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Reagents, methods, and libraries for bead-based sequencing

a technology of bead-based sequencing and reagents, which is applied in the field of bead-based sequencing reagents, methods, and libraries, can solve the problems of limiting the speed and accuracy of sequencing in many contexts, requiring a time-consuming separation step, and proving difficult to identify reversible terminators that can be incorporated by polymerase with high efficiency, so as to achieve high throughput sequencing and efficient implementation of methods

Inactive Publication Date: 2009-07-16
APPL BIOSYSTEMS INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

These methods enable high-throughput sequencing by identifying nucleotides in each cycle without the need for fragment separation, improving speed and accuracy, and are suitable for rapid sequence determination, including identifying sequence variants relevant to personalized medicine.

Problems solved by technology

Although currently available sequencing technologies have allowed the achievement of major landmarks such as the sequencing of a number of complete genomes, these techniques have a number of disadvantages, and considerable need for improvement remains in a number of areas.
However, this step has proven to be a major bottleneck limiting both the speed and accuracy of sequencing in many contexts.
For example, CAE still requires a time-consuming separation step and still involves discrimination based on size, which can be inaccurate.
However, it has proven difficult to identify reversible terminators that can be incorporated by polymerase with high efficiency, probably due to the fact that given the small size of a nucleotide, modifications that affect the ability of the nucleotide to act as a terminator also affect its incorporation into a growing polynucleotide strand.
While avoiding the need for electrophoretic separation, pyrosequencing suffers from a large number of drawbacks that have as yet limited its widespread applicability (Franca, et al., Quarterly Reviews of Biophysics, 35(2):169-200, 2002).
Sequencing by hybridization has also been proposed as an alternative (U.S. Pat. No. 5,202,231; WO 99 / 60170; WO 00 / 56937; Drmanac, et al., Advances in Biochemical Engineering / Biotechnology, 77:76-101, 2002) but has a number of disadvantages including the potential for error in discriminating between highly similar sequences.
However, various technical hurdles remain to be overcome before realization of this potential (Stephan, et al., 2001).

Method used

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  • Reagents, methods, and libraries for bead-based sequencing
  • Reagents, methods, and libraries for bead-based sequencing
  • Reagents, methods, and libraries for bead-based sequencing

Examples

Experimental program
Comparison scheme
Effect test

example 1

Efficient Cleavage and Ligation of Phosphorothiolated Oligonucleotides

[0347]This example describes an experiment demonstrating efficient ligation and cleavage of extension oligonucleotides containing a 3′-S phosphorothiolate linkage.

[0348]Materials and Methods

[0349]Ligation Sequencing Protocol

[0350]Template Preparation: To demonstrate evaluate the potential of sequencing by cycled oligonucleotide ligation and cleavage and to explore the effect of variations in certain aspects of the method, two sets of model bead-based template populations were prepared. In preferred implementations, as described in the Examples, cycled oligonucleotide ligation and cleavage extends strands in the 3′→5′ direction. Therefore, to evaluate ligation efficiencies, model templates were bound to beads at the 5′ end and designed with the same binding region at the 3′ end. One set was comprised of short (70 bp) oligonucleotides bound to streptavidin-coated magnetic beads (1 micron) via a dual biotin moiety. E...

example 2

Efficient Cleavage and Ligation of Phosphorothiolated Oligonucleotides Containing Degeneracy-Reducing Nucleotides

[0363]A competing consideration to probe length, however, is the fidelity of the extended oligonucleotide and its effect on subsequent ligation efficiency. The fidelity of T4 DNA ligase has been shown to decrease rapidly following the 5th base after the junction (Luo et al., Nucleic Acid Res., 24: 3071-3078 and 3079-3085, 1996). If mismatches are introduced at the 5′ side of a new ligation junction, the ligation efficiency may be reduced by attrition, however, no dephasing or increase in background signal will be generated (a major obstacle encountered in polymerase-based sequencing by synthesis methods).

[0364]Probe sets should preferably be capable of hybridizing to any DNA sequence in order to permit de novo sequencing of uncharacterized DNA. However, the complexity of a labeled probe set grows exponentially with the length and number of 4-fold degenerate bases. In addi...

example 3

Fidelity of Probe Ligation

[0369]Bacterial NAD-dependent ligases, such as Taq DNA ligase, have been reported to have high sequence fidelity across ligation junctions, with mismatches on the 3′ side having essentially no nick-closure activity, but mismatches on the 5′ side being tolerated to some degree (Luo et al., Nucleic Acid Res., 24: 3071-3078 and 3079-3085, 1996). T4 DNA ligase, on the other hand, has been reported to be somewhat less stringent, allowing mismatches on both the 3′- and 5′-sides of the junction. It was therefore of interest to evaluate the fidelity of probe ligation with T4 DNA ligase in comparison to Taq DNA ligase in the context of our system.

[0370]We developed two methods to evaluate the sequence fidelity of ligated oligonucleotides using standard ABI sequencing technology. The first method was designed to clone and sequence ligation products. In this method, ligation extension products were attached to adapter sequences, cloned and transformed into bacteria. I...

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Abstract

The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled probes containing phosphorothiolate linkages. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application claims priority to and the benefit of provisional applications U.S. Ser. No. 60 / 649,294, filed Feb. 1, 2005; U.S. Ser. No. 60 / 656,599, filed Feb. 25, 2005; U.S. Ser. No. 60 / 673,749, filed Apr. 21, 2005, U.S. Ser. No. 60 / 699,541, filed Jul. 15, 2005, U.S. Ser. No. 60 / 722,526, filed Sep. 30, 2005, and U.S. Ser. No. 11 / 345,979, filed Feb. 1, 2006, all of which are herein incorporated by reference.BACKGROUND OF THE INVENTION[0002]Nucleic acid sequencing techniques are of major importance in a wide variety of fields ranging from basic research to clinical diagnosis. The results available from such technologies can include information of varying degrees of specificity. For example, useful information can consist of determining whether a particular polynucleotide differs in sequence from a reference polynucleotide, confirming the presence of a particular polynucleotide sequence in a sample, determining partial sequence informati...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/68
CPCB82Y15/00B82Y30/00C12Q1/6837C12Q1/6844C12Q1/6869C12Q2565/537C12Q2565/518C12Q2565/513C12Q2565/137C12Q2565/102C12Q2533/107C12Q2537/165G16B50/00C12Q1/68C12Q1/6874
Inventor MCKERNAN, KEVINBLANCHARD, ALANKOTLER, LEVCOSTA, GINA
Owner APPL BIOSYSTEMS INC
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