Sequenzprotokoll zweite Version.txt
 SEQUENCE LISTING 

<110> Cellphenomics GmbH 

<120> Method for determination whether to start or to continue a treatment of cancer, a 
biomarker corresponding to at least one marker gene, and a use of the biomarker in the 
inventive method 

<130> 0426 PA 19001WO 

<150> DE102020102143.7 

<151> 2020-01-29 

<160> 16 

<170> BiSSAP 1.3.6 

<210> 1 

<211> 1659 

<212> DNA 

<213> Homo sapiens 

<220> 

<223> SMAD4 wt 

<400> 1 
atggacaata tgtctattac gaatacacca acaagtaatg atgcctgtct gagcattgtg 60 
catagtttga tgtgccatag acaaggtgga gagagtgaaa catttgcaaa aagagcaatt 120 
gaaagtttgg taaagaagct gaaggagaaa aaagatgaat tggattcttt aataacagct 180 
ataactacaa atggagctca tcctagtaaa tgtgttacca tacagagaac attggatggg 240 
aggcttcagg tggctggtcg gaaaggattt cctcatgtga tctatgcccg tctctggagg 300 
tggcctgatc ttcacaaaaa tgaactaaaa catgttaaat attgtcagta tgcgtttgac 360 
ttaaaatgtg atagtgtctg tgtgaatcca tatcactacg aacgagttgt atcacctgga 420 
attgatctct caggattaac actgcagagt aatgctccat caagtatgat ggtgaaggat 480 
gaatatgtgc atgactttga gggacagcca tcgttgtcca ctgaaggaca ttcaattcaa 540 
accatccagc atccaccaag taatcgtgca tcgacagaga catacagcac cccagctctg 600 
ttagccccat ctgagtctaa tgctaccagc actgccaact ttcccaacat tcctgtggct 660 

Page 1 

tccacaagtc agcctgccag tatactgggg ggcagccata gtgaaggact gttgcagata 720 
gcatcagggc ctcagccagg acagcagcag aatggattta ctggtcagcc agctacttac 780 
catcataaca gcactaccac ctggactgga agtaggactg caccatacac acctaatttg 840 
cctcaccacc aaaacggcca tcttcagcac cacccgccta tgccgcccca tcccggacat 900 
tactggcctg ttcacaatga gcttgcattc cagcctccca tttccaatca tcctgctcct 960 
gagtattggt gttccattgc ttactttgaa atggatgttc aggtaggaga gacatttaag 1020 
gttccttcaa gctgccctat tgttactgtt gatggatacg tggacccttc tggaggagat 1080 
cgcttttgtt tgggtcaact ctccaatgtc cacaggacag aagccattga gagagcaagg 1140 
ttgcacatag gcaaaggtgt gcagttggaa tgtaaaggtg aaggtgatgt ttgggtcagg 1200 
tgccttagtg accacgcggt ctttgtacag agttactact tagacagaga agctgggcgt 1260 
gcacctggag atgctgttca taagatctac ccaagtgcat atataaaggt ctttgatttg 1320 
cgtcagtgtc atcgacagat gcagcagcag gcggctactg cacaagctgc agcagctgcc 1380 
caggcagcag ccgtggcagg aaacatccct ggcccaggat cagtaggtgg aatagctcca 1440 
gctatcagtc tgtcagctgc tgctggaatt ggtgttgatg accttcgtcg cttatgcata 1500 
ctcaggatga gttttgtgaa aggctgggga ccggattacc caagacagag catcaaagaa 1560 
acaccttgct ggattgaaat tcacttacac cgggccctcc agctcctaga cgaagtactt 1620 
cataccatgc cgattgcaga cccacaacct ttagactga 1659 

<210> 2 

<211> 1659 

<212> DNA 

<213> Homo sapiens 

<220> 

<223> SMAD4 R361H - Loss-of-function mutation at postition 1082 

<400> 2 
atggacaata tgtctattac gaatacacca acaagtaatg atgcctgtct gagcattgtg 60 

catagtttga tgtgccatag acaaggtgga gagagtgaaa catttgcaaa aagagcaatt 120 

gaaagtttgg taaagaagct gaaggagaaa aaagatgaat tggattcttt aataacagct 	180 
Page 2 

ataactacaa atggagctca tcctagtaaa tgtgttacca tacagagaac attggatggg 240 
aggcttcagg tggctggtcg gaaaggattt cctcatgtga tctatgcccg tctctggagg 300 
tggcctgatc ttcacaaaaa tgaactaaaa catgttaaat attgtcagta tgcgtttgac 360 
ttaaaatgtg atagtgtctg tgtgaatcca tatcactacg aacgagttgt atcacctgga 420 
attgatctct caggattaac actgcagagt aatgctccat caagtatgat ggtgaaggat 480 
gaatatgtgc atgactttga gggacagcca tcgttgtcca ctgaaggaca ttcaattcaa 540 
accatccagc atccaccaag taatcgtgca tcgacagaga catacagcac cccagctctg 600 
ttagccccat ctgagtctaa tgctaccagc actgccaact ttcccaacat tcctgtggct 660 
tccacaagtc agcctgccag tatactgggg ggcagccata gtgaaggact gttgcagata 720 
gcatcagggc ctcagccagg acagcagcag aatggattta ctggtcagcc agctacttac 780 
catcataaca gcactaccac ctggactgga agtaggactg caccatacac acctaatttg 840 
cctcaccacc aaaacggcca tcttcagcac cacccgccta tgccgcccca tcccggacat 900 
tactggcctg ttcacaatga gcttgcattc cagcctccca tttccaatca tcctgctcct 960 
gagtattggt gttccattgc ttactttgaa atggatgttc aggtaggaga gacatttaag 1020 
gttccttcaa gctgccctat tgttactgtt gatggatacg tggacccttc tggaggagat 1080 
cacttttgtt tgggtcaact ctccaatgtc cacaggacag aagccattga gagagcaagg 1140 
ttgcacatag gcaaaggtgt gcagttggaa tgtaaaggtg aaggtgatgt ttgggtcagg 1200 
tgccttagtg accacgcggt ctttgtacag agttactact tagacagaga agctgggcgt 1260 
gcacctggag atgctgttca taagatctac ccaagtgcat atataaaggt ctttgatttg 1320 
cgtcagtgtc atcgacagat gcagcagcag gcggctactg cacaagctgc agcagctgcc 1380 
caggcagcag ccgtggcagg aaacatccct ggcccaggat cagtaggtgg aatagctcca 1440 
gctatcagtc tgtcagctgc tgctggaatt ggtgttgatg accttcgtcg cttatgcata 1500 
ctcaggatga gttttgtgaa aggctgggga ccggattacc caagacagag catcaaagaa 1560 
acaccttgct ggattgaaat tcacttacac cgggccctcc agctcctaga cgaagtactt 1620 
cataccatgc cgattgcaga cccacaacct ttagactga 1659 

Page 3 

<210> 3 

<211> 22 

<212> DNA 

<213> Artificial Sequence 

<220> 

<223> Primer 1 (SMAD4 fw2) 

<400> 3 
aaattctcag ttgacctggt cc 22 

<210> 4 

<211> 22 

<212> DNA 

<213> Artificial Sequence 

<220> 

<223> Primer 2 (SMAD4 rev2) 

<400> 4 
accgacaatt aagatggagt gc 22 

<210> 5 

<211> 1411 

<212> DNA 

<213> Homo sapiens 

<220> 

<223> FBXW7 wt 

<400> 5 
caacagcaaa ggcactgaga agagaaagtc aaaaagtcca gtttggcaga aaccattttg 60 

aaaactggat cgaggatttc ttccttaatt cgttagtcaa cagtaggctc aaaaagactt 120 

aagaactggg cagtgacact atcataatta taaaaggact atatgtcagc tgtataaaac 180 

ataagataac caagttagaa agctgtgaca atagttcaga atgagagaac aaattaccca 240 

caggcctcag cttttgccta gacttagaga tagggtgggt gtaaggtggg taggtaattt 300 

aaaaaggctc agacgcttga agcctgaatt tgtcccactt gcggaaataa gaatatcaaa 360 

Page 4 

aaaagagaga gaaaacatga tttctgcttg aatatgatga gtcatcaaag atacagaaca 420 
acaaaaagga ttagagatta gagagtagag agtttcaaac aggaagctga caacactagc 480 
aaatgagaaa ggaaatttac agacaatcac caattttaag acaaaacgct atggctttcc 540 
tagaatagaa acatctgaag tgtaataatt aaatctaatt taagagcaca ctgtcactat 600 
ttcagtaact ctacacagaa agggcccaaa ttcaccaata atagaggaag aagtcccaac 660 
catgacaaga ttttccctta ccttttttca tgaagatgca tacaacgcac agtggaagta 720 
tgcccatata aggtgtgtat acattctcca gtctctgcat tccacacttt gagtgtccga 780 
tctgtagatc cactaatgat gatgttgtct ctcatttgtg atgaccatac tccacctgta 840 
tgtcccacta atgttctcag acactggaaa aacacttaag atgattactt ttgggtagaa 900 
aggaaaagtg atttaaataa aatttaatag ctcattaaaa tttggagtaa agttacttat 960 
ttaatttgtt tggctcttca gaaaatatta catccgtata aaatgatccc atcactattt 1020 
attgttttgt ttattcaaaa gcattataaa tttatataag cacaagcaat tgtgtatgta 1080 
gtatgtagaa agcaaacata tgatataaaa catgatataa taaaaaggaa acacgacatg 1140 
aaagcagtta tgatagctct ggcctggcct ctttgatgaa ataatactga aattgcaact 1200 
gggtttcttc catgggaata gattcaatga aagtatgcca acagtattgg gtgtggctac 1260 
ataccacatt tcatctgaat ctgccccagg gcagtagtta ggagccagtg aagctacttc 1320 
tagacaagta aagacagaca ttaaagccct gtaataaatc ccaaactaat attacactat 1380 
ggaaatataa agctgcttta aaaaatttta a 1411 

<210> 6 

<211> 1411 

<212> DNA 

<213> Homo sapiens 

<220> 

<223> FBXW7 R465H - Loss-of function mutation at position 826 

<400> 6 
caacagcaaa ggcactgaga agagaaagtc aaaaagtcca gtttggcaga aaccattttg 60 

aaaactggat cgaggatttc ttccttaatt cgttagtcaa cagtaggctc aaaaagactt 	120 
Page 5 

aagaactggg cagtgacact atcataatta taaaaggact atatgtcagc tgtataaaac 180 
ataagataac caagttagaa agctgtgaca atagttcaga atgagagaac aaattaccca 240 
caggcctcag cttttgccta gacttagaga tagggtgggt gtaaggtggg taggtaattt 300 
aaaaaggctc agacgcttga agcctgaatt tgtcccactt gcggaaataa gaatatcaaa 360 
aaaagagaga gaaaacatga tttctgcttg aatatgatga gtcatcaaag atacagaaca 420 
acaaaaagga ttagagatta gagagtagag agtttcaaac aggaagctga caacactagc 480 
aaatgagaaa ggaaatttac agacaatcac caattttaag acaaaacgct atggctttcc 540 
tagaatagaa acatctgaag tgtaataatt aaatctaatt taagagcaca ctgtcactat 600 
ttcagtaact ctacacagaa agggcccaaa ttcaccaata atagaggaag aagtcccaac 660 
catgacaaga ttttccctta ccttttttca tgaagatgca tacaatgcac agtggaagta 720 
tgcccatata aggtgtgtat acattctcca gtctctgcat tccacacttt gagtgtccga 780 
tctgtagatc cactaatgat gatgttgtct ctcatttgtg atgaccatac tccacctgta 840 
tgtcccacta atgttctcag acactggaaa aacacttaag atgattactt ttgggtagaa 900 
aggaaaagtg atttaaataa aatttaatag ctcattaaaa tttggagtaa agttacttat 960 
ttaatttgtt tggctcttca gaaaatatta catccgtata aaatgatccc atcactattt 1020 
attgttttgt ttattcaaaa gcattataaa tttatataag cacaagcaat tgtgtatgta 1080 
gtatgtagaa agcaaacata tgatataaaa catgatataa taaaaaggaa acacgacatg 1140 
aaagcagtta tgatagctct ggcctggcct ctttgatgaa ataatactga aattgcaact 1200 
gggtttcttc catgggaata gattcaatga aagtatgcca acagtattgg gtgtggctac 1260 
ataccacatt tcatctgaat ctgccccagg gcagtagtta ggagccagtg aagctacttc 1320 
tagacaagta aagacagaca ttaaagccct gtaataaatc ccaaactaat attacactat 1380 
ggaaatataa agctgcttta aaaaatttta a 1411 

<210> 7 

<211> 21 

<212> DNA 

<213> Artificial Sequence 
Page 6 

<220> 

<223> FBXW7 fw (F) - Primer 

<400> 7 
caaacaggaa gctgacaaca c 21 

<210> 8 

<211> 21 

<212> DNA 

<213> Artificial Sequence 

<220> 

<223> FBXW7 rev (R) - Primer 

<400> 8 
agtgggacaa attcaggctt c 21 

<210> 9 

<211> 1411 

<212> DNA 

<213> Homo sapiens 

<220> 

<223> ARID1A wt 

<400> 9 
gagtaggctg tcaaatattt tttttgaatg aaaactaaat gaaagagaga accaaagtag 60 

cttagtgatt ttcacactgt ctgaattact aaaccttagg ttttcagttg gttgagccag 120 

gctgctattg actattcatt gtggttaggg tacagattcc taacacttat aaaaacagtc 180 

taggccgtga taaaaagagt taggctcact ggtagaaaca gctgctctca aacttatgtt 240 

gcccaaatag taaatagtgt aaattttcag tggataaatg tagtccactt gtaaacaaac 300 

cacctaaaaa cccagcttgg ccgtccttcc tggctcagtt taggcagggt gagagaaaaa 360 

ccctgggcct cctaagtatg aggccttgca tgcttgcttt ctatactcat catcagtgca 420 

tagcttctca caaaacactt catctttcct catgcaggag agtcagtgct aaaagtatat 480 

tttcctttcc tacagattcc tccttatgga caacaaggcc ccagcgggta tggtcaacag 540 

Page 7 

ggccagactc catattacaa ccagcaaagt cctcaccctc agcagcagca gccaccctac 600 
tcccagcaac caccgtccca gacccctcat gcccaacctt cgtatcagca gcagccacag 660 
tctcaaccac cacagctcca gtcctctcag cctccatact cccagcagcc atcccagcct 720 
ccacatcagc agtccccggc tccatacccc tcccagcagt cgacgacaca gcagcacccc 780 
cagagccagc ccccctactc acagccacag gctcagtctc cttaccagca gcagcaacct 840 
cagcagccag caccctcgac gctctcccag caggctgcgt atcctcagcc ccagtctcag 900 
cagtcccagc aaactgccta ttcccagcag cgcttccctc caccgcaggt aagatatccc 960 
tgcctcctgc ccttccctgt gtgtgactac agacagcttg ggggttagtg tcatgagaac 1020 
tttgctgtac agagtggttc tctaacgtgc acttaaagac caattaaact ctgggtaaac 1080 
atgataactg gattgattga actaataaag gcataacctc cttaactgca taaagacctg 1140 
tagctctcct taatgatgaa gaaatagggc aatggaaagt tgcatagatg gataagaaat 1200 
taaagataat gggactggtt tttttatttt attttatttt attttatttt gtaaatcaac 1260 
atcagaactt cagcatctaa gtgagttggt cttttttcaa aacagtcact ttgagaggca 1320 
gtactgtaca ttcactccaa ctgccattcc attctgctat cgctcaaaat acttggatcc 1380 
cttcatttgg aattgccacc agagctgata c 1411 

<210> 10 

<211> 1411 

<212> DNA 

<213> Homo sapiens 

<220> 

<223> ARID1A Q521* - Loss-of function mutation at position 826 

<400> 10 
gagtaggctg tcaaatattt tttttgaatg aaaactaaat gaaagagaga accaaagtag 60 
cttagtgatt ttcacactgt ctgaattact aaaccttagg ttttcagttg gttgagccag 120 
gctgctattg actattcatt gtggttaggg tacagattcc taacacttat aaaaacagtc 180 
taggccgtga taaaaagagt taggctcact ggtagaaaca gctgctctca aacttatgtt 240 
gcccaaatag taaatagtgt aaattttcag tggataaatg tagtccactt gtaaacaaac 300 
Page 8 

cacctaaaaa cccagcttgg ccgtccttcc tggctcagtt taggcagggt gagagaaaaa 360 
ccctgggcct cctaagtatg aggccttgca tgcttgcttt ctatactcat catcagtgca 420 
tagcttctca caaaacactt catctttcct catgcaggag agtcagtgct aaaagtatat 480 
tttcctttcc tacagattcc tccttatgga caacaaggcc ccagcgggta tggtcaacag 540 
ggccagactc catattacaa ccagcaaagt cctcaccctc agcagcagca gccaccctac 600 
tcccagcaac caccgtccca gacccctcat gcccaacctt cgtatcagca gcagccacag 660 
tctcaaccac cacagctcca gtcctctcag cctccatact cccagtagcc atcccagcct 720 
ccacatcagc agtccccggc tccatacccc tcccagcagt cgacgacaca gcagcacccc 780 
cagagccagc ccccctactc acagccacag gctcagtctc cttaccagca gcagcaacct 840 
cagcagccag caccctcgac gctctcccag caggctgcgt atcctcagcc ccagtctcag 900 
cagtcccagc aaactgccta ttcccagcag cgcttccctc caccgcaggt aagatatccc 960 
tgcctcctgc ccttccctgt gtgtgactac agacagcttg ggggttagtg tcatgagaac 1020 
tttgctgtac agagtggttc tctaacgtgc acttaaagac caattaaact ctgggtaaac 1080 
atgataactg gattgattga actaataaag gcataacctc cttaactgca taaagacctg 1140 
tagctctcct taatgatgaa gaaatagggc aatggaaagt tgcatagatg gataagaaat 1200 
taaagataat gggactggtt tttttatttt attttatttt attttatttt gtaaatcaac 1260 
atcagaactt cagcatctaa gtgagttggt cttttttcaa aacagtcact ttgagaggca 1320 
gtactgtaca ttcactccaa ctgccattcc attctgctat cgctcaaaat acttggatcc 1380 
cttcatttgg aattgccacc agagctgata c 1411 

<210> 11 

<211> 20 

<212> DNA 

<213> Artificial Sequence 

<220> 

<223> ARID1A fw (F) - Primer 

<400> 11 
Page 9 

ggtatggtca acagggccag 20 

<210> 12 

<211> 20 

<212> DNA 

<213> Artificial Sequence 

<220> 

<223> ARID1A rev (R) - Primer 

<400> 12 
tcatacttag gaggcccagg 20 

<210> 13 

<211> 1411 

<212> DNA 

<213> Homo sapiens 

<220> 

<223> BMPR2 wt 

<400> 13 
acaaatctgc ataccacaaa tgttgcacag tcaattgggc caacccctgt ctgcttacag 60 
ctgacagaag aagacttgga aaccaacaag ctagacccaa aagaagttga taagaacctc 120 
aaggaaagct ctgatgagaa tctcatggag cactctctta aacagttcag tggcccagac 180 
ccactgagca gtactagttc tagcttgctt tacccactca taaaacttgc agtagaagca 240 
actggacagc aggacttcac acagactgca aatggccaag catgtttgat tcctgatgtt 300 
ctgcctactc agatctatcc tctccccaag cagcagaacc ttcccaagag acctactagt 360 
ttgcctttga acaccaaaaa ttcaacaaaa gagccccggc taaaatttgg cagcaagcac 420 
aaatcaaact tgaaacaagt cgaaactgga gttgccaaga tgaatacaat caatgcagca 480 
gaacctcatg tggtgacagt caccatgaat ggtgtggcag gtagaaacca cagtgttaac 540 
tcccatgctg ccacaaccca atatgccaat gggacagtac tatctggcca aacaaccaac 600 
atagtgacac atagggccca agaaatgttg cagaatcagt ttattggtga ggacacccgg 660 
ctgaatatta attccagtcc tgatgagcat gagcctttac tgagacgaga gcaacaagct 720 

Page 10 

ggccatgatg aaggtgttct ggatcgtctt gtggacagga gggaacggcc actagaaggt 780 
ggccgaacta attccaataa caacaacagc aatccatgtt cagaacaaga tgttcttgca 840 
cagggtgttc caagcacagc agcagatcct gggccatcaa agcccagaag agcacagagg 900 
cctaattctc tggatctttc agccacaaat gtcctggatg gcagcagtat acagagtaag 960 
tggagggatc atataatctc tcctgtgtgt cttttggggc catttaaata actatttaga 1020 
atcaactaat agatatattt caactagtga ttatttacct ttaccacttt tgtaaatgat 1080 
ccatttgagg cggggcacag tggctcacac ctgtaatcct agcactttgg gaggccaagg 1140 
gaggtggatc acctgaggtc aggagttcaa gaccaacctg gccaacatgg cgaaacccca 1200 
tctctactaa aaaataaaaa aaattaggcc aggcgcggtg gctcacgcct gtaatcccag 1260 
cactttggga ggccaaggcg ggcagattac ttgagatcag gagttcaaga ccagcctggc 1320 
caacatggtg aaaccccatc tctaaaaaat acaaaaatta gccaggcgtg gtggcgtgca 1380 
cctgtaatcc cagccgagat cacgacactt c 1411 

<210> 14 

<211> 1411 

<212> DNA 

<213> Homo sapiens 

<220> 

<223> BMPR2 R873* - Loss-of function mutation at position 826 

<400> 14 
acaaatctgc ataccacaaa tgttgcacag tcaattgggc caacccctgt ctgcttacag 60 
ctgacagaag aagacttgga aaccaacaag ctagacccaa aagaagttga taagaacctc 120 
aaggaaagct ctgatgagaa tctcatggag cactctctta aacagttcag tggcccagac 180 
ccactgagca gtactagttc tagcttgctt tacccactca taaaacttgc agtagaagca 240 
actggacagc aggacttcac acagactgca aatggccaag catgtttgat tcctgatgtt 300 
ctgcctactc agatctatcc tctccccaag cagcagaacc ttcccaagag acctactagt 360 
ttgcctttga acaccaaaaa ttcaacaaaa gagccccggc taaaatttgg cagcaagcac 420 
aaatcaaact tgaaacaagt cgaaactgga gttgccaaga tgaatacaat caatgcagca 480 
Page 11 

gaacctcatg tggtgacagt caccatgaat ggtgtggcag gtagaaacca cagtgttaac 540 
tcccatgctg ccacaaccca atatgccaat gggacagtac tatctggcca aacaaccaac 600 
atagtgacac atagggccca agaaatgttg cagaatcagt ttattggtga ggacacccgg 660 
ctgaatatta attccagtcc tgatgagcat gagcctttac tgagatgaga gcaacaagct 720 
ggccatgatg aaggtgttct ggatcgtctt gtggacagga gggaacggcc actagaaggt 780 
ggccgaacta attccaataa caacaacagc aatccatgtt cagaacaaga tgttcttgca 840 
cagggtgttc caagcacagc agcagatcct gggccatcaa agcccagaag agcacagagg 900 
cctaattctc tggatctttc agccacaaat gtcctggatg gcagcagtat acagagtaag 960 
tggagggatc atataatctc tcctgtgtgt cttttggggc catttaaata actatttaga 1020 
atcaactaat agatatattt caactagtga ttatttacct ttaccacttt tgtaaatgat 1080 
ccatttgagg cggggcacag tggctcacac ctgtaatcct agcactttgg gaggccaagg 1140 
gaggtggatc acctgaggtc aggagttcaa gaccaacctg gccaacatgg cgaaacccca 1200 
tctctactaa aaaataaaaa aaattaggcc aggcgcggtg gctcacgcct gtaatcccag 1260 
cactttggga ggccaaggcg ggcagattac ttgagatcag gagttcaaga ccagcctggc 1320 
caacatggtg aaaccccatc tctaaaaaat acaaaaatta gccaggcgtg gtggcgtgca 1380 
cctgtaatcc cagccgagat cacgacactt c 1411 

<210> 15 

<211> 20 

<212> DNA 

<213> Artificial Sequence 

<220> 

<223> BMPR2 fw (F) - Primer 

<400> 15 
tgcagcagaa cctcatgtgg 20 

<210> 16 

<211> 20 

<212> DNA 
Page 12 

<213> Artificial Sequence 

<220> 

<223> BMPR2 rev (R) - Primer 

<400> 16 
acactgtggt ttctacctgc 

Page 13 

