METHODS AND COMPOSITIONS FOR ENRICHMENT OF TARGET POLYNUCLEOTIDES
First Claim
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1. A method of enriching a plurality of different target polynucleotides in a sample, the method comprising:
- (a) joining an adapter oligonucleotide to each of the target polynucleotides, wherein the adapter oligonucleotide comprises sequence Y;
(b) hybridizing a plurality of different oligonucleotide primers to adapted target polynucleotides, wherein each oligonucleotide primer comprises sequence Z and sequence W;
wherein sequence Z is common among all oligonucleotide primers; and
further wherein sequence W is different for each different oligonucleotide primer, is positioned at the 3′
end of each oligonucleotide primer, and is complementary to a sequence comprising a causal genetic variant or a sequence within 200 nucleotides of a causal genetic variant;
(c) in an extension reaction, extending the oligonucleotide primers along the adapted target polynucleotides to produce extended primers comprising sequence Z and sequence Y′
, wherein sequence Y′
is complementary to sequence Y; and
(d) exponentially amplifying the purified extension products using a pair of amplification primers comprising (i) a first amplification primer comprising sequence V and sequence Z, wherein sequence Z is positioned at the 3′
end of the first amplification primer; and
(ii) a second amplification primer comprising sequence X and sequence Y, wherein sequence Y is positioned at the 3′
end of the second amplification primer;
wherein sequences W, Y, and Z are different sequences and comprise 5 or more nucleotides each.
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Abstract
The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant.
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Citations
38 Claims
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1. A method of enriching a plurality of different target polynucleotides in a sample, the method comprising:
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(a) joining an adapter oligonucleotide to each of the target polynucleotides, wherein the adapter oligonucleotide comprises sequence Y; (b) hybridizing a plurality of different oligonucleotide primers to adapted target polynucleotides, wherein each oligonucleotide primer comprises sequence Z and sequence W;
wherein sequence Z is common among all oligonucleotide primers; and
further wherein sequence W is different for each different oligonucleotide primer, is positioned at the 3′
end of each oligonucleotide primer, and is complementary to a sequence comprising a causal genetic variant or a sequence within 200 nucleotides of a causal genetic variant;(c) in an extension reaction, extending the oligonucleotide primers along the adapted target polynucleotides to produce extended primers comprising sequence Z and sequence Y′
, wherein sequence Y′
is complementary to sequence Y; and(d) exponentially amplifying the purified extension products using a pair of amplification primers comprising (i) a first amplification primer comprising sequence V and sequence Z, wherein sequence Z is positioned at the 3′
end of the first amplification primer; and
(ii) a second amplification primer comprising sequence X and sequence Y, wherein sequence Y is positioned at the 3′
end of the second amplification primer;wherein sequences W, Y, and Z are different sequences and comprise 5 or more nucleotides each. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
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20. A method of enriching a plurality of different target polynucleotides in a sample, the method comprising:
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(a) hybridizing a plurality of different oligonucleotide primers to the target polynucleotides, wherein each oligonucleotide primer comprises sequence Z and sequence W;
wherein sequence Z is common among all oligonucleotide primers; and
further wherein sequence W is different for each different oligonucleotide primer, is positioned at the 3′
end of each oligonucleotide primer, and is complementary to a sequence comprising a causal genetic variant or a sequence within 200 nucleotides of a causal genetic variant;(b) in an extension reaction, extending the oligonucleotide primers along the target polynucleotides to produce extended primers; (c) joining an adapter oligonucleotide to each extended primer, wherein the adapter oligonucleotide comprises sequence Y′
, and further wherein sequence Y′
is the complement of a sequence Y; and(d) exponentially amplifying the purified extension products using a pair of amplification primers comprising (i) a first amplification primer comprising sequence V and sequence Z, wherein sequence Z is positioned at the 3′
end of the first amplification primer; and
(ii) a second amplification primer comprising sequence X and sequence Y, wherein sequence Y is positioned at the 3′
end of the second amplification primer;wherein sequences W, Y, and Z are different sequences and comprise 5 or more nucleotides each. - View Dependent Claims (21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38)
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Specification