DNA sequencing

• US 10,544,454 B2
• Filed: 05/02/2013
• Issued: 01/28/2020
• Est. Priority Date: 05/02/2012
• Status: Active Grant

• Current Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Original Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Inventors: Eshoo, Mark W.
• Primary Examiner(s): Chunduru, Suryaprabha
• Application Number:
  US14/398,304
• Publication Number:
  US 20150111763A1
• Time in Patent Office: 2,462 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/20 Sequence assembly

Abstract

Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using two or more labels and signal ratios to distinguish bases.

Claims

1. A method for sequencing a target nucleic acid and a calibration oligonucleotide, the method comprising:

a) determining a signal ratio produced from a plurality of a nucleotide base in a calibration oligonucleotide in which a first fraction of said plurality of said nucleobase is labeled with a first label and a second fraction of said plurality of said nucleobase is labeled with a second different label, wherein each nucleotide base is labeled at a specific known ratio of said first and said second different labels, wherein said specific known ratios differ between a plurality of nucleotide bases in said calibration oligonucleotide, wherein said calibration oligonucleotide comprises each of four different bases in known order;

b) determining a signal ratio produced from a plurality of a nucleotide base in said target nucleic acid in which a first fraction of said plurality of said nucleobase is labeled with a first label and a second fraction of said plurality of said nucleobase is labeled with a second different label, wherein each nucleotide base is labeled at a specific known ratio of said first and said different labels, wherein said specific known ratios differ between a plurality of nucleotide bases in said target nucleic acid, wherein the same said nucleotide base in said calibration oligonucleotide and in said target nucleic acid is labeled with the same known ratio of said two different labels; and

c) associating said signal ratios with said nucleotide bases in said calibration oligonucleotide and in said target nucleic acid to identify said nucleotide bases in said calibration oligonucleotide and in said target nucleic acid wherein the method for sequencing said calibration oligonucleotide and said target nucleic acid is ensemble sequencing by synthesis wherein the calibration oligonucleotide sequence and the target sequence are determined by detecting said ratio of signals produced by said two labels after each base incorporation.

2. The method of claim 1 wherein the signal ratio produced by the plurality of the nucleotide base is detectably different than a second signal ratio produced by a second plurality of a second nucleotide base.

3. The method of claim 1 wherein the first fraction of the plurality produces a first signal having a first intensity and the second fraction of the plurality produces a second signal having a second intensity and the signal ratio is a ratio of the first intensity relative to the second intensity.

4. The method of claim 3 wherein the first intensity is a first fluorescence emission amplitude and the second intensity is a second fluorescence emission amplitude.

5. The method of claim 3 wherein the first intensity is a first peak height and the second intensity is a second peak height.

6. The method of claim 1 further comprising providing a first plurality of a first nucleotide base and a second plurality of a second nucleotide base, wherein a first ratio of a first portion of the first plurality labeled with the first label relative to a second portion of the first plurality labeled with the second label is detectably different than a second ratio of a third portion of the second plurality labeled with the first label relative to a fourth portion of the second plurality labeled with the second label.

7. The method of claim 1 further comprising providing a first plurality of a first nucleotide base, a second plurality of a second nucleotide base, a third plurality of a third nucleotide base, and a fourth plurality of a fourth nucleotide base, wherein a first ratio of a first portion of the first plurality labeled with the first label relative to a second portion of the first plurality labeled with the second label, a second ratio of a third portion of the second plurality labeled with the first label relative to a fourth portion of the second plurality labeled with the second label, a third ratio of a fifth portion of the third plurality labeled with the first label relative to a sixth portion of the third plurality labeled with the second label, and a fourth ratio of a seventh portion of the fourth plurality labeled with the first label relative to an eighth portion of the fourth plurality labeled with the second label are all detectably different from each other.

8. The method of claim 7 wherein the first nucleotide base is A, the second nucleotide base is C, the third nucleotide base is G, and the fourth nucleotide base is T.

9. The method of claim 7 wherein the first label is a first fluorescent moiety with an emission peak at a first wavelength and the second label is a second fluorescent moiety with an emission peak at a second wavelength.

10. The method of claim 1 further comprising monitoring a first channel and a second channel, wherein the first label produces a signal in the first channel and the second label produces a signal in the second channel.

11. The method of claim 1 further comprising incorporating by polymerization the plurality of the nucleotide base into a plurality of a nucleic acid that is complementary to the target nucleic acid.

12. The method of claim 10 comprising monitoring with an optical device.

13. The method of claim 1 further comprising providing a calibration oligonucleotide comprising a known sequence.

14. The method of claim 1 further comprising analyzing a dataset of ordered signal ratios to produce a nucleotide sequence of the target nucleic acid.