                               SEQUENCE LISTING

<110> FOUNDATION MEDICINE, INC.
 
<120> METHODS OF TREATING UROTHELIAL CARCINOMAS

<130> F2036-7050WO

<140> PCT/US2014/046857
<141> 2014-07-16

<150> 61/847,532
<151> 2013-07-17

<160> 2     

<170> PatentIn version 3.5

<210> 1
<211> 1255
<212> PRT
<213> Homo sapiens

<400> 1
Met Glu Leu Ala Ala Leu Cys Arg Trp Gly Leu Leu Leu Ala Leu Leu 
1               5                   10                  15      


Pro Pro Gly Ala Ala Ser Thr Gln Val Cys Thr Gly Thr Asp Met Lys 
            20                  25                  30          


Leu Arg Leu Pro Ala Ser Pro Glu Thr His Leu Asp Met Leu Arg His 
        35                  40                  45              


Leu Tyr Gln Gly Cys Gln Val Val Gln Gly Asn Leu Glu Leu Thr Tyr 
    50                  55                  60                  


Leu Pro Thr Asn Ala Ser Leu Ser Phe Leu Gln Asp Ile Gln Glu Val 
65                  70                  75                  80  


Gln Gly Tyr Val Leu Ile Ala His Asn Gln Val Arg Gln Val Pro Leu 
                85                  90                  95      


Gln Arg Leu Arg Ile Val Arg Gly Thr Gln Leu Phe Glu Asp Asn Tyr 
            100                 105                 110         


Ala Leu Ala Val Leu Asp Asn Gly Asp Pro Leu Asn Asn Thr Thr Pro 
        115                 120                 125             


Val Thr Gly Ala Ser Pro Gly Gly Leu Arg Glu Leu Gln Leu Arg Ser 
    130                 135                 140                 


Leu Thr Glu Ile Leu Lys Gly Gly Val Leu Ile Gln Arg Asn Pro Gln 
145                 150                 155                 160 


Leu Cys Tyr Gln Asp Thr Ile Leu Trp Lys Asp Ile Phe His Lys Asn 
                165                 170                 175     


Asn Gln Leu Ala Leu Thr Leu Ile Asp Thr Asn Arg Ser Arg Ala Cys 
            180                 185                 190         


His Pro Cys Ser Pro Met Cys Lys Gly Ser Arg Cys Trp Gly Glu Ser 
        195                 200                 205             


Ser Glu Asp Cys Gln Ser Leu Thr Arg Thr Val Cys Ala Gly Gly Cys 
    210                 215                 220                 


Ala Arg Cys Lys Gly Pro Leu Pro Thr Asp Cys Cys His Glu Gln Cys 
225                 230                 235                 240 


Ala Ala Gly Cys Thr Gly Pro Lys His Ser Asp Cys Leu Ala Cys Leu 
                245                 250                 255     


His Phe Asn His Ser Gly Ile Cys Glu Leu His Cys Pro Ala Leu Val 
            260                 265                 270         


Thr Tyr Asn Thr Asp Thr Phe Glu Ser Met Pro Asn Pro Glu Gly Arg 
        275                 280                 285             


Tyr Thr Phe Gly Ala Ser Cys Val Thr Ala Cys Pro Tyr Asn Tyr Leu 
    290                 295                 300                 


Ser Thr Asp Val Gly Ser Cys Thr Leu Val Cys Pro Leu His Asn Gln 
305                 310                 315                 320 


Glu Val Thr Ala Glu Asp Gly Thr Gln Arg Cys Glu Lys Cys Ser Lys 
                325                 330                 335     


Pro Cys Ala Arg Val Cys Tyr Gly Leu Gly Met Glu His Leu Arg Glu 
            340                 345                 350         


Val Arg Ala Val Thr Ser Ala Asn Ile Gln Glu Phe Ala Gly Cys Lys 
        355                 360                 365             


Lys Ile Phe Gly Ser Leu Ala Phe Leu Pro Glu Ser Phe Asp Gly Asp 
    370                 375                 380                 


Pro Ala Ser Asn Thr Ala Pro Leu Gln Pro Glu Gln Leu Gln Val Phe 
385                 390                 395                 400 


Glu Thr Leu Glu Glu Ile Thr Gly Tyr Leu Tyr Ile Ser Ala Trp Pro 
                405                 410                 415     


Asp Ser Leu Pro Asp Leu Ser Val Phe Gln Asn Leu Gln Val Ile Arg 
            420                 425                 430         


Gly Arg Ile Leu His Asn Gly Ala Tyr Ser Leu Thr Leu Gln Gly Leu 
        435                 440                 445             


Gly Ile Ser Trp Leu Gly Leu Arg Ser Leu Arg Glu Leu Gly Ser Gly 
    450                 455                 460                 


Leu Ala Leu Ile His His Asn Thr His Leu Cys Phe Val His Thr Val 
465                 470                 475                 480 


Pro Trp Asp Gln Leu Phe Arg Asn Pro His Gln Ala Leu Leu His Thr 
                485                 490                 495     


Ala Asn Arg Pro Glu Asp Glu Cys Val Gly Glu Gly Leu Ala Cys His 
            500                 505                 510         


Gln Leu Cys Ala Arg Gly His Cys Trp Gly Pro Gly Pro Thr Gln Cys 
        515                 520                 525             


Val Asn Cys Ser Gln Phe Leu Arg Gly Gln Glu Cys Val Glu Glu Cys 
    530                 535                 540                 


Arg Val Leu Gln Gly Leu Pro Arg Glu Tyr Val Asn Ala Arg His Cys 
545                 550                 555                 560 


Leu Pro Cys His Pro Glu Cys Gln Pro Gln Asn Gly Ser Val Thr Cys 
                565                 570                 575     


Phe Gly Pro Glu Ala Asp Gln Cys Val Ala Cys Ala His Tyr Lys Asp 
            580                 585                 590         


Pro Pro Phe Cys Val Ala Arg Cys Pro Ser Gly Val Lys Pro Asp Leu 
        595                 600                 605             


Ser Tyr Met Pro Ile Trp Lys Phe Pro Asp Glu Glu Gly Ala Cys Gln 
    610                 615                 620                 


Pro Cys Pro Ile Asn Cys Thr His Ser Cys Val Asp Leu Asp Asp Lys 
625                 630                 635                 640 


Gly Cys Pro Ala Glu Gln Arg Ala Ser Pro Leu Thr Ser Ile Ile Ser 
                645                 650                 655     


Ala Val Val Gly Ile Leu Leu Val Val Val Leu Gly Val Val Phe Gly 
            660                 665                 670         


Ile Leu Ile Lys Arg Arg Gln Gln Lys Ile Arg Lys Tyr Thr Met Arg 
        675                 680                 685             


Arg Leu Leu Gln Glu Thr Glu Leu Val Glu Pro Leu Thr Pro Ser Gly 
    690                 695                 700                 


Ala Met Pro Asn Gln Ala Gln Met Arg Ile Leu Lys Glu Thr Glu Leu 
705                 710                 715                 720 


Arg Lys Val Lys Val Leu Gly Ser Gly Ala Phe Gly Thr Val Tyr Lys 
                725                 730                 735     


Gly Ile Trp Ile Pro Asp Gly Glu Asn Val Lys Ile Pro Val Ala Ile 
            740                 745                 750         


Lys Val Leu Arg Glu Asn Thr Ser Pro Lys Ala Asn Lys Glu Ile Leu 
        755                 760                 765             


Asp Glu Ala Tyr Val Met Ala Gly Val Gly Ser Pro Tyr Val Ser Arg 
    770                 775                 780                 


Leu Leu Gly Ile Cys Leu Thr Ser Thr Val Gln Leu Val Thr Gln Leu 
785                 790                 795                 800 


Met Pro Tyr Gly Cys Leu Leu Asp His Val Arg Glu Asn Arg Gly Arg 
                805                 810                 815     


Leu Gly Ser Gln Asp Leu Leu Asn Trp Cys Met Gln Ile Ala Lys Gly 
            820                 825                 830         


Met Ser Tyr Leu Glu Asp Val Arg Leu Val His Arg Asp Leu Ala Ala 
        835                 840                 845             


Arg Asn Val Leu Val Lys Ser Pro Asn His Val Lys Ile Thr Asp Phe 
    850                 855                 860                 


Gly Leu Ala Arg Leu Leu Asp Ile Asp Glu Thr Glu Tyr His Ala Asp 
865                 870                 875                 880 


Gly Gly Lys Val Pro Ile Lys Trp Met Ala Leu Glu Ser Ile Leu Arg 
                885                 890                 895     


Arg Arg Phe Thr His Gln Ser Asp Val Trp Ser Tyr Gly Val Thr Val 
            900                 905                 910         


Trp Glu Leu Met Thr Phe Gly Ala Lys Pro Tyr Asp Gly Ile Pro Ala 
        915                 920                 925             


Arg Glu Ile Pro Asp Leu Leu Glu Lys Gly Glu Arg Leu Pro Gln Pro 
    930                 935                 940                 


Pro Ile Cys Thr Ile Asp Val Tyr Met Ile Met Val Lys Cys Trp Met 
945                 950                 955                 960 


Ile Asp Ser Glu Cys Arg Pro Arg Phe Arg Glu Leu Val Ser Glu Phe 
                965                 970                 975     


Ser Arg Met Ala Arg Asp Pro Gln Arg Phe Val Val Ile Gln Asn Glu 
            980                 985                 990         


Asp Leu Gly Pro Ala Ser Pro Leu  Asp Ser Thr Phe Tyr  Arg Ser Leu 
        995                 1000                 1005             


Leu Glu  Asp Asp Asp Met Gly  Asp Leu Val Asp Ala  Glu Glu Tyr 
    1010                 1015                 1020             


Leu Val  Pro Gln Gln Gly Phe  Phe Cys Pro Asp Pro  Ala Pro Gly 
    1025                 1030                 1035             


Ala Gly  Gly Met Val His His  Arg His Arg Ser Ser  Ser Thr Arg 
    1040                 1045                 1050             


Ser Gly  Gly Gly Asp Leu Thr  Leu Gly Leu Glu Pro  Ser Glu Glu 
    1055                 1060                 1065             


Glu Ala  Pro Arg Ser Pro Leu  Ala Pro Ser Glu Gly  Ala Gly Ser 
    1070                 1075                 1080             


Asp Val  Phe Asp Gly Asp Leu  Gly Met Gly Ala Ala  Lys Gly Leu 
    1085                 1090                 1095             


Gln Ser  Leu Pro Thr His Asp  Pro Ser Pro Leu Gln  Arg Tyr Ser 
    1100                 1105                 1110             


Glu Asp  Pro Thr Val Pro Leu  Pro Ser Glu Thr Asp  Gly Tyr Val 
    1115                 1120                 1125             


Ala Pro  Leu Thr Cys Ser Pro  Gln Pro Glu Tyr Val  Asn Gln Pro 
    1130                 1135                 1140             


Asp Val  Arg Pro Gln Pro Pro  Ser Pro Arg Glu Gly  Pro Leu Pro 
    1145                 1150                 1155             


Ala Ala  Arg Pro Ala Gly Ala  Thr Leu Glu Arg Pro  Lys Thr Leu 
    1160                 1165                 1170             


Ser Pro  Gly Lys Asn Gly Val  Val Lys Asp Val Phe  Ala Phe Gly 
    1175                 1180                 1185             


Gly Ala  Val Glu Asn Pro Glu  Tyr Leu Thr Pro Gln  Gly Gly Ala 
    1190                 1195                 1200             


Ala Pro  Gln Pro His Pro Pro  Pro Ala Phe Ser Pro  Ala Phe Asp 
    1205                 1210                 1215             


Asn Leu  Tyr Tyr Trp Asp Gln  Asp Pro Pro Glu Arg  Gly Ala Pro 
    1220                 1225                 1230             


Pro Ser  Thr Phe Lys Gly Thr  Pro Thr Ala Glu Asn  Pro Glu Tyr 
    1235                 1240                 1245             


Leu Gly  Leu Asp Val Pro Val  
    1250                 1255 


<210> 2
<211> 3768
<212> DNA
<213> Homo sapiens

<400> 2
atggagctgg cggccttgtg ccgctggggg ctcctcctcg ccctcttgcc ccccggagcc       60

gcgagcaccc aagtgtgcac cggcacagac atgaagctgc ggctccctgc cagtcccgag      120

acccacctgg acatgctccg ccacctctac cagggctgcc aggtggtgca gggaaacctg      180

gaactcacct acctgcccac caatgccagc ctgtccttcc tgcaggatat ccaggaggtg      240

cagggctacg tgctcatcgc tcacaaccaa gtgaggcagg tcccactgca gaggctgcgg      300

attgtgcgag gcacccagct ctttgaggac aactatgccc tggccgtgct agacaatgga      360

gacccgctga acaataccac ccctgtcaca ggggcctccc caggaggcct gcgggagctg      420

cagcttcgaa gcctcacaga gatcttgaaa ggaggggtct tgatccagcg gaacccccag      480

ctctgctacc aggacacgat tttgtggaag gacatcttcc acaagaacaa ccagctggct      540

ctcacactga tagacaccaa ccgctctcgg gcctgccacc cctgttctcc gatgtgtaag      600

ggctcccgct gctggggaga gagttctgag gattgtcaga gcctgacgcg cactgtctgt      660

gccggtggct gtgcccgctg caaggggcca ctgcccactg actgctgcca tgagcagtgt      720

gctgccggct gcacgggccc caagcactct gactgcctgg cctgcctcca cttcaaccac      780

agtggcatct gtgagctgca ctgcccagcc ctggtcacct acaacacaga cacgtttgag      840

tccatgccca atcccgaggg ccggtataca ttcggcgcca gctgtgtgac tgcctgtccc      900

tacaactacc tttctacgga cgtgggatcc tgcaccctcg tctgccccct gcacaaccaa      960

gaggtgacag cagaggatgg aacacagcgg tgtgagaagt gcagcaagcc ctgtgcccga     1020

gtgtgctatg gtctgggcat ggagcacttg cgagaggtga gggcagttac cagtgccaat     1080

atccaggagt ttgctggctg caagaagatc tttgggagcc tggcatttct gccggagagc     1140

tttgatgggg acccagcctc caacactgcc ccgctccagc cagagcagct ccaagtgttt     1200

gagactctgg aagagatcac aggttaccta tacatctcag catggccgga cagcctgcct     1260

gacctcagcg tcttccagaa cctgcaagta atccggggac gaattctgca caatggcgcc     1320

tactcgctga ccctgcaagg gctgggcatc agctggctgg ggctgcgctc actgagggaa     1380

ctgggcagtg gactggccct catccaccat aacacccacc tctgcttcgt gcacacggtg     1440

ccctgggacc agctctttcg gaacccgcac caagctctgc tccacactgc caaccggcca     1500

gaggacgagt gtgtgggcga gggcctggcc tgccaccagc tgtgcgcccg agggcactgc     1560

tggggtccag ggcccaccca gtgtgtcaac tgcagccagt tccttcgggg ccaggagtgc     1620

gtggaggaat gccgagtact gcaggggctc cccagggagt atgtgaatgc caggcactgt     1680

ttgccgtgcc accctgagtg tcagccccag aatggctcag tgacctgttt tggaccggag     1740

gctgaccagt gtgtggcctg tgcccactat aaggaccctc ccttctgcgt ggcccgctgc     1800

cccagcggtg tgaaacctga cctctcctac atgcccatct ggaagtttcc agatgaggag     1860

ggcgcatgcc agccttgccc catcaactgc acccactcct gtgtggacct ggatgacaag     1920

ggctgccccg ccgagcagag agccagccct ctgacgtcca tcatctctgc ggtggttggc     1980

attctgctgg tcgtggtctt gggggtggtc tttgggatcc tcatcaagcg acggcagcag     2040

aagatccgga agtacacgat gcggagactg ctgcaggaaa cggagctggt ggagccgctg     2100

acacctagcg gagcgatgcc caaccaggcg cagatgcgga tcctgaaaga gacggagctg     2160

aggaaggtga aggtgcttgg atctggcgct tttggcacag tctacaaggg catctggatc     2220

cctgatgggg agaatgtgaa aattccagtg gccatcaaag tgttgaggga aaacacatcc     2280

cccaaagcca acaaagaaat cttagacgaa gcatacgtga tggctggtgt gggctcccca     2340

tatgtctccc gccttctggg catctgcctg acatccacgg tgcagctggt gacacagctt     2400

atgccctatg gctgcctctt agaccatgtc cgggaaaacc gcggacgcct gggctcccag     2460

gacctgctga actggtgtat gcagattgcc aaggggatga gctacctgga ggatgtgcgg     2520

ctcgtacaca gggacttggc cgctcggaac gtgctggtca agagtcccaa ccatgtcaaa     2580

attacagact tcgggctggc tcggctgctg gacattgacg agacagagta ccatgcagat     2640

gggggcaagg tgcccatcaa gtggatggcg ctggagtcca ttctccgccg gcggttcacc     2700

caccagagtg atgtgtggag ttatggtgtg actgtgtggg agctgatgac ttttggggcc     2760

aaaccttacg atgggatccc agcccgggag atccctgacc tgctggaaaa gggggagcgg     2820

ctgccccagc cccccatctg caccattgat gtctacatga tcatggtcaa atgttggatg     2880

attgactctg aatgtcggcc aagattccgg gagttggtgt ctgaattctc ccgcatggcc     2940

agggaccccc agcgctttgt ggtcatccag aatgaggact tgggcccagc cagtcccttg     3000

gacagcacct tctaccgctc actgctggag gacgatgaca tgggggacct ggtggatgct     3060

gaggagtatc tggtacccca gcagggcttc ttctgtccag accctgcccc gggcgctggg     3120

ggcatggtcc accacaggca ccgcagctca tctaccagga gtggcggtgg ggacctgaca     3180

ctagggctgg agccctctga agaggaggcc cccaggtctc cactggcacc ctccgaaggg     3240

gctggctccg atgtatttga tggtgacctg ggaatggggg cagccaaggg gctgcaaagc     3300

ctccccacac atgaccccag ccctctacag cggtacagtg aggaccccac agtacccctg     3360

ccctctgaga ctgatggcta cgttgccccc ctgacctgca gcccccagcc tgaatatgtg     3420

aaccagccag atgttcggcc ccagccccct tcgccccgag agggccctct gcctgctgcc     3480

cgacctgctg gtgccactct ggaaaggccc aagactctct ccccagggaa gaatggggtc     3540

gtcaaagacg tttttgcctt tgggggtgcc gtggagaacc ccgagtactt gacaccccag     3600

ggaggagctg cccctcagcc ccaccctcct cctgccttca gcccagcctt cgacaacctc     3660

tattactggg accaggaccc accagagcgg ggggctccac ccagcacctt caaagggaca     3720

cctacggcag agaacccaga gtacctgggt ctggacgtgc cagtgtga                  3768


