplification PIK3CA H1047R, PIK3CA I1058L, 82 Breast arimidex for ER+ YES CSF1R V32G IGF1R amplification, GATA3 83 Breast exemestane for ER+ NO M401fs*45+ SRC amplification, TOP1 amplification, MDM2 amplification, CCND1 amplification, CDK4 amplification, AURKA amplification, NKX2-1 84 Breast exemestane for ER+ NO amplification, NFKBIA amplification, ARID1A 253fs*111, FGF19 amplification, FGF3 amplification, FGF4 amplification, GATA3 G335fs*18, ZNF217 amplification 85 Breast RPTOR amplification, CDKN2A/B letrozole for ER+ NO loss, CCND1 amplification, TP53 H168R, SMAD4 loss, NKX2-1 amplification, BCL2L2 amplification, FGF19 amplification, FGF3

18 amplification, FGF4 amplification, GATA3 N332fs*21 AURKA amplification –

equivocal⌘, CCND1

amplification, FGF3 amplification, FGF4 86 Breast amplification, FGF19 exemestane for ER+ NO amplification, MLL2 A4571T, EMSY amplification, ZNF217 amplification, ARFRP1

amplification – equivocal⌘

pertuzumab + 87 Breast PIK3CA H1047R, FGFR2 NO amplification trastuzumab for HER2+ 132 Abbreviations: GI: gastrointestinal; GU: genitourinary; ER+: estrogen receptor positive; HER2+: human epidermal growth factor receptor 2 positive; AR+: androgen 133 receptor positive; SD ≥ 6 months or PR or CR: Stable disease ≥ 6 months or partial response or complete response of any duration. N=87 patients were matched; 134 N=30/87 (34.5%) achieved SD ≥ 6 months/PR/CR. 13 of the 87 patients (15%, see patients number 75-87) were matched on basis of non-NGS marker only (these 135 patients were considered matched as next-generation sequencing results were used in context of standard of care). aESR1 is generally a resistance mutation, but patients 136 with such alterations may respond to certain hormonal modulators, depending on the mutation36(p1),37,38(p1)

19 137 Supplemental Figure 1. Overall survival analysis