Optimized oligonucleotides and methods of using same for the screening, detection, isolation, quantitation, monitoring and sequencing of prostate cancer associated viruses and host biomarkers
AssigneeIntelligent Medical Devices, Inc.
InventorsAlice A. Jacobs, Chesley Leslin, David L. Dolinger
Life of this patent
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Abstract
Described herein are oligonucleotides useful for screening, detecting, isolating, quantitating, monitoring and sequencing of viruses and host biomarkers associated with prostate cancer and methods and kits of using the described oligonucleotides.
Claims38
An isolated nucleic acid sequence comprising a sequence selected from the group consisting of SEQ ID NOS:
- 1-61.
A method of hybridizing one or more isolated nucleic acid sequences comprising:
- a sequence selected from the group consisting of SEQ ID NOS:
- 1-61 to a RNAse L, PAP, Pim-1, Pim-2, Hepsin or PSMA sequence, further comprising contacting one or more isolated nucleic acid sequences to a sample comprising the RNAse L, PAP, Pim-1, Pim-2, Hepsin or PSMA sequence under conditions suitable for hybridization.
A primer set comprising at least one forward primer selected from the group consisting of SEQ ID NOS:
- 1, 4, 5, 7, 9, 19, 28, 31, 34, 39, 42 and 52 and at least one reverse primer selected from the group consisting of SEQ ID NOS:
- 3, 11, 20, 30, 36, 44, 47, 49, 51 and 54.
A primer comprising a sequence selected from the group consisting of SEQ ID NOS:
- 1, 3, 4, 5, 7, 9, 11, 19, 20, 28, 30, 31, 34, 36, 39, 42, 44, 47, 49, 51, 52 and 54 for the production of cDNA from RNAse L, PAP, Pim-1, Pim-2, Hepsin or PSMA RNA.
A method of producing a nucleic acid product, comprising contacting one or more isolated nucleic acid sequences selected from the group consisting of SEQ ID NOS:
- 1, 3, 4, 5, 7, 9, 11, 19, 20, 28, 30, 31, 34, 36, 39, 42, 44, 47, 49, 51, 52 and 54 to a sample comprising a RNAse L, PAP, Pim-1, Pim-2, Hepsin or PSMA sequence under conditions suitable for nucleic acid polymerization.
A method for detecting RNAse L, PAP, Pim-1, Pim-2, Hepsin or PSMA RNA or DNA in a sample, comprising:
- a) contacting the sample with at least one forward primer comprising a sequence selected from the group consisting of SEQ ID NOS:
- 1, 4, 5, 7, 9, 19, 28, 31, 34, 39, 42 and 52, and at least one reverse primer comprising a sequence selected from the group consisting of SEQ ID NOS:
- 3, 11, 20, 30, 36, 44, 47, 49, 51 and 54 under conditions such that nucleic acid amplification occurs to yield an amplicon;
- and
- b) contacting the amplicon with one or more probes comprising one or more sequences selected from the group consisting of SEQ ID NOS:
- 2, 6, 8, 10, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 32, 33, 35, 37, 38, 40, 41, 43, 45, 46, 48, 50, 53, 55, 56, 57, 58, 59, 60 and 61, under conditions such that hybridization of the probe to the amplicon occurs;
- wherein hybridization of the probe is indicative of the presence of RNAse L, PAP, Pim-1, Pim-2, Hepsin or PSMA in the sample.
A kit for detecting, quantitating and sequencing RNAse L, PAP, Pim-1, Pim-2, Hepsin or PSMA RNA or DNA in a sample, comprising one or more probes comprising a sequence selected from the group consisting of SEQ ID NOS:
- 2, 6, 8, 10, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 32, 33, 35, 37, 38, 40, 41, 43, 45, 46, 48, 50, 53, 55, 56, 57, 58, 59, 60 and 61
A kit for detecting and quantitating a targeted RNAse L, PAP, Pim-1, Pim-2, Hepsin or PSMA sequence derived from an artificial construct, such as a plasmid, comprising:
- a) at least one forward primer comprising the sequence selected from the group consisting of SEQ ID NOS:
- 1, 4, 5, 7, 9, 19, 28, 31, 34, 39, 42 and 52;
- b) at least one reverse primer comprising the sequence selected from the group consisting of SEQ ID NOS:
- 3, 11, 20, 30, 36, 44, 47, 49, 51 and 54;
- and
- c) one or more probes comprising a sequence selected from the group consisting of SEQ ID NOS:
- 2, 6, 8, 10, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 32, 33, 35, 37, 38, 40, 41, 43, 45, 46, 48, 50, 53, 55, 56, 57, 58, 59, 60 and 61.
A kit for binding, amplifying and sequencing RNAseL, PAP, PIM-1, PIM-2, Hepsin or PSMA RNA, DNA or proviral DNA in a sample, comprising:
- a) at least one forward primer comprising the sequence selected from the group consisting of:
- SEQ ID NOS:
- 1, 4, 5, 7, 9, 19, 28, 31, 34, 39, 42 and 52;
- b) at least one reverse primer comprising the sequence selected from the group consisting of:
- SEQ ID NOS:
- 3, 11, 20, 30, 36, 44, 47, 49, 51 and 54;
- and
- c) reagents for the sequencing of amplified DNA fragments.
A method of diagnosing prostate cancer, comprising:
- a) contacting a sample with at least one forward and reverse primer set selected from the group consisting of:
- Groups 1-40 of Table 2;
- b) conducting an amplification reaction, thereby producing an amplicon;
- and
- c) detecting the amplicon using one or more probes selected from the group consisting of:
- SEQ ID NOS:
- 2, 6, 8, 10, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 32, 33, 35, 37, 38, 40, 41, 43, 45, 46, 48, 50, 53, 55, 56, 57, 58, 59, 60 and 61;
- wherein the detection of an amplicon is indicative of the presence of RNAseL, PAP, PIM-1, PIM-2, HEPSIN or PSMA in the sample.
A method for diagnosing prostate cancer, comprising:
- a) contacting a sample with at least one forward and reverse primer pair selected from the group consisting of:
- Groups 1-40 of Table 2;
- b) conducting a reverse transcriptase-polymerase chain reaction, a polymerase chain reaction or signal amplification;
- c) detecting the generation of an amplified product using one or more probes selected from the group consisting of SEQ ID NOS:
- 2, 6, 8, 10, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 32, 33, 35, 37, 38, 40, 41, 43, 45, 46, 48, 50, 53, 55, 56, 57, 58, 59, 60 and 61;
- wherein the generation of an amplified product indicates the presence of RNAseL, PAP, PIM-1, PIM-2, HEPSIN or PSMA in the sample;
- and
- d) determining expression levels of RNAseL, PAP, PIM-1, PIM-2, HEPSIN or PSMA RNA.
Dependencies are inferred from the claim text.