Methods and compositions for tagging and identifying polynucleotides
First Claim
1. A method of sequencing comprising:
- sequencing a plurality of genomic fragments, wherein the genomic fragments are obtained from a plurality of different sources, and wherein;
i. each of said genomic fragments comprises an oligonucleotide tag that comprises a unique nucleotide sequence that indicates from which source a genomic fragment is derived; and
, separate from said unique nucleotide sequence, a binding site for a sequencing primer;
ii. said sequencing of the plurality of genomic fragments is done using said sequencing primer; and
iii. said genomic fragments correspond to one or more selected portions of a genome that have been isolated from a pooled genomic sample by specific hybridization;
to obtain, for each of the sequenced fragments, the unique nucleotide sequence of an oligonucleotide tag and the nucleotide sequence of at least a portion of a genomic fragment.
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Abstract
The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g. by hybridization of the oligonucleotide tag to its tag complement on an addressable array; or such analysis can be carried out serially by successive hybridizations of labeled word complements.
309 Citations
13 Claims
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1. A method of sequencing comprising:
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sequencing a plurality of genomic fragments, wherein the genomic fragments are obtained from a plurality of different sources, and wherein; i. each of said genomic fragments comprises an oligonucleotide tag that comprises a unique nucleotide sequence that indicates from which source a genomic fragment is derived; and
, separate from said unique nucleotide sequence, a binding site for a sequencing primer;ii. said sequencing of the plurality of genomic fragments is done using said sequencing primer; and iii. said genomic fragments correspond to one or more selected portions of a genome that have been isolated from a pooled genomic sample by specific hybridization; to obtain, for each of the sequenced fragments, the unique nucleotide sequence of an oligonucleotide tag and the nucleotide sequence of at least a portion of a genomic fragment. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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Specification