# US 2014/0155280 A1 · Method of diagnosing neoplasms

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- Number: US 2014/0155280 A1
- Document ID: US20140155280A1
- Status: Published application
- Kind: A1
- Application number: 14/115,698
- Filed: 2012-05-04
- Published: 2014-06-05
- Earliest claimed: 2011-05-05
- Assignees: Commonwealth Scientific and Industrial Research Organisation; Clinical Genomics Pty. Ltd.
- Inventors: Lawrence Charles Lapointe; Susanne Kartin Pedersen; Peter Molloy
- Web page: https://patentgrep.com/patent/US20140155280A1

## CPC

- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- G01N 33/57535: of the large intestine, e.g. colon, rectum or anus
- C12Q 2600/158: Expression markers
- G01N 2800/50: Determining the risk of developing a disease
- G01N 2800/52: Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
- G01N 2800/56: Staging of a disease; Further complications associated with the disease
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)

## Abstract

The present invention relates generally to a method for screening a subject for the onset, predisposition to the onset and/or progression of a colorectal neoplasm by screening for modulation in the level of expression of one or more nucleic acid markers. More particularly, the present invention provides a method for screening a subject for the onset, predisposition to the onset and/or progression of a colorectal neoplasm by screening for modulation in the level of expression of one or more gene markers in membranous microvesicles. The expression profiles of the present invention are useful in a range of applications including, but not limited to, those relating to the diagnosing and/or monitoring of colorectal neoplasms, such as colorectal adenoma and adenocarcinomas.

## Claims

### Claim 1

A method of screening for the onset or a predisposition to the onset of a large intestine neoplasm in an individual, said method comprising measuring the level of expression of:
(i) any one or more genes selected from:
1. KIAA1199
2. CRNDE
3. OLFM4
4. DPEP1
5. TESC
6. SLC12A2
7. ITGA6
8. REG4
9. S100A11
10. ACAA2
11. ANPEP
12. ANXA3
13. APP
14. APPL2
15. AZGP1
16. BGN
17. c20orf199
18. CALR
19. CAP1
20. COL12A1
21. CSE1L
22. CTSC
23. CXCL3
24. DMBT1
25. ENO1
26. EPS8L3
27. FAT
28. FTH1
29. GALNT6
30. GMDS
31. GNB2L1
32. GPRC5A
33. HEPH
34. HLADRB1
35. HPGD
36. HSP9OAA1
37. IFITM1
38. IFITM2
39. KRT8
40. LCN2
41. LDHB
42. LIMA1
43. LOC440264
44. LRPPRC
45. LRSAM1
46. MLLT3
47. MMP7
48. MUC13
49. MYO5B
50. NDRG1
51. NEBL
52. NQO1
53. OLA1
54. PIGR
55. PRDX1
56. PROS1
57. PSAT1
58. PUS7
59. RAB8A
60. RPL6
61. RPS4X
62. RPS7
63. S100A1
64. S100A6
65. S100P
66. SLC39A5
67. SLC7A5
68. SLK
69. SOD1
70. SORD
71. TACSTD2
72. TCP1
73. TFRC
74. TGFBI
75. THBS2
76. TM7SF3
77. TUBB6
78. VAMP3 or
79. VAT1;
or
(ii) any one of more of the regions defined by Hg19 coordinates:
1. chr15: 81,071,712-81,243,999
2. chr16: 54,952,778-54,963,079
3. chr13: 53,602,876-53,626,196
4. chr16: 89,687,000-89,704,839
5. chr12: 117,476,728-117,537,251
6. chr5: 127,419,483-127,525,380
7. chr2: 173,292,314-173,371,181
8. chr1: 120,336,641-120,354,203
9. chr1: 152,004,982-152,009,511
10. chr18: 47,309,874-47,340,251
11. chr15: 90,328,126-90,358,072
12. chr4: 79,472,742-79,531,605
13. chr21: 27,252,861-27,543,138
14. chr12: 105,567,075-105,630,008
15. chr7: 99,564,350-99,573,735
16. chrX: 152,760,347-152,775,004
17. chr20: 47894715-47905797
18. chr20: 47894715-47905797
19. chr20: 47894715-47905797
20. chr20: 47894715-47905797
21. chr20: 47894808-47905797
22. chr20: 47895179-47905797
23. chr20: 47895179-47905797
24. chr19: 13,049,414-13,055,304
25. chr1: 40,506,255-40,538,321
26. chr6: 75,794,042-75,915,623
27. chr20: 47,662,838-47,713,486
28. chr11: 88,026,760-88,070,941
29. chr4: 74,902,312-74,904,490
30. chr10: 124,320,181-124,403,252
31. chr1: 8,921,059-8,939,151
32. chr1: 110,292,702-110,306,644
33. chr4: 126315091-126414087
34. chr5: 150935821-150948505
35. chr4: 187627717-187647850
36. chr4: 187508937-187516980
37. chr5: 150883653-150948505
38. chr5: 150883653-150911531
39. chr4: 187508937-187644987
40. chr4: 126237567-126414087
41. chr4: 126369616-126412943
42. chr11: 92085262-92629635
43. chr11: 92573728-92629635
44. chr11: 61,731,757-61,735,132
45. chr12: 51,745,833-51,785,200
46. chr6: 1,624,035-2,245,868
47. chr5: 180,663,928-180,670,906
48. chr12: 13,043,956-13,066,600
49. chrX: 65,382,433-65,487,230
50. chr6 : 3,774,425-3,787,546
51. chr4: 175,411,328-175,443,792
52. chr14: 102547075-102606086
53. chr11: 313,991-315,272
54. chr11: 308,107-309,410
55. chr12: 53,290,971-53,298,868
56. chr9: 130,911,732-130,915,734
57. chr12: 21,788,275-21,810,789
58. chr12: 50,569,563-50,677,353
59. chr15: 30,262,050-30,265,947
60. chr2: 44,113,363-44,223,144
61. chr9: 130,214,534-130,265,780
62. chr9: 20,344,968-20,622,514
63. chr11: 102,391,239-102,401,478
64. chr3: 124,624,289-124,653,595
65. chr18: 47,349,156-47,721,451
66. chr8: 134,249,414-134,309,547
67. chr10: 21,068,903-21,186,531
68. chr16: 69,743,304-69,760,533
69. chr2: 174,937,175-175,113,365
70. chr1: 207,101,867-207,119,811
71. chr1: 45,976,707-45,988,562
72. chr3: 93,591,881-93,692,934
73. chr9: 80,912,059-80,945,009
74. chr7: 105,096,960-105,162,685
75. chr19: 16,222,490-16,244,445
76. chr12: 112,842,994-112,847,443
77. chrX: 71,492,453-71,497,141
78. chr2: 3,622,853-3,628,509
79. chr1: 153,600,873-153,604,513
80. chr1: 153,507,076-153,508,717
81. chr4: 6,695,566-6,698,897
82. chr12: 56,623,820-56,631,629
83. chr16: 87,863,629-87,903,100
84. chr10: 105,727,470-105,787,342
85. chr21: 33,031,935-33,041,243
86. chr15: 45,315,302-45,367,287
87. chr1: 59,041,095-59,043,166
88. chr6: 160,199,530-160,210,735
89. chr3: 195,776,155-195,809,032
90. chr5: 135,364,584-135,399,507
91. chr6: 169,615,875-169,654,137
92. chr12: 27,124,506-27,167,339
93. chr18: 12,308,257-12,326,568
94. chr1: 7,831,329-7,841,492 or
95. chr17: 41,166,622-41,174,459
in a membranous microvesicle sample from said individual wherein an increase in the level of expression of any one or more of said genes or any one of more of said regions defined by Hg19 coordinates relative to a control level of expression is indicative of the onset or the predisposition to the onset of a large intestine neoplasm in said individual.

### Claim at position 2

2-13. (canceled)

### Claim 14 (depends on 1)

The method according to claim 1 wherein said large intestine neoplasm is an adenoma.

### Claim 15 (depends on 1)

The method according to claim 1 wherein said large intestine neoplasm is an adenocarcinoma.

### Claim 16 (depends on 1)

The method according to claim 1 wherein said large intestine neoplasm is a colorectal neoplasm.

### Claim 17 (depends on 1)

The method according to claim 1 wherein either the level of RNA transcribed of any one or more of said genes or any one of more of said regions defined by Hg19 coordinates or cDNA reverse transcribed therefrom is measured.

### Claim 18 (depends on 17)

The method according to claim 17 wherein said RNA is mRNA.

### Claim 19 (depends on 1)

The method according to claim 1 wherein the level of a protein expression product or fragment thereof of said any one or more of said genes or any one of more of said regions defined by Hg19 coordinates is measured.

### Claim 20 (depends on 1)

The method according to claim 1 wherein said microvesicle is an exosome, apoptotic bleb, microparticle, apoptotic body or a cellular bleb.

### Claim 21 (depends on 1)

The method according to claim 1 wherein said microvesicle is an exosome.

### Claim 22 (depends on 1)

The method according to claim 1 wherein said biological sample is blood, serum, plasma, urine, stool, saliva, tears or ascites fluid.

### Claim 23 (depends on 1)

The method according to claim 1 wherein any one or more of the following genes are measured:
(i)
1. KIAA1199
2. CRNDE
3. OLFM4
4. DPEP1
5. TESC
6. SLC12A2
7. ITGA6
8. REG4 or
9. S100A11;
or
(ii) any one or more of the following regions defined by Hg19 coordinates are measured:
1. chr15: 81,071,712-81,243,999
2. chr16: 54,952,778-54,963,079
3. chr13: 53,602,876-53,626,196
4. chr16: 89,687,000-89,704,839
5. chr12: 117,476,728-117,537,251
6. chr5: 127,419,483-127,525,380
7. chr2: 173,292,314-173,371,181
8. chr1: 120,336,641-120,354,203 or
9. chr1: 152,004,982-152,009,511.

### Claim 24 (depends on 23)

The method according to claim 23 wherein any one or more of the following genes are measured:
(i)
1. KIAA1199
2. CRNDE or
3. OLFM4;
or
(ii) any one or more of the following regions defined by Hg19 coordinates are measured:
1. chr15: 81,071,712-81,243,999
2. chr16: 54,952,778-54,963,079 or
3. chr13: 53,602,876-53,626,196.

### Claim 25 (depends on 1)

The method according claim 1 wherein said individual is a human.