# US 10,246,705 B2 · Linking sequence reads using paired code tags

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- Number: US 10,246,705 B2
- Document ID: US10246705B2
- Status: Granted
- Kind: B2
- Application number: 15/159,588
- Filed: 2016-05-19
- Published: 2016-09-01
- Granted: 2019-04-02
- Earliest claimed: 2011-02-10
- Assignees: Ilumina, Inc.
- Applicants: Illumina, Inc.
- Inventors: Frank J. Steemers; Kevin L. Gunderson; Thomas Royce; Natasha Pignatelli; Igor Goryshin; Nicholas Caruccio
- Web page: https://patentgrep.com/patent/US10246705B2

## CPC

- C12N 15/1082: {Preparation or screening gene libraries by chromosomal integration of polynucleotide sequences, HR-, site-specific-recombination, transposons, viral vectors}
- C12Q 1/6869: Methods for sequencing
- C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- 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

Artificial transposon sequences having code tags and target nucleic acids containing such sequences. Methods for making artificial transposons and for using their properties to analyze target nucleic acids.

## Claims

### Claim 1

An artificial transposon, comprising:
a first transposase recognition site,
a second transposase recognition site,
a barcode disposed therebetween, wherein the barcode comprises a double-stranded nucleic acid sequence comprising
a first strand barcode and
a second strand barcode, wherein the first strand barcode and the second strand barcode comprise non-complementary sequences; and
a fragmentation site disposed within the first strand barcode and the second strand barcode.

### Claim 2 (depends on 1)

The transposon of claim 1, wherein the first transposase recognition site comprises a hyperactive Tn5 transposase recognition site.

### Claim 3 (depends on 1)

The transposon of claim 1, wherein the first transposase recognition site comprises a Mu transposase recognition site.

### Claim 4 (depends on 1)

The transposon of claim 1, wherein the first transposase recognition site comprises an IS911 transposase recognition site.

### Claim 5 (depends on 1)

The transposon of claim 1, further comprising at least one universal primer site.

### Claim 6 (depends on 1)

An isolated template nucleic acid, comprising at least a portion of a target nucleic acid or copy thereof and at least a first transposon and second transposon of claim 1, wherein the barcode of the first transposon is different from the barcode of the second transposon.

### Claim 7 (depends on 1)

The transposon of claim 1, wherein both the first strand barcode and the second strand barcode are at least four nucleotides in length.

### Claim 8 (depends on 1)

The transposon of claim 1, wherein the fragmentation site comprises a nickase recognition site.

### Claim 9

A DNA library preparation kit, comprising:
a plurality of artificial transposons, wherein each artificial transposon of the plurality of artificial transposon comprises:
a first transposase recognition site;
a second transposase recognition site;
a barcode disposed therebetween, wherein the barcode comprises a double-stranded nucleic acid sequence comprising
a first strand barcode and
a second strand barcode, wherein the first strand barcode and the second strand barcode comprise non-complementary sequences; and
a fragmentation site disposed within the first strand barcode and the second strand barcode; and
wherein each barcode of each artificial transposon of the plurality of artificial transposons is distinguishable from one another.

### Claim 10 (depends on 9)

The DNA library preparation kit of claim 9, wherein both the first strand barcode and the second strand barcode are at least four nucleotides in length.