Chase Ligation Sequencing
First Claim
1. A method for determining a sequence of nucleotides in a template polynucleotide, the method comprising the steps of:
- (a) providing a population of probe-template duplexes, each duplex comprising an initializing oligonucleotide probe hybridized to a template polynucleotide, the initializing oligonucleotide probe having an extendable terminus;
(b) ligating a labeled oligonucleotide extension probe to at least a fraction of the extendable termini of the population of probe-template duplexes to form labeled extended probe-template duplexes;
(c) ligating an unlabeled oligonucleotide extension probe to at least a fraction of the extendable termini of the population of probe-template duplexes that do not have a labeled oligonucleotide extension probe ligated thereto to form unlabeled extended probe-template duplexes;
(d) identifying after step (b) and before step (e) at least one nucleotide in the template polynucleotide;
(e) generating an extendable terminus on the oligonucleotide extension probe portion of at least a fraction of the labeled extended probe-template duplexes and the unlabeled extended probe-template duplexes; and
(f) repeating steps (b), (c), (d), and (e) until a sequence of nucleotides in the template polynucleotide is determined.
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Accused Products
Abstract
In various embodiments, the present teachings provide sequencing methods which facilitate enhancing the efficiency of ligation and/or increasing sequencing reads. Various embodiments of the methods enable sequencing through template regions for which complementary labeled extension probes are unavailable or insufficient. In various embodiments, one or more rounds of ligation with unlabeled extension probes can be used in addition to a round of ligation with labeled extension probe. In various embodiments, for example, such methods can facilitate extension on template polynucleotides that do not bind labeled extension probe in the first round of ligation.
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Citations
44 Claims
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1. A method for determining a sequence of nucleotides in a template polynucleotide, the method comprising the steps of:
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(a) providing a population of probe-template duplexes, each duplex comprising an initializing oligonucleotide probe hybridized to a template polynucleotide, the initializing oligonucleotide probe having an extendable terminus; (b) ligating a labeled oligonucleotide extension probe to at least a fraction of the extendable termini of the population of probe-template duplexes to form labeled extended probe-template duplexes; (c) ligating an unlabeled oligonucleotide extension probe to at least a fraction of the extendable termini of the population of probe-template duplexes that do not have a labeled oligonucleotide extension probe ligated thereto to form unlabeled extended probe-template duplexes; (d) identifying after step (b) and before step (e) at least one nucleotide in the template polynucleotide; (e) generating an extendable terminus on the oligonucleotide extension probe portion of at least a fraction of the labeled extended probe-template duplexes and the unlabeled extended probe-template duplexes; and (f) repeating steps (b), (c), (d), and (e) until a sequence of nucleotides in the template polynucleotide is determined. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21)
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22. A method for determining information about a sequence of nucleotides in a template polynucleotide using a first collection of at least 2 distinguishably labeled extension probe families, the method comprising the steps of.
(a) providing a population of probe-template duplexes, each duplex comprising an initializing oligonucleotide probe hybridized to a template polynucleotide, the initializing oligonucleotide probe having an extendable terminus; -
(b) contacting the population of probe-template duplexes with a mixture of labeled oligonucleotide extension probes from at least 2 distinguishably labeled oligonucleotide extension probe families to ligate a labeled oligonucleotide extension probe to at least a fraction of the extendable termini of the population of probe-template duplexes to form labeled extended probe-template duplexes; (c) ligating an unlabeled oligonucleotide extension probe to at least a fraction of the extendable termini of the population of probe-template duplexes that do not have a labeled oligonucleotide extension probe or a second labeled oligonucleotide extension probe ligated thereto to form unlabeled extended probe-template duplexes; (d) detecting after step (b) and before step (e) the labels of at least a portion of the labeled extended probe-template duplexes; (e) generating an extendable terminus on the oligonucleotide extension probe portion of at least a fraction of the labeled extended probe-template duplexes and the unlabeled extended probe-template duplexes; (f) eliminating after step (d) and before step (g) one or more possibilities for the sequence of nucleotides in the template polynucleotide portion of the labeled extended probe-template duplexes based at least on the labels detected in step (d) to produce a list of potential sequences; and (g) repeating steps (b), (c), (d), (e), and (f) until a sequence of nucleotides in the template polynucleotide is determined. - View Dependent Claims (23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44)
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Specification