Method of determining the nucleotide sequence of oligonucleotides and DNA molecules

• US 10,214,774 B2
• Filed: 05/02/2014
• Issued: 02/26/2019
• Est. Priority Date: 05/01/1998
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Williams, Peter, Williams, Daniel J. B., Bloom, Linda, Taylor, Thomas J.
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US14/268,224
• Publication Number:
  US 20140335509A1
• Time in Patent Office: 1,761 Days
• Field of Search: 435 61, 435 911
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2533/101 Primer extension
• CPC Class Codes: C12Q 2563/103 luminescence
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2563/116 electrical properties of nucleic acids, e.g. impedance, conductivity or resistance
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)
• CPC Class Codes: C12Q 2565/629 being a microfluidic device
• CPC Class Codes: G01N 33/573 for enzymes or isoenzymes
• CPC Class Codes: G01N 33/6863 Cytokines, i.e. immune system proteins modifying a biological response such as cell growth proliferation or differentiation, e.g. TNF, CNF, GM-CSF, lymphotoxin, MIF or their receptors

Abstract

The present invention relates to a novel method for analyzing nucleic acid sequences based on real-time detection of DNA polymerase-catalyzed incorporation of each of the four nucleotide bases, supplied individually and serially in a microfluidic system, to a reaction cell containing a template system comprising a DNA fragment of unknown sequence and an oligonucleotide primer. Incorporation of a nucleotide base into the template system can be detected by any of a variety of methods including but not limited to fluorescence and chemiluminescence detection. Alternatively, microcalorimetic detection of the heat generated by the incorporation of a nucleotide into the extending template system using thermopile, thermistor and refractive index measurements can be used to detect extension reactions.

Claims

1. A method for phase error compensation during nucleic acid sequencing, comprising:

providing a plurality of template nucleic acid strands;

performing a first series of sequential nucleotide incorporation reactions resulting in one or more nucleotide incorporations into the plurality of template nucleic acid strands, the nucleotide incorporation reactions using a sequence of individual deoxynucleoside triphosphates introduced to react with the template nucleic acid strands;

after each incorporation reaction detecting a signal transmitted from the incorporation of the one or more nucleotides, the signal having an amplitude corresponding to a number of nucleotide incorporations;

in response to identifying an error component of the detected signal that is attributable to a fraction of the template nucleic acid strands that are out of phase based on extension of the template nucleic acids strands resulting from nucleotide incorporations, subtracting the error component of the detected signal from the detected signal to obtain a corrected detected signal, thereby maintaining the sequencing of the plurality of template nucleic acid strands.

2. The method of claim 1, wherein the plurality of template nucleic acid strands are hybridized to a primer.

3. The method of claim 1, wherein the sequence of deoxynucleoside triphosphates introduced to react with the template nucleic acid strands comprises each of four differing deoxynucleoside triphosphates.

4. The method of claim 1, wherein the fraction of the template nucleic acid strands that are out of phase trail behind in extension based on nucleotide incorporations relative to an in-phase fraction of the template nucleic acid strands because of extension failures.

5. The method of claim 4, wherein identifying the error component of the detected signal comprises quantifying the error component by measuring out of phase signals and monitoring a percentage associated with the fraction of the template nucleic acid strands that trail behind in extension.

6. The method of claim 4, wherein identifying the error component of the detected signal comprises determining a size of the fraction of the template nucleic acid strands having undergone extension failure by prediction based on simulation of occurrences of extension failures.

7. The method of claim 4, further comprising controlling conditions of the initial and subsequent nucleotide incorporation reactions to tolerate a higher probability of extension failures while minimizing the probability of misincorporations, and countering the increase in extension failures using computer-aided signal discrimination.

8. The method of claim 1, wherein the fraction of the template nucleic acid strands that are out of phase lead in extension resulting from nucleotide incorporations relative to an in-phase fraction of the template nucleic acid strands because of incorrect extensions.

9. The method of claim 8, wherein identifying an error component of the detected signal comprises retroactively estimating the effects of the fraction of the template nucleic acid strands having undergone incorrect extension.

10. A method for phase error compensation during nucleic acid sequencing, comprising:

providing a plurality of template nucleic acid strands;

performing a first series of sequential nucleotide incorporation reactions resulting in one or more nucleotide incorporations into the plurality of template nucleic acid strands, the series of sequential nucleotide incorporation reactions using a sequence of individual deoxynucleoside triphosphates introduced to react with the template nucleic acid strands;

after each incorporation reaction detecting a signal transmitted from the incorporation of the one or more nucleotides, the signal having an amplitude corresponding to a number of nucleotide incorporations;

in response to identifying an error component of the detected signal that is attributable to a fraction of the template nucleic acid strands that are out of phase based on extension of the template nucleic acids strands resulting from nucleotide incorporations, subtracting the error component of the detected signal from the detected signal to obtain a corrected detected signal, wherein the error component of the detected signal corresponds to a fraction of the template nucleic acid strands that are out of phase relative to an in-phase fraction of the template nucleic acid strands because of extension failures; and

maintaining sequencing of the plurality of template nucleic acid strands as a result of the subtracting.

11. The method of claim 10, wherein the sequence of individual deoxynucleoside triphosphates comprises each of four differing deoxynucleoside triphosphates.

12. The method of claim 10, wherein identifying the error component of the detected signal comprises quantifying the error component by measuring out of phase signals and monitoring a percentage associated with the trailing fraction of the template nucleic acid strands.

13. The method of claim 10, wherein identifying the error component of the detected signal comprises determining a size of the fraction of the template nucleic acid strands that trail behind in extension in response to having undergone extension failure by prediction based on simulation of occurrences of extension failures.

14. The method of claim 10, further comprising controlling conditions of the initial and subsequent series of sequential nucleotide incorporation reactions to tolerate a higher probability of extension failures while minimizing the probability of misincorporations, and countering the increase in extension failures using computer-aided signal discrimination.

15. A method for phase error compensation during nucleic acid sequencing, comprising:

providing a plurality of template nucleic acid strands;

performing a first series of sequential nucleotide incorporation reactions resulting in one or more nucleotide incorporations into the plurality of template nucleic acid strands, the first series of sequential nucleotide incorporation reactions using a sequence of individual deoxynucleoside triphosphates introduced to react with the template nucleic acid strands;

after each incorporation reaction detecting a signal transmitted from the incorporation of the one or more nucleotides, the signal having an amplitude that varies based on a number of nucleotide incorporations;

in response to identifying an error component of the detected signal that is attributable to a fraction of the template nucleic acid strands that are out of phase based on extension of the template nucleic acids strands resulting from nucleotide incorporations, subtracting the error component of the detected signal from the detected signal to obtain a corrected detected signal, wherein the error component of the detected signal corresponds to a fraction of the template nucleic acid strands that are out of phase relative to an in-phase fraction of the template nucleic acid strands because of incorrect extensions, thereby maintaining the sequencing of the plurality of template nucleic acid strands.

16. The method of claim 15, wherein identifying an error component of the detected signal comprises retroactively estimating the effects of the fraction of the template nucleic acid strands having undergone incorrect extension.