CA2360073A1 - Probes and primers for detecting prostate specific antigen (psa) in a biological sample - Google Patents
Probes and primers for detecting prostate specific antigen (psa) in a biological sample Download PDFInfo
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- CA2360073A1 CA2360073A1 CA002360073A CA2360073A CA2360073A1 CA 2360073 A1 CA2360073 A1 CA 2360073A1 CA 002360073 A CA002360073 A CA 002360073A CA 2360073 A CA2360073 A CA 2360073A CA 2360073 A1 CA2360073 A1 CA 2360073A1
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- seq
- sequence
- psa
- oligonucleotide
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/158—Expression markers
Abstract
Nucleic acid sequences for detecting the presence of nucleic acids, particularly mRNA, encoding human prostate-associated genetic markers encoding prostate-specific antigen (PSA), prostate specific membrane antigen (PSMA) or human kallikrein 2 (hK2) are disclosed. Preferred combinations of nucleic acid sequences amplifying and detecting the prostate-associated genetic markers RNA, used in methods that include amplification of the target sequences and detection of the amplified sequences are disclosed. Methods of detecting the presence of prostate-associated genetic marker nucleic acids, particularly mRNA, in a biological sample of non-prostate origin are disclosed.
Claims (20)
1. An isolated oligonucleotide having the sequence of any one of SEQ ID NO:1 to SEQ ID
NO:43, SEQ ID NO:46 to SEQ ID NO:50, or a complementary or RNA equivalent thereof.
NO:43, SEQ ID NO:46 to SEQ ID NO:50, or a complementary or RNA equivalent thereof.
2. An oligonucleotide comprising a target-binding sequence consisting of the sequence of any one of SEQ ID NO:15 to SEQ ID NO:43, SEQ IDNO:46, SEQ ID NO:48 or a complementary or equivalent RNA thereof, and an optional contiguous sequence having a function used in an amplification reaction.
3. The oligonucleotide of claim 2, wherein the contiguous sequence is a polymerase binding sequence.
4. A combination of oligonucleotides that form a subset of oligonucleotides according to Claim 1, used in a detection assay specific for a prostate specific antigen (PSA) target nucleic acid sequence, comprising:
a first oligonucleotide that serves as a first amplification primer that hybridizes specifically to a first PSA-specific sequence contained in an exon of a PSA
expressed gene sequence, or that spans a joining point linking two exons of a PSA
expressed gene sequence;
a second oligonucleotide that serves as a second amplification primer that specifically hybridizes to a different, non-overlapping second PSA-specific sequence contained in an exon of a PSA expressed gene sequence, or that spans a joining point linking two exons of a PSA expressed gene sequence; and a third oligonucleotide that serves as a detection probe that specifically hybridizes to a third PSA-specific sequence contained in one or more exons of a PSA
expressed gene sequence.
a first oligonucleotide that serves as a first amplification primer that hybridizes specifically to a first PSA-specific sequence contained in an exon of a PSA
expressed gene sequence, or that spans a joining point linking two exons of a PSA
expressed gene sequence;
a second oligonucleotide that serves as a second amplification primer that specifically hybridizes to a different, non-overlapping second PSA-specific sequence contained in an exon of a PSA expressed gene sequence, or that spans a joining point linking two exons of a PSA expressed gene sequence; and a third oligonucleotide that serves as a detection probe that specifically hybridizes to a third PSA-specific sequence contained in one or more exons of a PSA
expressed gene sequence.
5. The combination of oligonucleotides of Claim 4, wherein the first oligonucleotide hybridizes specifically to a first PSA-specific sequence contained in exon 2, exon 3 or exon 4, or spans a joining point linking exons 2 and 3 or exons 3 and 4, and wherein the second oligonucleotide hybridizes specifically to a second PSA-specific sequence contained in exon 3, exon 4 or exon 5, or spanning a joining point linking exons 3 and 4 or exons 4 and 5.
6. The combination of oligonucleotides of Claim 4, wherein the third oligonucleotide hybridizes specifically to a third PSA-specific sequence contained in exon 2, exon 3, exon 4 or exon 5, or that spans a joining point linking exons 2 and 3, exons 3 and 4, or exons 4 and 5 of a PSA expressed gene sequence.
7. The combination of oligonucleotides of Claim 4, wherein:
the first oligonucleotide comprises a sequence selected from the group consisting of SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID
NO:21 and SEQ ID NO:26, or a complementary or equivalent RNA thereof;
the second oligonucleotide comprises a sequence selected from the group consisting of SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID
NO:34, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:41, or a complementary or equivalent RNA thereof; and the third oligonucleotide comprises a sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:14, or a complementary or equivalent RNA thereof.
the first oligonucleotide comprises a sequence selected from the group consisting of SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID
NO:21 and SEQ ID NO:26, or a complementary or equivalent RNA thereof;
the second oligonucleotide comprises a sequence selected from the group consisting of SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID
NO:34, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:41, or a complementary or equivalent RNA thereof; and the third oligonucleotide comprises a sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:14, or a complementary or equivalent RNA thereof.
8. The combination of oligonucleotides of Claim 4, wherein the combinations of first, second and third oligonucleotides, in that order, consist of the sequences of:
SEQ ID NO:15, SEQ ID NO:30 and SEQ ID NO:1;
SEQ ID NO:17, SEQ ID NO:30 and SEQ ID NO:1;
SEQ ID NO:18, SEQ ID NO:30 and SEQ ID NO:1;
SEQ ID NO:18, SEQ ID NO:35 and SEQ ID NO:1;
SEQ ID NO:18, SEQ ID NO:30 and SEQ ID NO:4;
SEQ ID NO:18, SEQ ID NO:30 and SEQ ID NO:5;
SEQ ID NO:18, SEQ ID NO:30 and SEQ ID NO:6;
SEQ ID NO:16, SEQ ID NO:31 and SEQ ID NO:2;
SEQ ID NO:16, SEQ ID NO:31 and SEQ ID NO:3;
SEQ ID NO:16, SEQ ID NO:33 and SEQ ID NO:2;
SEQ ID NO:16, SEQ ID NO:33 and SEQ ID NO:3;
SEQ ID NO:16, SEQ ID NO:32 and SEQ ID NO:2;
SEQ ID NO:16, SEQ ID NO:32 and SEQ ID NO:3;
SEQ ID NO:16, SEQ ID NO:34 and SEQ ID NO:2;
SEQ ID NO:16, SEQ ID NO:34 and SEQ ID NO:3;
SEQ ID NO:20, SEQ ID NO:37 and SEQ ID NO:8;
SEQ ID NO:20, SEQ ID NO:38 and SEQ ID NO:8;
SEQ ID NO:21, SEQ ID NO:37 and SEQ ID NO:8;
SEQ ID NO:21, SEQ ID NO:38 and SEQ ID NO:8;
SEQ ID NO:21, SEQ ID NO:40 and SEQ ID NO:14;
SEQ ID NO:21, SEQ ID NO:37 and SEQ ID NO:14;
SEQ ID NO:21, SEQ ID NO:41 and SEQ ID NO:14;
SEQ ID NO:21, SEQ ID NO:40 and SEQ ID NO:8;
SEQ ID NO:21, SEQ ID NO:41 and SEQ ID NO:8;
SEQ ID NO:26, SEQ ID NO:37 and SEQ ID NO:8;
SEQ ID NO:26, SEQ ID NO:40 and SEQ ID NO:8; or SEQ ID NO:26, SEQ ID NO:41 and SEQ ID NO:8.
SEQ ID NO:15, SEQ ID NO:30 and SEQ ID NO:1;
SEQ ID NO:17, SEQ ID NO:30 and SEQ ID NO:1;
SEQ ID NO:18, SEQ ID NO:30 and SEQ ID NO:1;
SEQ ID NO:18, SEQ ID NO:35 and SEQ ID NO:1;
SEQ ID NO:18, SEQ ID NO:30 and SEQ ID NO:4;
SEQ ID NO:18, SEQ ID NO:30 and SEQ ID NO:5;
SEQ ID NO:18, SEQ ID NO:30 and SEQ ID NO:6;
SEQ ID NO:16, SEQ ID NO:31 and SEQ ID NO:2;
SEQ ID NO:16, SEQ ID NO:31 and SEQ ID NO:3;
SEQ ID NO:16, SEQ ID NO:33 and SEQ ID NO:2;
SEQ ID NO:16, SEQ ID NO:33 and SEQ ID NO:3;
SEQ ID NO:16, SEQ ID NO:32 and SEQ ID NO:2;
SEQ ID NO:16, SEQ ID NO:32 and SEQ ID NO:3;
SEQ ID NO:16, SEQ ID NO:34 and SEQ ID NO:2;
SEQ ID NO:16, SEQ ID NO:34 and SEQ ID NO:3;
SEQ ID NO:20, SEQ ID NO:37 and SEQ ID NO:8;
SEQ ID NO:20, SEQ ID NO:38 and SEQ ID NO:8;
SEQ ID NO:21, SEQ ID NO:37 and SEQ ID NO:8;
SEQ ID NO:21, SEQ ID NO:38 and SEQ ID NO:8;
SEQ ID NO:21, SEQ ID NO:40 and SEQ ID NO:14;
SEQ ID NO:21, SEQ ID NO:37 and SEQ ID NO:14;
SEQ ID NO:21, SEQ ID NO:41 and SEQ ID NO:14;
SEQ ID NO:21, SEQ ID NO:40 and SEQ ID NO:8;
SEQ ID NO:21, SEQ ID NO:41 and SEQ ID NO:8;
SEQ ID NO:26, SEQ ID NO:37 and SEQ ID NO:8;
SEQ ID NO:26, SEQ ID NO:40 and SEQ ID NO:8; or SEQ ID NO:26, SEQ ID NO:41 and SEQ ID NO:8.
9. The combination of oligonucleotides of Claim 4, wherein the combinations further include at least one helper probe oligonucleotide.
10. The combination of oligonucleotides of Claim 9, wherein the helper probe oligonucleotide comprises the sequence of SEQ ID NO:27 or SEQ ID NO:28, or is a combination of oligonucleotides of SEQ ID NO:27 and SEQ ID NO:28.
11. A method of detecting a prostate-associated target nucleic acid in a biological sample containing nucleic acid, comprising the steps of:
providing a nucleic acid sample containing a target nucleic acid that includes at least a portion of at least one expressed gene sequence encoding prostate-specific antigen (PSA), prostate-specific membrane antigen (PSMA) or human kallikrein 2 (hK2);
hybridizing to the target nucleic acid at least one primer oligonucleotide containing a sequence that hybridizes specifically to the target nucleic acid or a complement thereof;
producing a plurality of amplification products of the target nucleic acid by using at least one polymerase activity;
providing a probe oligonucleotide that hybridizes specifically to at least one amplification product of the target nucleic acid; and detecting a signal resulting from the probe hybridized to the amplification product.
providing a nucleic acid sample containing a target nucleic acid that includes at least a portion of at least one expressed gene sequence encoding prostate-specific antigen (PSA), prostate-specific membrane antigen (PSMA) or human kallikrein 2 (hK2);
hybridizing to the target nucleic acid at least one primer oligonucleotide containing a sequence that hybridizes specifically to the target nucleic acid or a complement thereof;
producing a plurality of amplification products of the target nucleic acid by using at least one polymerase activity;
providing a probe oligonucleotide that hybridizes specifically to at least one amplification product of the target nucleic acid; and detecting a signal resulting from the probe hybridized to the amplification product.
12. The method of Claim 11, wherein:
the target nucleic acid is a PSA mRNA;
the at least one primer oligonucleotide comprises a promoter-primer oligonucleotide consisting of a sequence complementary to at least a portion of the PSA mRNA and a sequence that is a promoter sequence, and at least one primer oligonucleotide that hybridizes specifically to a nucleic acid strand complementary to the PSA mRNA; and the probe oligonucleotide hybridizes specifically to amplification products of a sense that is the same as that of the PSA mRNA.
the target nucleic acid is a PSA mRNA;
the at least one primer oligonucleotide comprises a promoter-primer oligonucleotide consisting of a sequence complementary to at least a portion of the PSA mRNA and a sequence that is a promoter sequence, and at least one primer oligonucleotide that hybridizes specifically to a nucleic acid strand complementary to the PSA mRNA; and the probe oligonucleotide hybridizes specifically to amplification products of a sense that is the same as that of the PSA mRNA.
13. The method of Claim 11, wherein:
the target nucleic acid is a PSMA mRNA;
the at least one primer oligonucleotide comprises a promoter-primer oligonucleotide consisting of a sequence complementary to at least a portion of the PSMA mRNA and a sequence that is a promoter sequence, and at least one primer oligonucleotide that hybridizes specifically to a nucleic acid strand complementary to the PSMA mRNA; and the probe oligonucleotide hybridizes specifically to amplification products of a sense that is the same as that of the PSMA mRNA.
the target nucleic acid is a PSMA mRNA;
the at least one primer oligonucleotide comprises a promoter-primer oligonucleotide consisting of a sequence complementary to at least a portion of the PSMA mRNA and a sequence that is a promoter sequence, and at least one primer oligonucleotide that hybridizes specifically to a nucleic acid strand complementary to the PSMA mRNA; and the probe oligonucleotide hybridizes specifically to amplification products of a sense that is the same as that of the PSMA mRNA.
14. The method of Claim 11, wherein:
the target nucleic acid is a hK2 mRNA;
the at least one primer oligonucleotide comprises a promoter-primer oligonucleotide consisting of a sequence complementary to at least a portion of the hK2 mRNA and a sequence that is a promoter sequence, and at least one primer oligonucleotide that hybridizes specifically to a nucleic acid strand complementary to the hK2 mRNA; and the probe oligonucleotide hybridizes specifically to amplification products of a sense that is the same as that of the hK2 mRNA.
the target nucleic acid is a hK2 mRNA;
the at least one primer oligonucleotide comprises a promoter-primer oligonucleotide consisting of a sequence complementary to at least a portion of the hK2 mRNA and a sequence that is a promoter sequence, and at least one primer oligonucleotide that hybridizes specifically to a nucleic acid strand complementary to the hK2 mRNA; and the probe oligonucleotide hybridizes specifically to amplification products of a sense that is the same as that of the hK2 mRNA.
15. The method of Claim 11, wherein the at least one primer oligonucleotide comprises the sequence of any one of SEQ ID NO:15 to SEQ ID NO:29, SEQ ID NO:46, SEQ ID
NO:48, or a target-binding sequence of any one of SEQ ID NO:30 to SEQ ID NO:43, SEQ
ID
NO:47 or SEQ ID NO:49.
NO:48, or a target-binding sequence of any one of SEQ ID NO:30 to SEQ ID NO:43, SEQ
ID
NO:47 or SEQ ID NO:49.
16. The method of Claim 12, wherein the promoter-primer oligonucleotide comprises the sequence of any one of SEQ ID NO:30 to SEQ ID NO:43, and wherein the primer oligonucleotide that hybridizes specifically to a nucleic acid strand complementary to the PSA mRNA comprises the sequence of any one of SEQ ID NO:15 to SEQ ID NO:29.
17. The method of Claim 13, wherein the promoter-primer oligonucleotide comprises the sequence of SEQ ID NO:49, and wherein the primer oligonucleotide that hybridizes specifically to amplification products of a sense that is the same as that of the PSMA
mRNA comprises the sequence of SEQ ID NO:48.
mRNA comprises the sequence of SEQ ID NO:48.
18. The method of Claim 14, wherein the promoter-primer oligonucleotide comprises the sequence of SEQ ID NO:47, and wherein the primer oligonucleotide that hybridizes specifically to amplification products of a sense that is the same as that of the hK2 mRNA
comprises the sequence of SEQ ID NO:46.
comprises the sequence of SEQ ID NO:46.
19. The method of Claim 11, wherein the detecting step uses at least one probe oligonucleotide consisting of a sequence of any one of SEQ ID NO:1 to SEQ ID
NO:14, SEQ ID NO:27, SEQ ID NO:28 or SEQ ID NO:50.
NO:14, SEQ ID NO:27, SEQ ID NO:28 or SEQ ID NO:50.
20. The method of Claim 11, wherein the method comprises assaying for the expressed gene sequence encoding PSA and at least one expressed gene sequence encoding PSMA
or hK2.
or hK2.
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US11764099P | 1999-01-28 | 1999-01-28 | |
| US60/117,640 | 1999-01-28 | ||
| PCT/US2000/002270 WO2000044940A2 (en) | 1999-01-28 | 2000-01-28 | Nucleic acid sequences for detecting genetic markers for cancer in a biological sample |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CA2360073A1 true CA2360073A1 (en) | 2000-08-03 |
| CA2360073C CA2360073C (en) | 2011-01-18 |
Family
ID=22374015
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA2360073A Expired - Fee Related CA2360073C (en) | 1999-01-28 | 2000-01-28 | Probes and primers for detecting prostate specific antigen (psa) in a biological sample |
Country Status (6)
| Country | Link |
|---|---|
| US (5) | US6551778B1 (en) |
| EP (1) | EP1151142A2 (en) |
| JP (1) | JP4495349B2 (en) |
| AU (1) | AU767587B2 (en) |
| CA (1) | CA2360073C (en) |
| WO (1) | WO2000044940A2 (en) |
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- 2000-01-28 WO PCT/US2000/002270 patent/WO2000044940A2/en active IP Right Grant
- 2000-01-28 AU AU34755/00A patent/AU767587B2/en not_active Ceased
- 2000-01-28 CA CA2360073A patent/CA2360073C/en not_active Expired - Fee Related
- 2000-01-28 EP EP00913284A patent/EP1151142A2/en not_active Withdrawn
- 2000-01-28 US US09/493,491 patent/US6551778B1/en not_active Expired - Lifetime
- 2000-01-28 JP JP2000596180A patent/JP4495349B2/en not_active Expired - Fee Related
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- 2002-10-17 US US10/273,707 patent/US6811985B2/en not_active Expired - Lifetime
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2004
- 2004-10-28 US US10/978,145 patent/US7267956B2/en not_active Expired - Lifetime
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2007
- 2007-08-13 US US11/838,168 patent/US20080026398A1/en not_active Abandoned
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2008
- 2008-02-14 US US12/031,489 patent/US20090035773A1/en not_active Abandoned
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| US7267956B2 (en) | 2007-09-11 |
| JP4495349B2 (en) | 2010-07-07 |
| WO2000044940A3 (en) | 2000-12-07 |
| US20090035773A1 (en) | 2009-02-05 |
| CA2360073C (en) | 2011-01-18 |
| JP2002535014A (en) | 2002-10-22 |
| US6811985B2 (en) | 2004-11-02 |
| US20050118630A1 (en) | 2005-06-02 |
| US20030104448A1 (en) | 2003-06-05 |
| US6551778B1 (en) | 2003-04-22 |
| WO2000044940A2 (en) | 2000-08-03 |
| EP1151142A2 (en) | 2001-11-07 |
| AU767587B2 (en) | 2003-11-20 |
| AU3475500A (en) | 2000-08-18 |
| US20080026398A1 (en) | 2008-01-31 |
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