Enrichment of nucleic acids by complementary capture
AssigneeThe Johns Hopkins University
InventorsBert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Jian Wu
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Abstract
Assays can be used to detect mutations found in neoplasms of the pancreas, as well as for other neoplasms and other uses. Nucleic acids can be captured from body fluids such as cyst fluids. Thousands of oligonucleotides can be synthesized in parallel, amplified and ligated together. The ligated products can be further amplified. The amplified, ligated products are used to capture complementary DNA sequences, which can be analyzed, for example by massively parallel sequencing.
Claims21
A probe set for nucleic acid enrichment, the probe set comprising:
- a plurality of concatamers, wherein each concatamer comprises a plurality of subunits, each subunit comprising, in a 5′ to 3′ direction:
- a 5′ universal priming site;
- a portion complementary to plus or minus strands of a target nucleic acid;
- and a 3′ universal priming site;
- wherein the probe set is complementary to both the plus and minus strands of the target nucleic acid.
A method for enrichment of nucleic acid, the method comprising:
- providing a probe set comprising a plurality of concatamers wherein each concatamer comprises a plurality of subunits, each subunit comprising, in a 5′ to 3′ direction:
- a 5′ universal priming site, a portion complementary to plus or minus strands of a target nucleic acid, and a 3′ universal priming site;
- wherein the probe set is complementary to both the plus and minus strands of the target nucleic acid;
- contacting the plurality of concatamers with a sample comprising the target nucleic acid to capture the target nucleic acid;
- and
- removing uncaptured nucleic acids to enrich for the target nucleic acid.
A probe set for nucleic acid enrichment, the probe set comprising:
- a plurality of concatamers, wherein each concatamer comprises a plurality of subunits, each subunit comprising, in a 5′ to 3′ direction:
- a 5′ universal priming site;
- a portion complementary to plus or minus strands of a target nucleic acid;
- and a 3′ universal priming site,
- wherein the portions complementary to the plus or minus strands of the target nuclei acid have at least a 33-base overlap in a targeted portion of the plus or minus strands of the target nucleic acid.
Dependencies are inferred from the claim text.