Efficient shotgun sequencing methods
First Claim
1. A method for sequencing a target nucleic acid comprising:
- (a) sequencing the target nucleic acid to produce primary sequence information for the target nucleic acid;
(b) identifying missing sequences and/or low confidence sequences in the target nucleic acid from the primary sequence information determined in step (a);
(c) synthesizing a plurality of target-specific oligonucleotides,each corresponding to a sequence identified in step (b);
(d) hybridizing said plurality of target-specific oligonucleotides to a library of fragments of the target nucleic acid;
(e) hybridizing universal oligonucleotides to the library of fragments;
(f) ligating the universal oligonucleotides that have hybridized to the target nucleic acids to adjacently hybridized target-specific oligonucleotides, thereby producing universal oligonucleotide;
target-specific oligonucleotide ligation products; and
(g) preparing an enriched library of fragments of the target nucleic acid by capturing fragments of the target nucleic acid from the library that are hybridized to the universal oligonucleotide;
target-specific oligonucleotide ligation products.
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Abstract
Methods are provided for efficient shotgun sequencing to allow efficient selection and sequencing of nucleic acids of interest contained in a library. The nucleic acids of interest can be defined any time before or after preparation of the library. One example of nucleic acids of interest is missing or low confidence genome sequences resulting from an initial sequencing procedure. Other nucleic acids of interest include subsets of genomic DNA, RNA or cDNAs (exons, genes, gene sets, transciptomes). By designing an efficient (simple to implement, speedy, high specificity, low cost) selection procedure, a more complete sequence is achieved with less effort than by using highly redundant shotgun sequencing in an initial sequencing procedure.
142 Citations
25 Claims
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1. A method for sequencing a target nucleic acid comprising:
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(a) sequencing the target nucleic acid to produce primary sequence information for the target nucleic acid; (b) identifying missing sequences and/or low confidence sequences in the target nucleic acid from the primary sequence information determined in step (a); (c) synthesizing a plurality of target-specific oligonucleotides, each corresponding to a sequence identified in step (b); (d) hybridizing said plurality of target-specific oligonucleotides to a library of fragments of the target nucleic acid; (e) hybridizing universal oligonucleotides to the library of fragments; (f) ligating the universal oligonucleotides that have hybridized to the target nucleic acids to adjacently hybridized target-specific oligonucleotides, thereby producing universal oligonucleotide;
target-specific oligonucleotide ligation products; and(g) preparing an enriched library of fragments of the target nucleic acid by capturing fragments of the target nucleic acid from the library that are hybridized to the universal oligonucleotide;
target-specific oligonucleotide ligation products.- View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18)
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19. A method for sequencing a target nucleic acid, comprising:
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(a) obtaining nucleotide sequence information for at least a portion of the target nucleic acid; (b) identifying missing sequences and/or low confidence sequences in the nucleotide sequence information; (c) synthesizing a plurality of target-specific oligonucleotides, each corresponding to a sequence identified in step (b); (d) hybridizing said plurality of target-specific oligonucleotides to a library of fragments of the target nucleic acid; (e) hybridizing universal oligonucleotides to the library of fragments; (f) ligating the universal oligonucleotides that have hybridized to the target nucleic acids to adjacently hybridized target-specific oligonucleotides, thereby producing universal oligonucleotide;
target-specific oligonucleotide ligation products;(g) preparing an enriched library of fragments of the target nucleic acid by selecting fragments of the target nucleic acid from the library that are hybridized to the universal oligonucleotide;
target-specific oligonucleotide ligation products;(h) sequencing fragments in the enriched library; and (i) assembling sequence information determined in step (h) with the sequence information obtained in step (a), thereby obtaining more complete sequence information. - View Dependent Claims (20, 21, 22, 23, 24)
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25. A computer controlled apparatus configured and programmed for sequencing a genome of a human organism according to a method that comprises the following steps:
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(a) obtaining nucleotide sequence information for at least a portion of the genome; (b) identifying missing sequences and/or low confidence sequences in the nucleotide sequence information; (c) synthesizing a plurality of target-specific oligonucleotides, each corresponding to a sequence identified in step (b); (d) hybridizing said plurality of target-specific oligonucleotides to a library of fragments of the genome; (e) hybridizing universal oligonucleotides to the library of fragments; (f) ligating the universal oligonucleotides that have hybridized to the target nucleic acids to adjacently hybridized sequence-specific oligonucleotides, thereby producing universal oligonucleotide;
sequence-specific oligonucleotide ligation products;(g) preparing an enriched library of fragments of the genome by capturing fragments of the genome nucleic acid from the library that are hybridized to the universal oligonucleotide;
sequence-specific oligonucleotide ligation products;(h) sequencing fragments in the enriched library; and (i) assembling sequence information determined in step (h) with the primary sequence information obtained from step (a).
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Specification