Method of diagnosing neoplasms
Abstract
The present invention relates generally to nucleic acid molecules, the RNA and protein expression profiles of which are indicative of the onset, predisposition to the onset and/or progression of a neoplasm. More particularly, the present invention is directed to nucleic acid molecules, the expression profiles of which are indicative of the onset and/or progression of a large intestine neoplasm, such as an adenoma or an adenocarcinoma. The expression profiles of the present invention are useful in a range of applications including, but not limited to, those relating to the diagnosis and/or monitoring of colorectal neoplasms, such as colorectal adenocarcinomas. Accordingly, in a related aspect the present invention is directed to a method of screening a subject for the onset, predisposition to the onset and/or progression of a neoplasm by screening for modulation in the expression profile of one or more nucleic acid molecule markers.
Claims
exact text as granted — not AI-modified1 - 30 . (canceled)
31 . A method of screening for the onset or predisposition to the onset of a large intestine neoplasm or monitoring the progress of a neoplasm in an individual, said method comprising measuring the level of expression of one or more genes or transcripts selected from:
(i)
the gene, genes or transcripts detected by Affymetrix probeset IDs:
201563_at
204702_s_at
205828_at
201328_at
221577_x_at
205886_at
201341_at
221922_at
205890_s_at
201416_at
60474_at
205910_s_at
201417_at
222696_at
205941_s_at
201468_s_at
223447_at
206224_at
201506_at
223970_at
206976_s_at
201656_at
225541_at
207173_x_at
201925_s_at
225835_at
207457_s_at
201926_s_at
226360_at
208079_s_at
202286_s_at
227174_at
208712_at
202718_at
227475_at
209218_at
202831_at
228303_at
209309_at
202833_s_at
228653_at
209752_at
202935_s_at
228754_at
209773_s_at
202936_s_at
228915_at
209774_x_at
203124_s_at
229215_at
209792_s_at
203256_at
231832_at
209875_s_at
203313_s_at
231941_s_at
209955_s_at
203510_at
232176_at
210052_s_at
203860_at
232252_at
210511_s_at
203895_at
232481_s_at
210559_s_at
203896_s_at
234331_s_at
210766_s_at
203961_at
235210_s_at
211506_s_at
203962_s_at
235976_at
212281_s_at
204259_at
236894_at
212344_at
204351_at
238017_at
212353_at
204401_at
212354_at
204404_at
238984_at
213905_x_at
204855_at
241031_at
214022_s_at
204885_s_at
200660_at
214974_x_at
205174_s_at
200832_s_at
215091_s_at
205366_s_at
200903_s_at
217430_x_at
205470_s_at
201014_s_at
217996_at
205513_at
201112_s_at
218507_at
205765_at
201195_s_at
218963_s_at
205825_at
201261_x_at
218984_at
205927_s_at
201292_at
219787_s_at
205983_at
201338_x_at
219911_s_at
206239_s_at
201479_at
221729_at
206286_s_at
201577_at
221730_at
207158_at
201601_x_at
221731_x_at
207850_at
201666_at
221923_s_at
209369_at
202310_s_at
37892_at
210445_at
202311_s_at
222449_at
210519_s_at
202404_s_at
222450_at
211429_s_at
202431_s_at
222549_at
212063_at
202504_at
222608 s_at
212070_at
202779_s_at
223062_s_at
212190_at
202859_x_at
224428_s_at
212531_at
202954_at
224646_x_at
212942_s_at
202998_s_at
224915_x_at
213880_at
203083_at
225295_at
213975_s_at
203213_at
225520_at
214235_at
203878_s_at
225664_at
214651_s_at
204051_s_at
225681_at
217523_at
204127_at
225767_at
217867_x_at
204170_s_at
225799_at
218086_at
204320_at
225806_at
218211_s_at
204470_at
226227_x_at
218704_at
204475_at
226237_at
218796_at
204580_at
226311_at
218872_at
204620_s_at
226777_at
219630_at
205361_s_at
226835_s_at
219682_s_at
205476_at
227140_at
219727_at
205479_s_at
229802_at
219955_at
205713_s_at
231766_s_at
219956_at
205815_at
232151_at; and/or
200665_s_at
(ii)
SORD
NFE2L3
CDCA7
LOXL2
KIAA1199
RNF43
TDGF1
AZGP1
FOXQ1
CCL20
MTHFD1L
MYC
MMP1
CTSE
ANLN
COMP
TCN1
MSLN
H19
AURKA
MMP7
TIMP1
FAP
PAICS
WDR72
PCSK1
DACH1
PUS7
INHBA
CST1
VCAN
ZNRF3
COL11A1
BGN
SQLE
CCND1
GDF15
AXIN2
REG3A
CSE1L
CTHRC1
MET
TESC
PFDN4
COL1A1
SOX9
UBE2C
C20orf42
LGR5
TMEPAI
TMEM97
SLC11A2
DUSP27
CDH11
TRIM29
CEL
SERPINB5
MMP11
KLK11
NLF1
ASCL2
CXCL1
LY6G6D
NPDC1
SULF1
QPCT
SLC7A5
ENC1
SLC6A6
PDZK1IP1
FABP6
SERPINE2
TACSTD2
CD55
SLITRK6
UBE2S
NEBL
ECT2
MLPH
TOP2A
PCCA
COL12A1
HOXA9
CDC2
FLJ37644
L1TD1
TBX3
RFC3
KRT23
WDR51B
BACE2
LILRB1
CXCL3
HOXB6
GPX2
NPM1
MMP3
FAM84A
TPX2
RDHE2
SFRP4
COL5A2
KCNN4
PLAU
UBD
MMP12
LOC541471
HSPH1
SCD
PSAT1
CYP3A5
GTF3A
DPEP1
CXCL5
ANXA3
KLK10
LCN2
IGFBP2
CYP3A5P2
GPSM2
PLCB4
TGIF1
C14orf94
NME1
SPINK1
CXCL2
RP5-875H10.1
MUC20
DUOX2
SLCO4A1
RPL22L1
RPESP
SOX4
CKS2
APOBEC1
RRM2
THBS2
PHLDA1
HIG2
DKC1
CLDN1
SERPINA1
COL10A1
CD44
REG1B
COL1A2
AHCY
CDH3
IL8
SPARC
in a biological sample from said individual wherein a higher level of expression of the genes or transcripts of group (i) and/or group (ii) relative to control levels is indicative of a neoplastic large intestine cell or a cell predisposed to the onset of a neoplastic state.
32 . The method according to claim 31 wherein said one or more genes or transcripts are selected from:
(i) 201563_at, 204702_s_at; and/or (ii) SORD, NFE2L3.
33 . The method according to claim 31 wherein said one or more genes or transcripts are selected from:
(i) the gene, genes or transcripts detected by Affymetrix probeset IDs:
225681_at; 227140_at; and/or
(ii) CTHRC1; (ii) the gene, genes or transcripts detected by Affymetrix probeset IDs:
227475_at, 204475_at, 202859_x_at, 202404_s_at; and/or
FOXQ1, MMP1, IL8, COL1A2;
(iii) the gene, genes or transcripts detected by Affymetrix probeset IDs:
205513_at, 204259_at, 227174_at, 210511_s_at, 37892_at; and/or
TCN1, MMP7, WDR72, INHBA, COL11A1;
(i)
the gene, genes or transcripts detected by Affymetrix probeset IDs:
221577_x_at
212942_s_at
202310_s_at
213880_at
232252_at
204855_at
229215_at
212354_at
228754_at
202286_s_at
203962_s_at
203860_at
202935_s_at
218963_s_at
207850_at
205828_at
204051_s_at
205890_s_at
200832_s_at
205983_at
212531_at; and/or
KIAA1199
GDF15
COL1A1
LGR5
DUSP27
SERPINB5
ASCL2
SULF1
SLC6A6
TACSTD2
NEBL
PCCA
FLJ37644
KRT23
CXCL3
MMP3
SFRP4
UBD
SCD
DPEP1
LCN2;
34 . The method according to any one of claims 31 - 33 wherein said control level is a non-neoplastic level.
35 . The method according to claim 31 wherein said neoplastic cell is an adenoma or an adenocarcinoma.
36 . The method according to claim 31 wherein said neoplasm is an adenoma and said one or more genes or transcripts are selected from:
(i)
the gene, genes or transcripts detected by Affymetrix probeset IDs:
201328_at
205825_at
219956_at
201468_s_at
205927_s_at
221922_at
201656_at
206239_s_at
223447_at
201925_s_at
207158_at
223970_at
201926_s_at
210445_at
225835_at
202718_at
210519_s_at
226360_at
202831_at
211429_s_at
228303_at
202833_s_at
212063_at
228653_at
203124_s_at
213975_s_at
228915_at
203313_s_at
214235_at
231832_at
203860_at
214651_s_at
231941_s_at
203895_at
217523_at
232176_at
203896_s_at
217867_x_at
232481_s_at
204401_at
218086_at
234331_s_at
204885_s_at
218211_s_at
235210_s_at
205174_s_at
218796_at
235976_at
205366_s_at
219630_at
236894_at
205470_s_at
219682_s_at
238017_at
205513_at
219727_at
238984_at
205765_at
219955_at;
241031_at; and/or
(ii)
APOBEC1
HOXB6
QPCT
BACE2
IGFBP2
RDHE2
C20orf42
ITGA6
REG4
CD44
KCNN4
RETNLB
CD55
KLK11
RP5-875H10.1
CTSE
L1TD1
RPESP
CYP3A5
LILRB1
SERPINA1
CYP3A5P2
MLPH
SLC11A2
DACH1
MSLN
SLC12A2
DUOX2
MUC20
SLITRK6
ETS2
NLF1
SPINK1
FABP6
NPDC1
TBX3
FAM84A
NQO1
TCN1
GALNT6
PCCA
TGIF1
GPSM2
PCSK1
WDR51B
GPX2
PDZK1IP1
ZNRF3
HOXA9
PLCB4.
37 . The method according to claim 31 wherein said neoplasm is a cancer and said one or more genes or transcripts are selected from:
(i)
the gene, genes or transcripts detected by Affymetrix probeset IDs:
204702_s_at
205476_at
217430_x_at
200660_at
205479_s_at
217996_at
200665_s_at
205713_s_at
218507_at
200832_s_at
205815_at
218963_s_at
200903_s_at
205828_at
218984_at
201014_s_at
205886_at
219787_s_at
201112_s_at
205890_s_at
219911_s_at
201195_s_at
205910_s_at
221729_at
201261_x_at
205941_s_at
221730_at
201292_at
206224_at
221731_x_at
201338_x_at
206976_s_at
221923_s_at
201479_at
207173_x_at
37892_at
201577_at
207457_s_at
222449_at
201601_x_at
208079_s_at
222450_at
201666_at
208712_at
222549_at
202310_s_at
209218_at
222608_s_at
202311_s_at
209309_at
223062_s_at
202403_s_at
209752_at
224428_s_at
202404_s_at
209773_s_at
224646_x_at
202431_s_at
209774_x_at
224915_x_at
202504_at
209792_s_at
225295_at
202779_s_at
209875_s_at
225520_at
202859_x_at
209955_s_at
225664_at
202954_at
210052_s_at
225681_at
202998_s_at
210511_s_at
225767_at
203083_at
210559_s_at
225799_at
203213_at
210766_s_at
225806_at
203878_s_at
211506_s_at
226227_x_at
204051_s_at
212281_s_at
226237_at
204127_at
212344_at
226311_at
204170_s_at
212353_at
226777_at
204320_at
212354_at
226835_s_at
204470_at
213905_x_at
227140_at
204475_at
214022_s_at
229802_at
204580_at
214974_x_at
231766_s_at
204620_s_at
215091_s_at;
232151_at; and/or
205361_s_at
(ii)
NFE2L3
DKC1
PSAT1
AHCY
ECT2
PUS7
ANLN
FAP
REG1A
AURKA
GTF3A
REG1B
AZGP1
H19
REG3A
BGN
HIG2
RFC3
C14orf94
HSPH1
RRM2
C20orf199
IFITM1
S100A11
CCL20
IL8
SCD
CCND1
INHBA
SFRP4
CDC2
KLK10
SLC39A10
CDCA7
KRT23
SLC7A5
CDH11
LOC541471
SLCO4A1
CEL
LOXL2
SPARC
CKS2
LY6G6D
SPP1
CLDN1
MMP1
SQLE
COL10A1
MMP11
SULF1
COL11A1
MMP12
THBS2
COL12A1
MMP3
TIMP1
COL1A1
MTHFD1L
TMEM97
COL1A2
MYC
TMEPAI
COL5A2
NME1
TOP2A
COL8A1
NPM1
TPX2
COMP
PAICS
TRIM29
CSE1L
PFDN4
UBD
CST1
PHLDA1
UBE2C
CTHRC1
PLAU
UBE2S
CXCL1
VCAN
CXCL2
CXCL5.
38 . A method of screening for the onset of a large intestine neoplasm in an individual, said method comprising measuring the level of expression of one or more genes or transcripts selected from:
(i)
the gene, genes or transcripts detected by Affymetrix probeset IDs:
204702_s_at
235976_at
209309_at
202286_s_at
236894_at
211506_s_at
204259_at
214974_x_at
204885_s_at
238984_at
219787_s_at
205174_s_at
241031_at
37892_at
205825_at
202311_s_at
222608_s_at
207850_at
204320_at
223062_s_at
213880_at
204475_at
225806_at
217523_at
205910_s_at
226237_at
227174_at
206224_at
227140_at
228915_at
229802_at; and/or
232252_at
(ii)
NFE2L3
PCSK1
ANLN
MMP1
CST1
DACH1
MMP7
QPCT
COL11A1
LGR5
ECT2
C14orf94
WDR72
SLITRK6
AZGP1
COL11A1
L1TD1
REG4
COL1A1
KIAA1199
CEL
DUSP27
PSAT1
CD44
NLF1
CXCL5
COL8A1
IL8
CXCL3
TACSTD2
MSLN
in a biological sample from said individual wherein a higher level of expression of the genes or transcripts of group (i) and/or group (ii) relative to background levels is indicative of a neoplastic cell or a cell predisposed to the onset of a neoplastic state.
39 . The method according to claim 38 wherein said neoplastic cell is an adenoma or adenocarcinoma.
40 . The method according to claim 38 wherein said neoplasm is an adenoma and said one or more genes or transcripts are selected from:
(i) the gene, genes or transcripts detected by Affymetrix probeset IDs:
204885_s_at, 217523_at, 236894_at, 205174_s_at, 228915_at, 238984_at, 205825_at, 235976_at, 241031_at; and/or
(ii) CD44, MSLN, QPCT, DACH1, NLF1, REG4, L1TD1, PCSK1, SLITRK6.
41 . The method according to claim 38 wherein said neoplasm is a cancer and said one or more genes or transcripts are selected from:
(i)
the gene or genes detected by Affymetrix probeset IDs:
204702_s_at
209309_at
223062_s_at
202311_s_at
211506_s_at
225806_at
204320_at
214974_x_at
226237_at
204475_at
219787_s_at
227140_at
205910_s_at
37892_at
229802_at; and/or
206224_at
222608_s_at
(ii)
NFE2L3
COL1A1
IL8
ANLN
COL8A1
MMP1
AZGP1
CST1
C14orf94
CXCL5
CEL
ECT2.
PSAT1
COL11A1
42 . The method according to any one of claims 38 - 41 wherein said background level is the background of the testing methodology.
43 . A method of characterising a neoplastic cell or cellular population, which cell or cellular population is derived from the large intestine of an individual, said method comprising measuring the level of expression of one or more genes or transcripts selected from:
(i)
the gene, genes or transcripts detected by Affymetrix probeset IDs:
200884_at
214234_s_at
226248_s_at
203240_at
214235_at
226302_at
203963_at
214433_s_at
227676_at
204508_s_at
215125_s_at
227719_at
204607_at
215867_x_at
227725_at
204811_s_at
217109_at
228232_s_at
204895_x_at
217110_s_at
229070_at
204897_at
218211_s_at
231832_at
205259_at
219543_at
232176_at
205765_at
219955_at
232481_s_at
205927_s_at
221841_s_at
235976_at
208063_s_at
221874_at
236894_at
208937_s_at
223969_s_at
237521_x_at
210107_at
223970_at
242601_at
213106_at; and/or
(ii)
CLCA1
CTSE
ATP8B1
FCGBP
C6orf105
CACNA2D2
HMGCS2
CKB
KLF4
RETNLB
ATP8A1
CYP3A5P2
L1TD1
MUC4
CAPN9
SLITRK6
UGT1A1
NR3C2
VSIG2
SELENBP1
PBLD
LOC253012
PTGER4
CA12
ST6GALNAC1
MLPH
WDR51B
ID1
KIAA1324
FAM3D
CYP3A5
in said cell or cellular population wherein a higher level of expression of the genes or transcripts of group (i) and/or group (ii) relative to a gastrointestinal cancer cell level is indicative of an adenoma cell or a cell predisposed to the onset of an adenoma state.
44 . A method of characterising a neoplastic cell or cellular population, which cell or cellular population is derived from the large intestine of an individual, said method comprising measuring the level of expression of one or more genes or transcripts selected from:
(i)
the gene, genes or transcripts detected by Affymetrix probeset IDs:
200600_at
204006_s_at
213428_s_at
200665_s_at
204051_s_at
213524_s_at
200832_s_at
204122_at
213869_x_at
200974_at
204320_at
213905_x_at
200986_at
204475_at
214247_s_at
201058_s_at
204620_s_at
215049_x_at
201069_at
205479_s_at
215076_s_at
201105_at
205547_s_at
215646_s_at
201141_at
205828_at
216442_x_at
201147_s_at
207173_x_at
217430_x_at
201150_s_at
207191_s_at
217762_s_at
201162_at
208747_s_at
217763_s_at
201163_s_at
208782_at
217764_s_at
201185_at
208788_at
218468_s_at
201261_x_at
208850_s_at
218469_at
201289_at
208851_s_at
218559_s_at
201426_s_at
209101_at
218638_s_at
201438_at
209156_s_at
219087_at
201616_s_at
209218_at
221011_s_at
201645_at
209395_at
221729_at
201667_at
209396_s_at
221730_at
201744_s_at
209596_at
221731_x_at
201792_at
209875_s_at
37892_at
201842_s_at
209955_s_at
223122_s_at
201852_x_at
210095_s_at
223235_s_at
201859_at
210495_x_at
224560_at
201893_x_at
210511_s_at
224694_at
202237_at
210764_s_at
224724_at
202238_s_at
210809_s_at
225664_at
202283_at
211161_s_at
225681_at
202291_s_at
211571_s_at
225710_at
202310_s_at
211719_x_at
225799_at
202311_s_at
211813_x_at
226237_at
202403_s_at
211896_s_at
226311_at
202404_s_at
211959_at
226694_at
202450_s_at
211964_at
226777_at
202620_s_at
211966_at
226930_at
202766_s_at
211980_at
227099_s_at
202859_x_at
211981_at
227140_at
202878_s_at
212077_at
227566_at
202917_s_at
212344_at
229218_at
202998_s_at
212353_at
229802_at
203083_at
212354_at
231579_s_at
203325_s_at
212464_s_at
231766_s_at
203382_s_at
212488_at
231879_at
203477_at
212489_at
232458_at
203570_at
212667_at
233555_s_at
203645_s_at
213125_at
234994_at
203878_s_at; and/or
(ii)
COL1A2
LGALS1
SRGN
CTHRC1
ELOVL5
LBH
FN1
MGP
CTGF
POSTN
MMP2
TNC
SPP1
LOXL2
G0S2
MMP1
MYL9
SQLE
SPARC
DCN
EFEMP1
LUM
CALD1
APOE
GREM1
FBN1
MSN
IL8
MMP3
IGFBP3
IGFBP5
IGFBP7
SERPINF1
SFRP2
FSTL1
ISLR
SULF1
COL4A2
HNT
ASPN
VCAN
COL5A1
COL6A3
SMOC2
OLFML2B
COL8A1
HTRA1
KIAA1913
COL12A1
CYR61
PALM2-AKAP2
COL5A2
FAP
SERPING1
CDH11
VIM
TYROBP
THBS2
TIMP2
ACTA2
COL15A1
SCD
COL3A1
COL11A1
TIMP3
PLOD2
S100A8
AEBP1
MMP11
FNDC1
GJA1
CD163
SFRP4
NNMT
FCGR3B
INHBA
COL1A1
PLAU
COL6A2
SULF2
MAFB
ANTXR1
COL6A1
LOC541471
GPNMB
SPON2
LOC387763
BGN
CTSK
CHI3L1
TAGLN
MXRA5
THY1
COL4A1
C1S
LOXL1
RAB31
DKK3
CD93
in a biological sample from said individual wherein a higher level of expression of the genes or transcripts of group (i) and/or group (ii) relative to a gastrointestinal adenoma cell level is indicative of a cancer or a cell predisposed to the onset of a cancerous state.
45 . The method according to claim 43 wherein said one or more genes or transcripts are selected from:
(i) the gene or genes detected by Affymetrix probeset IDs:
210107_at; and/or
CLCA1;
(ii) the gene, genes or transcripts detected by Affymetrix probeset IDs:
203240_at, 219955_at, 242601_at, 204607_at, 232481_s_at, 227725_at, 223969_s_at, 228232_s_at; and/or
FCGBP, LITD1, LOC253012, HMGCS2, SLITRK6, ST6GALNAC1, RETNLB, VSIG2;
(iii) said control level is the background level of neoplastic tissue and said one or more genes or transcripts are selected from:
the gene, genes or transcripts detected by Affymetrix probeset IDs:
235976_at
236894_at; and/or
SLITRK6
L1TD1.
(iv) said control level is the background level of neoplastic tissue and said one or more genes or transcripts selected from:
the gene, genes or transcripts detected by Affymetrix probeset IDs:
202311_s_at, 209396_s_at, 226237_at, 204320_at, 215646_s_at, 227140_at, 204475_at, 37892_at, 229802_at, 209395_at; and/or,
COL1A1, VCAN, CHI3L1, MMP1, COL8A1, COL11A1.
46 . The method according to claim 44 wherein said one or more genes or transcripts are selected from:
(i) the gene, genes or transcripts detected by Affymetrix probeset IDs:
202404_s_at, 210809_s_at, 227140_at, 225681_at, 209875_s_at, 204475_at, 212464_s_at; and/or
COL1A2, FN1, SPP1, CTHRC1, POSTN, MMP1;
(ii) the gene, genes or transcripts detected by Affymetrix probeset IDs:
200665_s_at, 218468_s_at, 211959_at, 201744_s_at, 202859_x_at; and/or
SPARC, GREM1, IGFBP5, LUM, IL8;
(iii)
the gene, genes or transcripts detected by Affymetrix probeset IDs:
223122_s_at
207173_x_at
210511_s_at
212353_at
203083_at
209156_s_at
219087_at
203477_at
224694_at
201438_at
37892_at
201141_at
226237_at
202917_s_at
213905_x_at
225664_at
226930_at
205547_s_at
221730_at
204051_s_at;
and/or
SFRP2
CDH11
INHBA
SULF1
THBS2
COL6A2
ASPN
COL15A1
ANTXR1
COL6A3
COL11A1
GPNMB
COL8A1
S100A8
BGN
COL12A1
FNDC1
TAGLN
COL5A2
SFRP4.
47 . The method according to any one of claim 31 , 38 , 43 or 44 wherein said cell is a colorectal cell.
48 . The method according to any one of claim 31 , 38 , 43 or 44 wherein said biological sample is a faecal sample, enema wash, surgical resection, tissue biopsy or blood sample.
49 . The method according to any one of claim 31 , 38 , 43 or 44 wherein said level of expression is mRNA expression or protein expression.
50 . The method according to any one of claim 31 , 38 , 43 or 44 wherein said individual is a human.
51 . A molecular array, which array comprises a plurality of:
nucleic acid molecules comprising a nucleotide sequence corresponding to any one or more of the neoplastic marker genes listed in claim 31 or a sequence exhibiting at least 80% identity thereto or a functional derivative, fragment, variant or homologue of said nucleic acid molecule; or (ii) nucleic acid molecules comprising a nucleotide sequence capable of hybridising to any one or more of the sequences of (i) under medium stringency conditions or a functional derivative, fragment, variant or homologue of said nucleic acid molecule; or (iii) nucleic acid probes or oligonucleotides comprising a nucleotide sequence capable of hybridising to any one or more of the sequences of (i) under medium stringency conditions or a functional derivative, fragment, variant or homologue of said nucleic acid molecule; or (iv) probes capable of binding to any one or more of the proteins encoded by the nucleic acid molecules of (i) or a derivative, fragment or, homologue thereof wherein the level of expression of said marker genes of (i) or proteins of (iv) is indicative of the neoplastic state of a cell or cellular subpopulation derived from the large intestine.
52 . The method according to any one of claim 31 , 38 , 43 or 44 wherein said control level is a non-neoplastic level.Cited by (0)
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