# US 2020/0399696 A1 · Compositions and Methods for Detecting C1orf43 Nucleic Acid

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 2020/0399696 A1
- Document ID: US20200399696A1
- Status: Published application
- Kind: A1
- Application number: 16/763,387
- Filed: 2018-11-15
- Published: 2020-12-24
- Earliest claimed: 2017-11-17
- Assignees: Gen-Probe Incorporated
- Applicants: Gen-Probe Incorporated
- Inventors: Siobhán M. Miick; Paul M. Darby; Jo Ann Jackson; Damon Kittredge Getman
- Web page: https://patentgrep.com/patent/US20200399696A1

## CPC

- C12Q 1/6876: Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q 2563/107: fluorescence
- 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

## Abstract

This disclosure provides oligomers, combinations of oligomers, compositions, kits, uses, and methods for detecting a C1orf43 nucleic acid, such as C1orf43 mRNA, such as human C1orf43 mRNA, in a sample.

## Claims

### Claim 1

A combination of oligomers comprising at least first and second amplification oligomers, wherein the first and second amplification oligomers are reverse and forward amplification oligomers, respectively; each comprise at least 10 nucleotides; and are configured to specifically hybridize to first and second sites in the sequence of SEQ ID NO: 39 and generate an amplicon therefrom, respectively.

### Claim 2

A method of detecting the presence or absence of a C1orf43 nucleic acid in a sample, comprising:
contacting the sample with a combination of oligomers comprising at least first and second amplification oligomers,
performing a nucleic acid amplification reaction which produces at least a first amplicon in the presence of the C1orf43 nucleic acid,
and detecting the presence or absence of the first amplicon,
wherein:
the first amplicon is produced through extension of the first and second amplification oligomers in the presence of the C1orf43 nucleic acid; and
wherein the first and second amplification oligomers are reverse and forward amplification oligomers, respectively; each comprise at least 10 nucleotides; and are configured to specifically hybridize to first and second sites in the sequence of SEQ ID NO: 39, respectively.

### Claim 3 (depends on 1, 2)

The combination of claim 1 or method of claim 2, wherein at least one of the amplification oligomers is a promoter-primer.

### Claim 4

The combination or method of any one of the preceding claims, wherein the first amplification oligomer is a promoter-primer.

### Claim 5 (depends on 3, 4)

The combination or method of any one of claims 3-4, wherein the promoter-primer comprises a T7 promoter which is located 5′ of a target-hybridizing sequence.

### Claim 6 (depends on 5)

The combination or method of claim 5, wherein the T7 promoter comprises the sequence of SEQ ID NO: 58.

### Claim 7

The combination or method of any one of the preceding claims, wherein the first and second amplification oligomer are configured to generate an amplicon comprising at least 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, or 144 nucleotides of the sequence of SEQ ID NO: 40.

### Claim 8 (depends on 7)

The combination or method of claim 7, wherein the first and second amplification oligomer are configured to generate an amplicon comprising the sequence of SEQ ID NO: 41.

### Claim 9 (depends on 7)

The combination or method of claim 7, wherein the first and second amplification oligomer are configured to generate an amplicon comprising the sequence of SEQ ID NO: 42.

### Claim 10

The combination or method of any one of the preceding claims, wherein the first amplification oligomer is configured to specifically hybridize to a first site in the complement of SEQ ID NO: 52.

### Claim 11 (depends on 10)

The combination or method of claim 10, wherein the first site comprises the sequence of SEQ ID NO: 53.

### Claim 12 (depends on 10)

The combination or method of claim 10, wherein the first site comprises the sequence of SEQ ID NO: 54.

### Claim 13

The combination or method of any one of the preceding claims, wherein the first amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 27, optionally with up to two mismatches.

### Claim 14 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)

The combination or method of any one of claims 1-12, wherein the first amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 29, optionally with up to two mismatches.

### Claim 15 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)

The combination or method of any one of claims 1-12, wherein the first amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 31, optionally with up to two mismatches.

### Claim 16 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)

The combination or method of any one of claims 1-12, wherein the first amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 33, optionally with up to two mismatches.

### Claim 17

The combination or method of any one of the preceding claims, wherein the first amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 27, 29, 31, or 33.

### Claim 18

The combination or method of any one of the preceding claims, wherein the first amplification oligomer comprises the sequence of SEQ ID NO: 26, 28, 30, or 32.

### Claim 19

The combination or method of any one of the preceding claims, wherein the second amplification oligomer is configured to specifically hybridize to a second site in the complement of SEQ ID NO: 46.

### Claim 20 (depends on 19)

The combination or method of claim 19, wherein the second site comprises the sequence of SEQ ID NO: 47.

### Claim 21 (depends on 19)

The combination or method of claim 19, wherein the second site comprises the sequence of SEQ ID NO: 48.

### Claim 22

The combination or method of any one of the preceding claims, wherein the second amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 34, optionally with up to two mismatches.

### Claim 23 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21)

The combination or method of any one of claims 1-21, wherein the second amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 35, optionally with up to two mismatches.

### Claim 24 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21)

The combination or method of any one of claims 1-21, wherein the second amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 36, optionally with up to two mismatches.

### Claim 25 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21)

The combination or method of any one of claims 1-21, wherein the second amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 37, optionally with up to two mismatches.

### Claim 26 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21)

The combination or method of any one of claims 1-21, wherein the second amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 38, optionally with up to two mismatches.

### Claim 27

The combination or method of any one of the preceding claims, wherein the second amplification oligomer comprises a target-hybridizing sequence comprising the sequence of SEQ ID NO: 34, 35, 36, 37, or 38.

### Claim 28

The combination or method of any one of the preceding claims, wherein the combination further comprises at least one probe oligomer that comprises at least 10 nucleotides and is configured to specifically hybridize to an amplicon produced from the first and second amplification oligomers.

### Claim 29 (depends on 28)

The combination or method of claim 28, wherein the probe oligomer is configured to specifically hybridize to a detection site in a nucleic acid having the sequence of SEQ ID NO: 43.

### Claim 30

A probe oligomer that comprises at least 10 nucleotides and is configured to specifically hybridize to a detection site in a nucleic acid having the sequence of SEQ ID NO: 43.

### Claim 31 (depends on 28, 29, 30)

The combination, method, or probe oligomer of any one of claims 28-30, wherein the probe oligomer is configured to specifically hybridize to a detection site in the sequence of SEQ ID NO: 44.

### Claim 32 (depends on 28, 29, 30)

The combination, method, or probe oligomer of any one of claims 28-30, wherein the probe oligomer is configured to specifically hybridize to a detection site in a nucleic acid having the sequence of SEQ ID NO: 45.

### Claim 33 (depends on 28, 29, 30)

The combination, method, or probe oligomer of any one of claims 28-30, wherein the probe oligomer is configured to specifically hybridize to a detection site in a nucleic acid having the sequence of SEQ ID NO: 49.

### Claim 34 (depends on 33)

The combination, method, or probe oligomer of claim 33, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 50.

### Claim 35 (depends on 33)

The combination, method, or probe oligomer of claim 33, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 51.

### Claim 36 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 15 with up to two mismatches.

### Claim 37 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 17 with up to two mismatches.

### Claim 38 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 19 with up to two mismatches.

### Claim 39 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 21 with up to two mismatches.

### Claim 40 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 23 with up to two mismatches.

### Claim 41 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 25 with up to two mismatches.

### Claim 42 (depends on 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41)

The combination, method, or probe oligomer of any one of claims 28-41, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 15, 17, 19, 21, 23, or 25.

### Claim 43 (depends on 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41)

The combination, method, or probe oligomer of any one of claims 28-41, wherein the probe oligomer comprises the sequence of SEQ ID NO: 14, 16, 18, 20, 22, or 24.

### Claim 44 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 59 with up to two mismatches.

### Claim 45 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 60 with up to two mismatches.

### Claim 46 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 64 with up to two mismatches.

### Claim 47 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 66 with up to two mismatches.

### Claim 48 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 67 with up to two mismatches.

### Claim 49 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 68 with up to two mismatches.

### Claim 50 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 69 with up to two mismatches.

### Claim 51 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 70 with up to two mismatches.

### Claim 52 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 71 with up to two mismatches.

### Claim 53 (depends on 28, 29, 30, 31, 32, 33, 34, 35)

The combination, method, or probe oligomer of any one of claims 28-35, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 72 with up to two mismatches.

### Claim 54

A probe oligomer that comprises a target hybridizing sequence comprising the sequence of any one of SEQ ID NO: 61, 62, 63, or 65 with up to two mismatches

### Claim 55 (depends on 28, 54)

The combination, method, or probe oligomer of any one of claim 28 or 54, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 61 with up to two mismatches.

### Claim 56 (depends on 28, 54)

The combination, method, or probe oligomer of any one of claim 28 or 54, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 62 with up to two mismatches.

### Claim 57 (depends on 28, 54)

The combination, method, or probe oligomer of any one of claim 28 or 54, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 63 with up to two mismatches.

### Claim 58 (depends on 28, 54)

The combination, method, or probe oligomer of any one of claim 28 or 54, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 65 with up to two mismatches.

### Claim 59 (depends on 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58)

The combination, method, or probe oligomer of any one of claim 28-35 or 44-58, wherein the probe oligomer comprises a target hybridizing sequence comprising the sequence of any one of SEQ ID NOs: 59-72.

### Claim 60 (depends on 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59)

The combination, method, or probe oligomer of any one of claims 28-59, wherein the probe oligomer comprises 2′-O-methyl-ribose in its backbone.

### Claim 61 (depends on 60)

The combination, method, or probe oligomer of claim 60, wherein at least half, at least 90%, or all of the sugars in the probe oligomer are 2′-O-methyl-ribose.

### Claim 62 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27)

The combination or method of any one of claims 1-27, wherein one or more of the first and second amplification oligomers comprises a non-nucleotide detectable label.

### Claim 63 (depends on 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61)

The combination, method, or probe oligomer of any one of claims 28-61, wherein at least one probe oligomer comprises a non-nucleotide detectable label.

### Claim 64 (depends on 62, 63)

The combination, method, or probe oligomer of any one of claims 62-63, wherein the non-nucleotide detectable label is a fluorescent label.

### Claim 65 (depends on 63, 64)

The combination, method, or probe oligomer of claim 63 or 64, wherein the probe oligomer comprises a quencher.

### Claim 66 (depends on 65)

The combination, method, or probe oligomer of claim 65, wherein the non-nucleotide detectable label is a fluorescent label and the quencher absorbs fluorescence to a greater extent when the probe is free than when the probe is annealed to a target nucleic acid.

### Claim 67 (depends on 64, 65, 66)

The combination, method, or probe oligomer of any one of claims 64-66, wherein the fluorescent label is FAM, HEX, or acridine.

### Claim 68 (depends on 65, 66, 67)

The combination, method, or probe oligomer of any one of claims 65-67, wherein the quencher is DABCYL or ROX.

### Claim 69 (depends on 65, 66, 67, 68)

The combination, method, or probe oligomer of any one of claims 65-68, wherein the fluorescent label is attached to the 5′-terminus of the probe oligomer and the quencher is attached to the 3′-terminus of the probe oligomer, or the fluorescent label is attached to the 3′-terminus of the probe oligomer and the quencher is attached to the 5′-terminus of the probe oligomer.

### Claim 70 (depends on 62, 63)

The combination, method, or probe oligomer of any one of claims 62-63, wherein the non-nucleotide detectable label is a chemiluminescent label.

### Claim 71 (depends on 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70)

The combination, method, or probe oligomer of any one of claim 28-61 or 63-70, wherein the probe oligomer comprises a first self-complementary region at its 5′ end and a second self-complementary region at its 3′ end.

### Claim 72 (depends on 71)

The combination, method, or probe oligomer of claim 71, wherein the self-complementary regions can hybridize to form 3 to 7 Watson-Crick or wobble base pairs.

### Claim 73 (depends on 71)

The combination, method, or probe oligomer of claim 71, wherein the self-complementary regions can hybridize to form 4 Watson-Crick or wobble base pairs.

### Claim 74 (depends on 63, 64, 65, 66, 67, 68, 69, 70, 71)

The combination, method, or probe oligomer of any one of claims 63-71, wherein the probe oligomer is a linear probe oligomer.

### Claim 75 (depends on 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74)

A method of detecting the presence or absence of a C1orf43 nucleic acid in a sample, comprising:
contacting the sample with the probe oligomer of any one of claim 30-61 or 63-74;
performing a hybridization reaction which produces a complex of the probe oligomer and the C1orf43 nucleic acid in the presence of the C1orf43 nucleic acid;
and detecting the presence or absence of the complex of the probe oligomer and the C1orf43 nucleic acid.

### Claim 76 (depends on 75)

The method of claim 75, wherein the hybridization reaction is a hybridization protection assay.

### Claim 77 (depends on 75, 76)

The method of claim 75 or 76, wherein the hybridization reaction is a dual kinetic assay.

### Claim 78 (depends on 75, 76, 77)

The method of any one of claims 75-77, wherein the probe oligomer functions as a flasher probe in the dual kinetic assay.

### Claim 79 (depends on 75, 76, 77)

The method of any one of claims 75-77, wherein the probe oligomer functions as a glower probe in the dual kinetic assay.

### Claim 80 (depends on 75, 76, 77, 78, 79)

The method of any one of claims 75-79, wherein the C1orf43 nucleic acid comprises a C1orf43 amplicon.

### Claim 81 (depends on 75, 76, 77, 78, 79)

The method of any one of claims 75-79, wherein the C1orf43 nucleic acid comprises C1orf43 RNA from cells in the sample.

### Claim 82 (depends on 75, 76, 77, 78, 79, 80, 81)

The method of any one of claims 75-81, wherein the sample is contacted with a combination of oligomers comprising the probe oligomer.

### Claim 83 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56)

The combination or method of any one of claim 1-29, 31-56, or 82, wherein the combination further comprises at least one capture oligomer that comprises at least 10 nucleotides and is configured to specifically hybridize to a capture site in a C1orf43 nucleic acid.

### Claim 84 (depends on 83)

The combination or method of claim 83, wherein the capture site is in the sequence of SEQ ID NO: 1, 2, or 3.

### Claim 85 (depends on 83)

The combination or method of claim 83, wherein the capture site is in the sequence of SEQ ID NO: 39.

### Claim 86

A method of isolating C1orf43 nucleic acid from a sample, comprising:
contacting the sample with at least one capture oligomer under conditions permissive for forming one or more complexes of a capture oligomer and the C1orf43 nucleic acid, thereby forming a composition, wherein the capture oligomer comprises at least 10 nucleotides and is configured to specifically hybridize to a capture site in the sequence of SEQ ID NO: 39; and
isolating the capture oligomer from the composition.

### Claim 87 (depends on 86)

The method of claim 86, wherein isolating the capture oligomers comprises associating the capture oligomers with a solid support, and washing the solid support.

### Claim 88 (depends on 87)

The method of claim 87, wherein the solid support comprises a poly-N sequence that is complementary to a portion of the capture oligomer.

### Claim 89 (depends on 87)

The method of claim 87, wherein the solid support comprises a binding agent that recognizes an affinity tag present in the capture oligomer.

### Claim 90

A capture oligomer that comprises at least 10 nucleotides and is configured to specifically hybridize to a capture site in the sequence of SEQ ID NO: 39.

### Claim 91 (depends on 83, 84, 85, 86, 87, 88, 89, 90)

The combination, method, or capture oligomer of any one of claims 83-90, wherein the capture site is in the sequence of SEQ ID NO: 55.

### Claim 92 (depends on 83, 84, 85, 86, 87, 88, 89, 90)

The combination, method, or capture oligomer of any one of claims 83-90, wherein the capture oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 56.

### Claim 93 (depends on 83, 84, 85, 86, 87, 88, 89, 90)

The combination, method, or capture oligomer of any one of claims 83-90, wherein the capture oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 57.

### Claim 94 (depends on 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93)

The combination, method, or capture oligomer of any one of claims 83-93, wherein the capture oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 5 with up to two mismatches.

### Claim 95 (depends on 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93)

The combination, method, or capture oligomer of any one of claims 83-93, wherein the capture oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 7 with up to two mismatches.

### Claim 96 (depends on 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93)

The combination, method, or capture oligomer of any one of claims 83-93, wherein the capture oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 9 with up to two mismatches.

### Claim 97 (depends on 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93)

The combination, method, or capture oligomer of any one of claims 83-93, wherein the capture oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 11 with up to two mismatches.

### Claim 98 (depends on 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93)

The combination, method, or capture oligomer of any one of claims 83-93, wherein the capture oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 13 with up to two mismatches.

### Claim 99 (depends on 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93)

The combination, method, or capture oligomer of any one of claims 83-93, wherein the capture oligomer comprises a target hybridizing sequence comprising the sequence of SEQ ID NO: 5, 7, 9, 11, or 13.

### Claim 100 (depends on 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99)

The combination, method, or capture oligomer of any one of claims 83-99, wherein the capture oligomer comprises the sequence of SEQ ID NO: 4, 6, 8, 10, or 12.

### Claim 101 (depends on 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100)

The combination, method, or capture oligomer of any one of claims 83-100, wherein the capture oligomer comprises 2′-O-methyl-ribose in its backbone.

### Claim 102 (depends on 101)

The combination, method, or capture oligomer of claim 101, wherein at least half, at least 90%, or all of the sugars in the target hybridizing sequence of the capture oligomer are 2′-O-methyl-ribose.

### Claim 103 (depends on 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102)

The combination, method, or capture oligomer of any one of claims 83-102, wherein the capture oligomer further comprises a non-nucleotide affinity label.

### Claim 104 (depends on 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102)

The combination, method, or capture oligomer of any one of claims 83-102, wherein the capture oligomer further comprises a non-C1orf43 sequence.

### Claim 105 (depends on 104)

The combination, method, or capture oligomer of claim 104, wherein the non-C1orf43 sequence is a poly-N sequence.

### Claim 106 (depends on 105)

The combination, method, or capture oligomer of claim 105, wherein the poly-N sequence is a poly-A or poly-T sequence.

### Claim 107 (depends on 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106)

A combination comprising the capture oligomer according to any one of claims 90-106 and one or more amplification oligomers, wherein the amplification oligomer is configured to specifically hybridize to a site in the sequence of SEQ ID NO: 39.

### Claim 108 (depends on 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 107)

The combination of claim 107, wherein the one or more amplification oligomers includes the first amplification oligomer as recited in any one of claims 4-18.

### Claim 109 (depends on 19, 20, 21, 22, 23, 24, 25, 26, 27, 107, 108)

The combination of claim 107 or 108, wherein the one or more amplification oligomers includes the second amplification oligomer as recited in any one of claims 19-27.

### Claim 110 (depends on 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 107, 108, 109)

The combination of any one of claims 107-109, further comprising the probe oligomer as recited in any one of claim 28-61 or 63-74.

### Claim 111 (depends on 86, 87, 88, 89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106)

The method of any one of claim 86-89 or 91-106, further comprising performing a linear amplification wherein at least one amplification oligomer is extended.

### Claim 112 (depends on 111)

The method of claim 111, wherein prior to the linear amplification, the amplification oligomer is associated with a complex of C1orf43 nucleic acid and a capture oligomer and the complex is associated with a solid support, and the method comprises washing the solid support.

### Claim 113 (depends on 112)

The method of claim 112, wherein the solid support is a population of microbeads.

### Claim 114 (depends on 113)

The method of claim 113, wherein the microbeads of the population are magnetic.

### Claim 115 (depends on 112, 113, 114)

The method of any one of claims 112-114, wherein following the washing step, the method comprises adding one or more additional amplification oligomers oppositely oriented to an amplification oligomer associated with the complex of C1orf43 nucleic acid and the capture oligomer.

### Claim 116 (depends on 115)

The method of claim 115, wherein the one or more oppositely oriented additional amplification oligomers includes a promoter-primer.

### Claim 117 (depends on 116)

The method of claim 116, wherein the one or more oppositely oriented additional amplification oligomers includes an oligomer that is not a promoter-primer.

### Claim 118 (depends on 19, 20, 21, 22, 23, 24, 25, 26, 27, 115, 116, 117)

The method of any one of claims 115-117, wherein the one or more oppositely oriented additional amplification oligomers includes the second amplification oligomer as recited in any one of claims 19-27.

### Claim 119 (depends on 115, 116, 117, 118)

The method of any one of claims 115-118, further comprising performing an exponential amplification following the linear amplification.

### Claim 120 (depends on 119)

The method of claim 119, wherein the exponential amplification is transcription-mediated amplification.

### Claim 121 (depends on 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105)

The method of any one of claim 2-29, 31-89, 91-105, or 111-120, further comprising quantifying C1orf43 nucleic acid in the sample.

### Claim 122

A kit or composition comprising at least one, two, three, or four of a first amplification oligomer, a second amplification oligomer, a probe oligomer, or a capture oligomer recited in any one of the preceding claims.

### Claim 123 (depends on 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 122)

The kit or composition of claim 122, comprising at least one probe oligomer as recited in any one of claim 28-61 or 63-74.

### Claim 124 (depends on 83, 84, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 122, 123)

The kit or composition of any one of claims 122-123, comprising at least one capture oligomer as recited in any one of claim 83-85 or 90-106.

### Claim 125 (depends on 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 122, 123, 124)

The kit or composition of any one of claims 122-124, comprising the first amplification oligomer as recited in any one of claims 4-18 and the second amplification oligomer as recited in any one of claims 19-27.

### Claim 126 (depends on 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 122, 123, 124, 125)

A kit according to any one of claims 122-125 or comprising the combination of any one of claim 1, 3-62, 63-85, or 91-110.

### Claim 127 (depends on 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 122, 123, 124, 125)

A composition according to any one of claims 122-125 or comprising the combination of any one of claim 1, 3-62, 63-85, or 91-110.

### Claim 128 (depends on 127)

The composition of claim 127, which is aqueous, frozen, or lyophilized.

### Claim 129

Use of the combination, method, composition, capture oligomer, probe oligomer, or kit of any one of the preceding claims for detecting the presence or absence of a C1orf43 nucleic acid in a sample.

### Claim 130 (depends on 1, 128)

The combination, method, composition, capture oligomer, probe oligomer, or kit of any one of claims 1-128, for use in detecting the presence or absence of a C1orf43 nucleic acid in a sample.

### Claim 131 (depends on 1, 128)

Use of the combination, method, composition, capture oligomer, probe oligomer, or kit of any one of claims 1-128 for quantifying a C1orf43 nucleic acid in a sample.

### Claim 132 (depends on 1, 128)

The combination, method, composition, capture oligomer, probe oligomer, or kit of any one of claims 1-128, for use in quantifying a C1orf43 nucleic acid in a sample.

### Claim 133 (depends on 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121)

The use, combination, method, composition, capture oligomer, probe oligomer, or kit of any one of claim 2-29, 31-53, 55-89, 91-106, 111-121, or 126-132, wherein the sample comprises human mRNA.

### Claim 134 (depends on 133)

The use, combination, method, composition, or kit of claim 133, wherein the human mRNA comprises mRNA from bladder, ductus deferens, epididymis, kidney, lymph node, pancreas, peripheral blood lymphocytes, penis, prostate, seminal vesicle, or spleen.

### Claim 135 (depends on 133)

The use, combination, method, composition, or kit of claim 133, wherein the human mRNA comprises mRNA from a vaginal or cervical sample.

### Claim 136 (depends on 135)

The use, combination, method, composition, or kit of claim 135, wherein the vaginal or cervical sample is a vaginal or cervical swab.

### Claim 137 (depends on 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121)

The use, combination, method, composition, or kit of any one of claim 2-29, 31-53, 55-89, 91-106, 111-121, or 126-136, wherein the method or use further comprises detecting the presence or absence of at least one nucleic acid of a microbe or pathogen.

### Claim 138 (depends on 137)

The use, combination, method, composition, or kit of claim 137, wherein the at least one nucleic acid of a microbe or pathogen comprises human papillomavirus nucleic acid, Chlamydia trachomatis nucleic acid, Neisseria gonorrheae nucleic acid, Trichomonas vaginalis nucleic acid, or Mycoplasma genitalium nucleic acid.

### Claim 139 (depends on 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121)

The use, combination, method, composition, or kit of any one of claim 2-29, 31-53, 55-89, 91-106, 111-121, or 126-138, wherein the method or use further comprises detecting the presence or absence of at least one mRNA other than C1orf43.

### Claim 140 (depends on 139)

The use, combination, method, composition, or kit of claim 139, wherein the mRNA other than C1orf43 is a human mRNA other than C1orf43.