Profiling and treatment of hypermutant cancer
There is provided a method of profiling a tumour, the method comprising determining a relative proportion for each of 96 mutation types, wherein the 96 mutation types are defined as the six possible sequence changes C>A, C>G, C>T, T>A, T>C, or T>G in the context of each of four possible nucleotides (A, C, G, or T) at the position immediately 5′ to the mutation and each of four possible nucleotides at the position immediately 3′ to the mutation; assigning the tumour, using the determined relative proportion for each of the 96 mutation types, to at least one of eight clusters defined herein; and determining at least one tumour characteristic based on the assignment to a cluster.
1. A method of profiling a tumour, the method comprising:
sequencing nucleic acid from a sample obtained from the tumour to obtain nucleic acid sequences;
identifying mutations in the nucleic acid sequences relative to a reference sequence obtained from a healthy tissue, wherein each of said mutations is defined with respect to the pyrimidine of a base pair;
determining for the tumour, using the mutations, relative proportions of each of 96 mutation types, wherein the 96 mutation types are defined as each of six possible pyrimidine base changes C>A, C>G, C>T, T>A, T>C, or T>G in the context of each of four possible nucleotides (A, C, G, or T) at the position immediately 5′ to the mutation and each of four possible nucleotides (A, C, G, or T) at the position immediately 3′ to the mutation,
comparing the relative proportions of at least 48 of the 96 mutation types for the tumour to corresponding mean proportions for the mutation types for clusters 1 to 3 depicted in Table 1A:
TABLE 1A
Mean Proportion for Clusters
Mut
5′
3′
1
2
3
C > A
A
A
6.7E-05
0.001303
0.00119
C > A
A
C
0.002389
0.003823
0.003755
C > A
A
G
0
0.00119
0.000792
C > A
A
T
0.009421
0.002499
0.006822
C > A
C
A
0.003067
0.00708
0.003819
C > A
C
C
0.004592
0.011953
0.002766
C > A
C
G
0.00161
0.007254
0.002327
C > A
C
T
0.037945
0.029925
0.014682
C > A
G
A
0.001125
0.002937
0.002638
C > A
G
C
0.005352
0.004551
0.002743
C > A
G
G
0.001282
0.002862
0.00103
C > A
G
T
0.032471
0.008021
0.008659
C > A
T
A
0.002468
0.002416
0.030984
C > A
T
C
0.006074
0.004215
0.008444
C > A
T
G
0.000658
0.001553
0.003072
C > A
T
T
0.041834
0.006319
0.190779
C > G
A
A
0.000569
0.001268
0.000741
C > G
A
C
0.000114
0.002475
0.000842
C > G
A
G
0.000251
0.001332
0.000468
C > G
A
T
0
0.001943
0.000872
C > G
C
A
0.00032
0.00168
0.00023
C > G
C
C
0.000559
0.002767
0.001219
C > G
C
G
0.000379
0.003067
0.000998
C > G
C
T
0.000202
0.001803
0.001843
C > G
G
A
0.000238
0.001606
0.000929
C > G
G
C
0.000404
0.003352
0.001803
C > G
G
G
5.71E-05
0.001414
0.00021
C > G
G
T
7.05E-05
0.001991
0.001271
C > G
T
A
0
0.001682
0.000244
C > G
T
C
0.000343
0.002414
0.000753
C > G
T
G
0
0.001217
0.000503
C > G
T
T
0.001043
0.004031
0.000942
C > T
A
A
0.009098
0.015807
0.002356
C > T
A
C
0.021673
0.014512
0.007633
C > T
A
G
0.080822
0.098997
0.029695
C > T
A
T
0.01273
0.008974
0.006131
C > T
C
A
0.005011
0.009953
0.002726
C > T
C
C
0.013316
0.012312
0.003786
C > T
C
G
0.075944
0.103416
0.024621
C > T
C
T
0.013479
0.012866
0.006972
C > T
G
A
0.024254
0.028917
0.005288
C > T
G
C
0.059279
0.046541
0.024879
C > T
G
G
0.222447
0.148718
0.070994
C > T
G
T
0.038951
0.030229
0.021253
C > T
T
A
0.007213
0.010064
0.004939
C > T
T
C
0.028449
0.011086
0.016469
C > T
T
G
0.078732
0.052801
0.219143
C > T
T
T
0.027756
0.008177
0.02943
T > A
A
A
0.000295
0.001176
0.000209
T > A
A
C
0.001226
0.003815
0.000852
T > A
A
G
0.0004
0.001401
0.000458
T > A
A
T
0.001352
0.002917
0.001796
T > A
C
A
0
0.000781
0.000352
T > A
C
C
0.000369
0.002485
0.001001
T > A
C
G
0.0005
0.004052
0.001149
T > A
C
T
0.000809
0.001423
0.000821
T > A
G
A
0
0.0012
0.000226
T > A
G
C
0.002031
0.002942
0.000182
T > A
G
G
0.00019
0.003729
0.000445
T > A
G
T
0.000321
0.00107
0.000202
T > A
T
A
0
0.000781
0.000138
T > A
T
C
0.001246
0.00113
0.000725
T > A
T
G
0.000229
0.000808
0.00015
T > A
T
T
0.000267
0.000915
0.00279
T > C
A
A
0.006228
0.010066
0.004417
T > C
A
C
0.005627
0.00713
0.004952
T > C
A
G
0.004509
0.021637
0.005165
T > C
A
T
0.00324
0.007429
0.004211
T > C
C
A
0.001378
0.007187
0.000923
T > C
C
C
0.004677
0.009799
0.003691
T > C
C
G
0.003798
0.025847
0.003957
T > C
C
T
0.002998
0.009297
0.003321
T > C
G
A
0.014476
0.017372
0.01155
T > C
G
C
0.012038
0.011524
0.015514
T > C
G
G
0.012999
0.020376
0.008717
T > C
G
T
0.008026
0.011538
0.012768
T > C
T
A
0.002157
0.00638
0.002805
T > C
T
C
0.003458
0.007139
0.00666
T > C
T
G
0.002926
0.009561
0.005562
T > C
T
T
0.002948
0.005824
0.005819
T > G
A
A
6.7E-05
0.000486
0.001478
T > G
A
C
0.001077
0.001094
0.003775
T > G
A
G
0.000499
0.001114
0.001846
T > G
A
T
0.003055
0.00097
0.011338
T > G
C
A
0.000196
0.00167
0.002233
T > G
C
C
0.000731
0.004141
0.001955
T > G
C
G
0.000628
0.00923
0.003836
T > G
C
T
0.003131
0.005064
0.015868
T > G
G
A
0.000365
0.000912
0.001333
T > G
G
C
0.001875
0.001146
0.002466
T > G
G
G
0.001543
0.002292
0.00168
T > G
G
T
0.003994
0.003071
0.004097
T > G
T
A
0
0.000364
0.004756
T > G
T
C
0.001569
0.001778
0.006492
T > G
T
G
0.000386
0.001434
0.001971
T > G
T
T
0.006112
0.001191
0.048665
assigning the tumour to one of the clusters 1 to 3 based on the comparing,
wherein:
cluster 1 is indicative of an ultra-hypermutant tumour with microsatellite stability, a germline MMR gene mutation, or a POLE gene mutation secondary an MMR mutation;
cluster 2 is indicative of a hypermutant tumour with microsatellite instability, or an early MMR gene mutation; and
cluster 3 is indicative of an ultra-hypermutant tumour with microsatellite stability, an early POLE gene mutation, or an MMR gene mutation secondary to a POLE gene mutation; and
after assigning the tumor to one of the clusters 1 to 3, administering to the patient an immunotherapy or an immune checkpoint inhibitor.
2. The method of claim 1 , wherein the comparing is carried out using the relative proportions of the 96 mutation types determined for the tumour.
3. The method of claim 1 , wherein the step of assigning is carried out by matching the relative proportions determined for the tumour to one of the clusters by highest cosine similarity.
4. The method of claim 3 , wherein the matching requires a minimum cosine similarity of 0.75.
5. The method of claim 1 , wherein the at least one tumour characteristic is further determined based on the presence of one or more driver mutations as defined in Table 6:
TABLE 6
Specimen
Driver
Mutation
ID
Tumour Type
Gene
Mutation
Burden
Stage
Status
Drivers POLE
1
Colorectal Carcinoma
POLE
Y458H
342
Adult
New
2
Brain PNET
POLE
Y458H
85.02
Pediatric
New
3
Colon adenocarcinoma (CRC)
POLE
Y458C
753.2
Adult
New
4
Colon adenocarcinoma (CRC)
POLE
Y458C
13.5
Adult
New
5
Colon adenocarcinoma (CRC)
POLE
V411L
703.6
Adult
Known
6
Brain glioblastoma
POLE
V411L
699
Pediatric
Known
7
Ovary carcinosarcoma
POLE
V411L
650.5
Adult
Known
8
Uterus endometrial
POLE
V411L
636.9
Adult
Known
adenocarcinoma (NOS)
9
Brain glioblastoma (GBM)
POLE
V411L
578.4
Adult
Known
10
Kidney urothelial carcinoma
POLE
V411L
500
Adult
Known
11
Prostate neuroendocrine
POLE
V411L
371.2
Adult
Known
carcinoma
12
Colon adenocarcinoma (CRC)
POLE
V411L
360.4
Adult
Known
13
Uterus endometrial
POLE
V411L
345.9
Adult
Known
adenocarcinoma endometrioid
14
Uterus endometrial
POLE
V411L
324.3
Adult
Known
adenocarcinoma (NOS)
15
Brain glioma (NOS)
POLE
V411L
315.3
Adult
Known
16
Ovary epithelial carcinoma
POLE
V411L
309.9
Adult
Known
(NOS)
17
Prostate acinar
POLE
V411L
301.8
Adult
Known
adenocarcinoma
18
Prostate neuroendocrine
POLE
V411L
279.3
Adult
Known
carcinoma
19
Prostate acinar
POLE
V411L
245.9
Adult
Known
adenocarcinoma
20
Rectum adenocarcinoma
POLE
V411L
240.5
Adult
Known
(CRC)
21
Uterus endometrial
POLE
V411L
238.7
Adult
Known
adenocarcinoma (NOS)
22
Uterus endometrial
POLE
V411L
187.4
Adult
Known
adenocarcinoma (NOS)
23
Colon adenocarcinoma (CRC)
POLE
V411L
136
Adult
Known
24
Colon adenocarcinoma (CRC)
POLE
V411L
120.7
Adult
Known
25
Colon adenocarcinoma (CRC)
POLE
V411L
116.2
Adult
Known
26
Ovary clear cell carcinoma
POLE
V411L
105.4
Adult
Known
27
Colon adenocarcinoma (CRC)
POLE
V411L
104.5
Adult
Known
28
Rectum adenocarcinoma
POLE
V411L
100
Adult
Known
(CRC)
29
Uterus carcinosarcoma
POLE
V411L
77.5
Adult
Known
30
Brain glioblastoma (GBM)
POLE
V411L
45
Adult
Known
31
Colon adenocarcinoma (CRC)
POLE
V411L
39.6
Adult
Known
32
Brain glioblastoma (GBM)
POLE
S461T
447.8
Adult
Known
33
Brain glioblastoma
POLE
S461P
496.24
Pediatric
Known
34
Brain glioblastoma
POLE
S461P
208
Pediatric
Known
35
Unknown primary carcinoma
(NOS)
POLE
S459F
311.7
Adult
Known
36
Brain glioblastoma
POLE
S459F
295
Pediatric
Known
37
Rectum adenocarcinoma
(CRC)
POLE
S459F
146.8
Adult
Known
38
Brain glioblastoma (GBM)
POLE
S459F
117.1
Adult
Known
39
Uterus endometrial
POLE
S459F
102.7
Adult
Known
adenocarcinoma (NOS)
40
Duodenum adenocarcinoma
POLE
S459F
36.9
Adult
Known
41
Brain glioblastoma (GBM)
POLE
S297F
386.5
Adult
Known
42
Brain glioblastoma
POLE
S297F
218
Pediatric
Known
43
Skin melanoma
POLE
S297F
115.3
Adult
Known
44
Uterus endometrial
POLE
S297F
39.6
Adult
Known
adenocarcinoma (NOS)
45
Colorectal Carcinoma
POLE
P436S
433
Adult
New
46
Brain glioblastoma (GBM)
POLE
P436S
333.3
Adult
New
47
Brain glioblastoma
POLE
P436S
318.06
Pediatric
New
48
Brain glioblastoma
POLE
P436S
302
Pediatric
New
49
Osteochondroma
POLE
P436S
195
Pediatric
New
50
Colon adenocarcinoma (CRC)
POLE
P436R
493.7
Adult
New
51
Brain glioblastoma
POLE
P436H
541.36
Pediatric
New
52
Brain glioblastoma
POLE
P436H
532
Pediatric
New
53
Brain glioblastoma
POLE
P436H
409.18
Pediatric
New
54
Brain glioblastoma
POLE
P436H
359
Pediatric
New
55
Skin basal cell carcinoma
POLE
P286S
58.6
Adult
New
56
Unknown primary melanoma
POLE
P286S
42.3
Adult
New
57
Uterus endometrial
POLE
P286R
493.7
Adult
Known
adenocarcinoma (NOS)
58
Colon adenocarcinoma (CRC)
POLE
P286R
479.3
Adult
Known
59
Brain glioblastoma (GBM)
POLE
P286R
450.5
Adult
Known
60
Colon adenocarcinoma (CRC)
POLE
P286R
394.6
Adult
Known
61
Colon adenocarcinoma (CRC)
POLE
P286R
342.3
Adult
Known
62
Colon adenocarcinoma (CRC)
POLE
P286R
305.4
Adult
Known
63
Colon adenocarcinoma (CRC)
POLE
P286R
259.5
Adult
Known
64
Colon adenocarcinoma (CRC)
POLE
P286R
245
Adult
Known
65
Brain glioblastoma (GBM)
POLE
P286R
227.9
Adult
Known
66
Colon adenocarcinoma (CRC)
POLE
P286R
226.1
Adult
Known
67
Rectum adenocarcinoma
POLE
P286R
223.4
Adult
Known
(CRC)
68
Colon adenocarcinoma (CRC)
POLE
P286R
216.2
Adult
Known
69
Uterus endometrial
POLE
P286R
208.1
Adult
Known
adenocarcinoma (NOS)
70
Uterus endometrial
POLE
P286R
203.6
Adult
Known
adenocarcinoma (NOS)
71
Colon adenocarcinoma (CRC)
POLE
P286R
172.1
Adult
Known
72
Uterus carcinosarcoma
POLE
P286R
168.5
Adult
Known
73
Ovary neuroendocrine
POLE
P286R
163.1
Adult
Known
carcinoma
74
Rectum adenocarcinoma
POLE
P286R
162.2
Adult
Known
(CRC)
75
Colon adenocarcinoma (CRC)
POLE
P286R
155
Adult
Known
76
Uterus endometrial
POLE
P286R
153.2
Adult
Known
adenocarcinoma (NOS)
77
Uterus endometrial
POLE
P286R
145.9
Adult
Known
adenocarcinoma (NOS)
78
Colon adenocarcinoma (CRC)
POLE
P286R
133.3
Adult
Known
79
Uterus endometrial
POLE
P286R
123.4
Adult
Known
adenocarcinoma (NOS)
80
Pancreas ductal
POLE
P286R
100.9
Adult
Known
adenocarcinoma
81
Uterus endometrial
POLE
P286R
84.7
Adult
Known
adenocarcinoma (NOS)
82
rectum neuroendocrine
POLE
P286R
80.2
Adult
Known
carcinoma
83
Colon adenocarcinoma (CRC)
POLE
P286R
62.2
Adult
Known
84
Brain glioblastoma (GBM)
POLE
P286H
212
Adult
New
85
Brain glioblastoma (GBM)
POLE
M444K
116.2
Adult
Known
86
Colon adenocarcinoma (CRC)
POLE
M444K
91.9
Adult
Known
87
Uterus neuroendocrine
POLE
M444K
32.4
Adult
Known
carcinoma
88
Colorectal carcinoma
POLE
L424P
590
Pediatric
New
89
Brain glioblastoma
POLE
L424I
336
Pediatric
Known
90
Brain glioblastoma (GBM)
POLE
L424I
160.4
Adult
Known
91
Lung adenocarcinoma
POLE
L424I
154.1
Adult
Known
92
Liver cholangiocarcinoma
POLE
L424I
47.7
Adult
Known
93
Brain glioblastoma
POLE
F367L
472.56
Pediatric
New
94
Brain glioblastoma
POLE
F367L
238.18
Pediatric
New
95
Unknown primary squamous
POLE
E978K
80.2
Adult
New
cell carcinoma (SCC)
96
Brain glioblastoma
POLE
E978G
608.02
Pediatric
New
Uterus carcinosarcoma
POLE
E978G
26.1
Adult
New
98
Appendix adenocarcinoma
POLE
D368N
36
Adult
New
99
Lung adenocarcinoma
POLE
D275V
43.2
Adult
Known
100
Brain glioblastoma (GBM)
POLE
D275V
17.1
Adult
Known
101
Pancreas ducta
POLE
D275G
318.9
Adult
Known
adenocarcinoma
102
Brain glioblastoma (GBM)
POLE
D275A
226.1
Adult
Known
103
Rectum adenocarcinoma
POLE
C810G
854.1
Adult
New
(CRC)
104
Brain glioblastoma (GBM)
POLE
C810G
154.1
Adult
New
105
Lung squamous cell
POLE
A463V
231.5
Adult
New
carcinoma (SCC)
106
Uterus endometrial
POLE
A463V
55.9
Adult
New
adenocarcinoma (NOS)
107
Brain oligodendroglioma
POLE
A463T
809
Adult
New
108
Brain glioblastoma
POLE
A463D
532
Pediatric
New
109
Brain glioblastoma
POLE
A463D
359
Pediatric
New
110
Colon adenocarcinoma (CRC)
POLE
A456P
373.9
Adult
Known
111
Colon adenocarcinoma (CRC)
POLE
A456P
314.4
Adult
Known
112
Colon adenocarcinoma (CRC)
POLE
A456P
233.3
Adult
Known
113
Uterus endometrial
POLE
A456P
226.1
Adult
Known
adenocarcinoma (NOS)
114
Colon adenocarcinoma (CRC)
POLE
A456P
200
Adult
Known
115
Ovary endometrioid
POLE
A456P
69.4
Adult
adenocarcinoma
Known
116
Cervix squamous cel
POLE
A456P
33.3
Adult
Known
carcinoma (SCC)
117
Brain glioblastoma (GBM)
POLE
A288V
578.4
Adult
New
118
Brain glioblastoma (GBM)
POLE
A288V
386.5
Adult
New
119
Stomach neuroendocrine
POLE
A288V
155.9
Adult
New
carcinoma
Drivers POLD1
1
Colon adenocarcinoma (CRC)
POLD1
R689W
259.5
Adult
Known
2
Brain oligodendroglioma
POLD1
R689W
585.6
Adult
Known
3
Brain glioblastoma (GBM)
POLD1
R689W
578.4
Adult
Known
4
Brain glioblastoma (GBM)
POLD1
R689W
447.8
Adult
Known
5
Colon adenocarcinoma (CRC)
POLD1
R689W
12.6
Adult
Known
6
Vulva squamous cell
POLD1
R1016H
39.6
Adult
New
carcinoma (SCC)
7
Colon adenocarcinoma (CRC)
POLD1
R1016H
29.7
Adult
New
8
Brain glioma (NOS)
POLD1
R1016H
315.3
Adult
New
9
Unknown primary
POLD1
R1016H
69.4
Adult
New
adenocarcinoma
10
Uterus endometrial
POLD1
R1016H
636.9
Adult
New
adenocarcinoma (NOS)
11
Colon adenocarcinoma (CRC)
POLD1
R1016H
49.5
Adult
New
12
Brain medullobastoma
POLD1
L632M
141
Pediatric
New
13
Brain glioblastoma
POLD1
L632M
228
Pediatric
New
14
Brain glioblastoma
POLD1
L632M
296
Pediatric
New
15
Brain Glioblastoma
POLD1
L632M
121
Pediatric
New
16
Brain PNET
POLD1
L606M
196
Pediatric
Known
17
Brain PNET
POLD1
L606M
295
Pediatric
Known
18
Brain glioblastoma (GBM)
POLD1
L606M
228.8
Adult
Known
19
Brain glioblastoma (GBM)
POLD1
L606M
51.4
Adult
Known
20
Uterus carcinosarcoma
POLD1
L606M
311.7
Adult
Known
21
Brain PNET
POLD1
E318K
182
Pediatric
New
22
Lung non-small cell lung
carcinoma (NOS)
POLD1
E318K
13.5
Adult
New
23
Colon adenocarcinoma (CRC)
POLD1
E245K
76.6
Adult
New
24
Liver cholangiocarcinoma
POLD1
E245K
122.5
Adult
New
25
Colon adenocarcinoma (CRC)
POLD1
E245K
85.6
Adult
New.
6. The method of claim 1 , wherein the tumour is a hypermutant tumour.
7. The method of claim 6 , wherein the hypermutant tumour has mutation frequency of at least 5 mutations per megabase (Mb), and the tumour is a pediatric tumour.
8. The method of claim 6 , wherein the hypermutant tumour has a mutation frequency of at least 9.9 mutations per megabase (Mb), and the tumour is from an adult.
9. The method of claim 6 , wherein the hypermutant tumour is an ultra-hypermutant tumour having a mutation frequency of at least 100 mutations per megabase (Mb).
10. The method of claim 2 , wherein the step of assigning is carried out by matching the relative proportions determined for the tumour to one of the clusters by highest cosine similarity.
11. The method of claim 10 , wherein the matching requires a minimum cosine similarity of 0.75.