Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library regeneration
First Claim
Patent Images
1. A method for enriching for a nucleic acid sequence of interest in a sample comprising nucleic acids, the method comprising:
- (a) fragmenting nucleic acids in the sample comprising the nucleic acids, thereby generating nucleic acid fragments, wherein the nucleic acid fragments comprise the nucleic acid sequence of interest;
(b) ligating a first adaptor sequence to a 5′
end of the nucleic acid fragments, thereby generating nucleic acid fragments ligated to the first adaptor sequence;
(c) purifying the nucleic acid fragments ligated to the first adaptor sequence;
(d) annealing one or more oligonucleotides in solution to the nucleic acid sequence of interest in the purified nucleic acid fragments ligated to the first adaptor sequence, wherein the one or more oligonucleotides in solution comprise a 3′
portion with at least 10 bases that are complementary to the nucleic acid sequence of interest and a 5′
tail, wherein the 5′
tail comprises a second adaptor sequence non-complementary to the sequence of interest;
(e) extending the one or more oligonucleotides annealed to the nucleic acid sequence of interest in the nucleic acid fragments ligated to the first adaptor sequence with a polymerase in a reaction mixture, wherein the reaction mixture does not comprise a primer that anneals to sequence complementary to the first adaptor sequence, thereby generating one or more oligonucleotide extension products comprising sequence complementary to the ligated first adaptor sequence at a first end, sequence complementary to the nucleic acid sequence of interest, and the second adaptor sequence at a second end;
(f) amplifying the one or more oligonucleotide extension products using a first primer that anneals to the complement of the first adaptor sequence and a second primer that anneals to a complement of the second adaptor sequence to enrich for the nucleic acid sequence of interest, wherein products of the amplifying comprise a 3′
end with sequence complementary to a sequence on a surface, thereby providing an enriched nucleic acid sequence of interest;
(g) annealing a strand of the products of the amplifying to the sequence on the surface using the 3′
end with sequence complementary to the sequence on the surface; and
(h) sequencing the enriched nucleic acid sequence of interest on a massively parallel sequencing platform.
4 Assignments
0 Petitions
Accused Products
Abstract
The present invention provides methods, compositions and kits for targeted nucleic acid sequence enrichment in a nucleic acid sample and for high efficiency nucleic acid library generation for next generation sequencing (NGS). Specifically, the methods, compositions and kits provided herein are useful for the production and capture of amplification-ready, target-specific and strand-specific regions of interest from nucleic acid samples containing complex DNA.
375 Citations
37 Claims
-
1. A method for enriching for a nucleic acid sequence of interest in a sample comprising nucleic acids, the method comprising:
-
(a) fragmenting nucleic acids in the sample comprising the nucleic acids, thereby generating nucleic acid fragments, wherein the nucleic acid fragments comprise the nucleic acid sequence of interest; (b) ligating a first adaptor sequence to a 5′
end of the nucleic acid fragments, thereby generating nucleic acid fragments ligated to the first adaptor sequence;(c) purifying the nucleic acid fragments ligated to the first adaptor sequence; (d) annealing one or more oligonucleotides in solution to the nucleic acid sequence of interest in the purified nucleic acid fragments ligated to the first adaptor sequence, wherein the one or more oligonucleotides in solution comprise a 3′
portion with at least 10 bases that are complementary to the nucleic acid sequence of interest and a 5′
tail, wherein the 5′
tail comprises a second adaptor sequence non-complementary to the sequence of interest;(e) extending the one or more oligonucleotides annealed to the nucleic acid sequence of interest in the nucleic acid fragments ligated to the first adaptor sequence with a polymerase in a reaction mixture, wherein the reaction mixture does not comprise a primer that anneals to sequence complementary to the first adaptor sequence, thereby generating one or more oligonucleotide extension products comprising sequence complementary to the ligated first adaptor sequence at a first end, sequence complementary to the nucleic acid sequence of interest, and the second adaptor sequence at a second end; (f) amplifying the one or more oligonucleotide extension products using a first primer that anneals to the complement of the first adaptor sequence and a second primer that anneals to a complement of the second adaptor sequence to enrich for the nucleic acid sequence of interest, wherein products of the amplifying comprise a 3′
end with sequence complementary to a sequence on a surface, thereby providing an enriched nucleic acid sequence of interest;(g) annealing a strand of the products of the amplifying to the sequence on the surface using the 3′
end with sequence complementary to the sequence on the surface; and(h) sequencing the enriched nucleic acid sequence of interest on a massively parallel sequencing platform. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22)
-
-
23. A method for enriching for a nucleic acid sequence of interest from a library, wherein the library comprises nucleic acid inserts comprising the nucleic acid sequence of interest, wherein the nucleic acid inserts have a first adaptor sequence attached on a first end and a second adaptor sequence attached on a second end, the method comprising:
-
(a) denaturing the nucleic acid inserts with the first adaptor sequence on the first end and the second adaptor sequence on the second end, thereby generating a library of single-stranded nucleic acid inserts with the first adaptor sequence on a first end and the second adaptor sequence on a second end; (b) annealing one or more oligonucleotides in solution to the sequence of interest in the single-stranded nucleic acid inserts with the first adaptor sequence on the first end and the second adaptor sequence on the second end, wherein the one or more oligonucleotides in solution comprise a 3′
portion with at least 10 bases designed to be complementary to the nucleic acid sequence of interest present in the nucleic acid inserts and a 5′
tail, wherein the 5′
tail comprises a third adaptor sequence, wherein the third adaptor sequence is distinct from the first adaptor sequence and the second adaptor sequence, and the 5′
tail is non-complementary to the sequence of interest;(c) extending the one or more oligonucleotides with a polymerase in a reaction mixture, wherein the reaction mixture does not comprise a primer that anneals to sequence complementary to the first adaptor sequence or the second adaptor sequence, thereby generating one or more oligonucleotide extension products comprising sequence complementary to the first adaptor sequence at a first end, sequence complementary to the nucleic acid sequence of interest, and the third adaptor sequence at a second end; (d) amplifying the one or more oligonucleotide extension products using a first primer that anneals to the complement of the first adaptor sequence and a second primer that anneals to a complement of the third adaptor sequence to enrich for the nucleic acid sequence of interest, wherein products of the amplifying comprise a 3′
end with sequence complementary to a sequence on a surface, thereby providing an enriched nucleic acid sequence of interest;(e) purifying the products of the amplifying; (f) annealing a strand of the purified products of the amplifying to the sequence on the surface using the 3′
end with sequence complementary to the sequence on the surface; and(g) sequencing the enriched nucleic acid sequence of interest on a massively parallel sequencing platform. - View Dependent Claims (24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37)
-
Specification