# US 10,119,164 B2 · Capture primers and capture sequence linked solid supports for molecular diagnostic tests

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- Number: US 10,119,164 B2
- Document ID: US10119164B2
- Status: Granted
- Kind: B2
- Application number: 15/237,284
- Filed: 2016-08-15
- Published: 2017-02-16
- Granted: 2018-11-06
- Earliest claimed: 2009-07-31
- Assignees: Ibis Biosciences, Inc.
- Applicants: Ibis Biosciences, Inc.
- Inventors: Mark A. Hayden
- Web page: https://patentgrep.com/patent/US10119164B2

## CPC

- C12Q 1/6869: Methods for sequencing
- C12Q 1/686: Polymerase chain reaction [PCR]
- G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B 30/10: Sequence alignment; Homology search
- 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
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

## Abstract

The present invention provides systems, methods, and compositions for performing molecular tests. In particular, the present invention provides methods, compositions and systems for generating target sequence-linked solid supports (e.g., beads) using a solid support linked to a plurality of capture sequences and capture primers composed of a 3′ target-specific portion and a 5′ capture sequence portion. In certain embodiments, the target sequence linked solid support is used in sequencing methods (e.g., pyrosequencing, zero-mode waveguide type sequencing, nanopore sequencing, etc.) to determine the sequence of the target sequence (e.g., in order to detect the identity of a target nucleic acid in sample).

## Claims

### Claim 1

A method comprising:
a) contacting a sample suspected of containing a target nucleic acid with a capture primer and a reverse primer, wherein said capture primer comprises: i) a 3′ region configured to hybridize to said target nucleic acid such that it can be extended by a polymerase, and ii) a 5′ region comprising a capture sequence; and wherein said contacting is under conditions such that:
i) said 3′ region of said capture primer hybridizes to said target nucleic acid and is extended to generate a first amplification product, and
ii) said reverse primer hybridizes to said first amplification product and is extended to generate a second amplification product, wherein said second amplification product comprises a 3′ capture sequence complement capable of hybridizing to said capture sequence; and
b) treating said sample under conditions such that said second amplification product is separated from said first amplification product;
c) contacting said second amplification product with a solid support comprising a plurality of bound capture sequences under conditions such that said 3′ capture sequence complement of said second amplification product hybridizes to one of said bound capture sequences to generate a hybridized solid support; and
d) treating said hybridized solid support under conditions such that one of said bound capture sequences is extended along said second amplification product to generate a target sequence that is linked to said solid support; and
e) treating said target sequence linked to said solid support under conditions such that at least part of the nucleic acid sequence of said target sequence is determined by a method comprising contacting said target sequence with at least one nucleotide incorporating biocatalyst, labeled nucleotides, and at least one primer nucleic acid that is at least partially complementary to at least a subsequence of said target sequence, under conditions whereby said nucleotide incorporating biocatalyst extends said primer nucleic acid to produce an extended primer nucleic acid by incorporating said labeled nucleotides at a terminal end of said extended primer nucleic acid.

### Claim 2 (depends on 1)

The method of claim 1, further comprising f) contacting said solid support with a plurality of free capture sequences and a plurality of said reverse primers under conditions such that said plurality of bound capture sequences are extended to generate a clonally amplified solid support comprising a plurality of said target sequences.

### Claim 3 (depends on 2)

The method of claim 2, wherein said conditions comprise emulsion PCR conditions or bridge PCR conditions.

### Claim 4 (depends on 1)

The method of claim 1, wherein said 5′ region is configured to not hybridize to said target nucleic when said 3′ region of said capture primer is hybridized to said target nucleic acid.

### Claim 5 (depends on 1)

The method of claim 1, wherein said nucleic acid sequence of said target sequence is determined by a method employing at least one zero-mode waveguide.

### Claim 6 (depends on 1)

The method of claim 1, wherein said labels comprise different fluorescent labels and wherein said detectable signals are detected using a fluorescence microscope.

### Claim 7 (depends on 1)

The method of claim 1, wherein said at least one primer nucleic acid is a primer pair, wherein said primer pair is configured to hybridize with conserved regions of two or more different bioagents and flank variable regions of two or more different bioagents.

### Claim 8 (depends on 1)

The method of claim 1, wherein the terminal end of said extended primer nucleic acid is the 3′ terminal end.

### Claim 9 (depends on 1)

The method of claim 1, wherein said nucleotide incorporating biocatalyst comprises an enzyme selected from the group consisting of: a polymerase, a terminal transferase, a reverse transcriptase, a polynucleotide phosphorylase, and a telomerase.

### Claim 10 (depends on 1)

The method of claim 1, wherein said nucleotide incorporating biocatalyst comprises one or more modifications.

### Claim 11 (depends on 1)

The method of claim 1, wherein said nucleotide incorporating biocatalyst is an enzyme derived from an organism that is selected from the group consisting of: Thermus antranikianii, Thermus aquaticus, Thermus caldophilus, Thermus chliarophilus, Thermus filiformis, Thermus flavus, Thermus igniterrae, Thermus lacteus, Thermus oshimai, Thermus ruber, Thermus rubens, Thermus scotoductus, Thermus silvanus, Thermus species Z05, Thermus species sps 17, Thermus thermophilus, Thermotoga maritima, Thermotoga neapolitana, Thermosipho africanus, Anaerocellum thermophilum, Bacillus caldotenax, Pfu, KOD1, and Bacillus stearothermophilus.

### Claim 12 (depends on 1)

The method of claim 1, wherein said nucleotide incorporating biocatalyst comprises a phi29 DNA polymerase.

### Claim 13 (depends on 1)

The method of claim 1, wherein a label is attached to one of a heterocyclic base of a labeled nucleotide, a sugar moiety of a labeled nucleotide, and a phosphate group of a labeled nucleotide.

### Claim 14 (depends on 1)

The method of claim 1, wherein a linker attaches a label to a labeled nucleotide.

### Claim 15 (depends on 1)

The method of claim 1, wherein said extended primer nucleic acid is complementary to a subsequence of said target sequence.

### Claim 16 (depends on 1)

The method of claim 1, wherein said extended primer nucleic acid is complementary to a full-length sequence of said target sequence.

### Claim 17 (depends on 1)

The method of claim 1, wherein said primer nucleic acid comprises an intelligent primer.

### Claim 18 (depends on 1)

The method of claim 1, wherein said label comprises a fluorescent dye, a non-fluorescent label, a colorimetric label, a chemiluminescent label, a bioluminescent label, a radioisotope, an antibody, an antigen, biotin, a hapten, or an enzyme.

### Claim 19 (depends on 18)

The method of claim 18, wherein said label is a fluorescent dye selected from the group consisting of: a rhodamine dye, a fluorescein dye, a halofluorescein dye, a dichlororhodamine dye, an energy transfer dye, a Lucifer dye, Oregon Green, and a cyanine dye.

### Claim 20 (depends on 18)

The method of claim 18, wherein said label is a fluorescent dye selected from the group consisting of: JOE, VIC, TET, HEX, PAM, R6G, R110, TAMRA, and ROX.

### Claim 21 (depends on 18)

The method of claim 18, wherein said label is a radioisotope selected from the group consisting of: 3H, 14C, 22Na, 32P, 33P, 35S, 42K, 45Ca, 125I, and 203Hg.

### Claim 22 (depends on 1)

The method of claim 1, wherein said capture primer and said reverse primer are configured to hybridize with conserved regions of two or more different bioagents and flank variable regions of said two or more different bioagents.

### Claim 23 (depends on 1)

The method of claim 1, wherein the target nucleic acid comprises a mammalian nucleic acid, a bacterial nucleic acid, a viral nucleic acid, a fungal nucleic acid, or a protozoal nucleic acid.

### Claim 24 (depends on 1)

The method of claim 1, comprising obtaining said target nucleic acid from one or more sample sources selected from the group consisting of: an environmental sample and a sample derived from a subject.

### Claim 25 (depends on 1)

The method of claim 1, wherein said nucleic acid sequence of said target sequence is compared to a database in order to determine the organismal source of said target nucleic acid.

### Claim 26 (depends on 25)

The method of claim 25, wherein the organismal source is identified at one or more taxonomic rank levels selected from the group consisting of: a Domain, a Superphylum, a Superdivision, a Superclass, a Superorder, a Superfamily, a Superspecies, a Kingdom, a Phylum, a Division, a Class, a Legion, an Order, a Family, a Tribe, a Genus, a Species, a Subkingdom, a Subphylum, a Subclass, a Cohort, a Suborder, a Subfamily, a Subtribe, a Subgenus, a Subspecies, an Infrakingdom, a Branch, an Infraphylum, an Infraclass, an Infraorder, an Alliance, an Infraspecies, a Microphylum, a Pan/class, and a Parvorder.

### Claim 27 (depends on 1)

The method of claim 1, wherein said capture primer comprises a bar-code sequence between said 3′ region and said 5′ region.