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US 11,993,772 B2Granted
Linking sequence reads using paired code tags
AssigneeIllumina, Inc.
InventorsFrank J. Steemers, Kevin L Gunderson, Thomas Royce, Natasha Pignatelli, Igor Goryshin, Nicholas Caruccio
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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.
Claims17
A method for preparing a library of template nucleic acids comprising:
- (a) contacting a target nucleic acid with a plurality of transposons under conditions such that a portion of the plurality of transposons are inserted into the target nucleic acid, wherein at least one transposon of the plurality of transposons comprises:
- a double-stranded first transposase recognition site;
- a double-stranded second transposase recognition site;
- a barcode disposed therebetween, wherein the barcode comprises:
- a first barcode sequence of the at least one transposon;
- a second barcode sequence of the at least one transposon;
- and
- a linker disposed between the first and second barcode sequences, wherein the linker comprises a first primer site, a second primer site and a non-amplifiable site disposed between the first and second primer sites;
- and
- (b) amplifying said target nucleic acid using one or both of the first primer site and the second primer site to separate the first barcode sequence from the second barcode sequence.
7 more elements
A method for preparing a library of template nucleic acids, comprising:
- (a) contacting a target nucleic acid with a plurality of transposons under conditions such that a portion of the plurality of transposons are inserted into the target nucleic acid, wherein at least one transposon of the plurality of transposons comprises:
- a double-stranded first transposase recognition site;
- a double-stranded second transposase recognition site
- a barcode disposed therebetween, wherein the barcode comprises:
- a first barcode sequence of the at least one transposon;
- a second barcode sequence of the at least one transposon;
- and
- a linker disposed between the first and second barcode sequences, wherein the linker comprises a first primer site, a second primer site and a non-amplifiable site disposed between the first and second primer sites,
- (b) hybridizing a primer to the first primer site;
- and
- (c) amplifying a portion of the at least one transposon.
8 more elements
A method of analyzing a target nucleic acid comprising:
- contacting a target nucleic acid with a plurality of transposons under conditions such that a portion of the plurality of transposons are inserted into the target nucleic acid to prepare the target nucleic acid for sequencing, wherein at least one transposon of the plurality of transposons comprises:
- a double-stranded first transposase recognition site;
- a double-stranded second transposase recognition site;
- and
- a barcode disposed therebetween, wherein the barcode comprises:
- a first barcode sequence of the at least one transposon;
- a second barcode sequence of the at least one transposon;
- and
- a linker disposed between the first and second barcode sequences, wherein the
- linker comprises a first primer site, a second primer site and a non-amplifiable
- site disposed between the first and second primer sites;
- hybridizing a primer to the first primer site;
- amplifying a portion of the at least one transposon to generate fragments of the target nucleic acid comprising the first barcode;
- obtaining sequence data from the fragments of the target nucleic acid including the portion of the at least one transposon comprising the first barcode;
- and
- assembling a representation of the target nucleic acid from the sequence data based on the first barcode sequence.
13 more elements
Dependencies are inferred from the claim text.