Compositions and methods for detecting rare sequence variants
First Claim
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1. A method of performing rolling circle amplification, the method comprising:
- (a) in a reaction mixture, circularizing starting template polynucleotides in a plurality of starting template polynucleotides to form a plurality of circular polynucleotides using a ligase enzyme, wherein each polynucleotide of the plurality of polynucleotides has a 5′
end and a 3′
end prior to circularizing;
(b) adding a heat labile protease to said reaction mixture to degrade the ligase enzyme; and
(c) amplifying the circular polynucleotides after step (b) without isolating the circular polynucleotides from said reaction mixture between steps (a) and (c) to produce amplified polynucleotides,wherein said method yields a higher level of recovery of the starting template polynucleotides as compared to performing a rolling circle amplification comprising steps (a) and (c) alone,wherein the higher level of recovery is evidenced by an increased library complexity, andwherein the increased library complexity is represented by an increased number of unique sequences amplified from said starting template polynucleotides.
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Abstract
In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, or two different sheared polynucleotides as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described methods.
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Citations
30 Claims
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1. A method of performing rolling circle amplification, the method comprising:
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(a) in a reaction mixture, circularizing starting template polynucleotides in a plurality of starting template polynucleotides to form a plurality of circular polynucleotides using a ligase enzyme, wherein each polynucleotide of the plurality of polynucleotides has a 5′
end and a 3′
end prior to circularizing;(b) adding a heat labile protease to said reaction mixture to degrade the ligase enzyme; and (c) amplifying the circular polynucleotides after step (b) without isolating the circular polynucleotides from said reaction mixture between steps (a) and (c) to produce amplified polynucleotides, wherein said method yields a higher level of recovery of the starting template polynucleotides as compared to performing a rolling circle amplification comprising steps (a) and (c) alone, wherein the higher level of recovery is evidenced by an increased library complexity, and wherein the increased library complexity is represented by an increased number of unique sequences amplified from said starting template polynucleotides. - 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, 24)
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25. A method of generating a sequencing library, comprising:
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(a) in a reaction mixture, circularizing individual starting template polynucleotides in a plurality of starting template polynucleotides to form a plurality of circular polynucleotides using a ligase enzyme, wherein each polynucleotide of the plurality of starting template polynucleotides has a 5′
end and a 3′
end prior to circularizing;(b) adding a heat labile protease to said reaction mixture to degrade the ligase enzyme; and (c) amplifying the circular polynucleotides after step (b) without isolating the circular polynucleotides from said reaction mixture between steps (a) and (c) to produce a sequencing library comprising amplified polynucleotides, wherein the method generates a sequencing library with a complexity that is at least one-fold greater than a control library generated by performing a method comprising steps (a) and (c) alone, without performing step (b). - View Dependent Claims (26, 27, 28, 29, 30)
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Specification