Sequential sequencing
First Claim
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1. A method, comprising:
- coupling a nucleic acid template strand to a solid support in a sequencing platform;
sequencing the template strand using a first primer to produce a first sequencing read, the first primer comprising a 3′
portion that anneals to a first binding site in the template strand;
removing the first primer and an extension product from the template strand;
annealing a second primer to a genomic location in the template strand that is more than 5 nucleotides away from a binding site of the first primer, wherein a 3′
portion of the second primer is complementary to the genomic location in the template strand; and
sequencing the template strand using the second primer to produce a second sequencing read, wherein at least one of the sequencing steps comprises sequencing by synthesis.
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Abstract
Described herein are improved methods, compositions and kits for next generation sequencing (NGS). The methods, compositions and kits described herein enable phasing of two or more nucleic acid sequences in a sample, i.e. determining whether the nucleic acid sequences (which can comprise regions of sequence variation) are located on the same chromosome and/or the same chromosomal fragment. Phasing information can be obtained by performing multiple, successive sequencing reactions from the same immobilized nucleic acid template. The methods, compositions and kits provided herein can be useful, for example, for haplotyping, SNP phasing, or for determining downstream exons in RNA-seq.
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Citations
17 Claims
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1. A method, comprising:
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coupling a nucleic acid template strand to a solid support in a sequencing platform; sequencing the template strand using a first primer to produce a first sequencing read, the first primer comprising a 3′
portion that anneals to a first binding site in the template strand;removing the first primer and an extension product from the template strand; annealing a second primer to a genomic location in the template strand that is more than 5 nucleotides away from a binding site of the first primer, wherein a 3′
portion of the second primer is complementary to the genomic location in the template strand; andsequencing the template strand using the second primer to produce a second sequencing read, wherein at least one of the sequencing steps comprises sequencing by synthesis. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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Specification