Systems for and methods of hybrid pyrosequencing

• US 8,901,043 B2
• Filed: 07/06/2012
• Issued: 12/02/2014
• Est. Priority Date: 07/06/2011
• Status: Expired due to Fees

• Current Assignee: Advanced Liquid Logic, Inc. (Illumina Incorporated)
• Original Assignee: Advanced Liquid Logic, Inc. (Illumina Incorporated)
• Inventors: Eckhardt, Allen E., Benton, Jonathan, Boles, Deborah
• Primary Examiner(s): Vivlemore, Tracy
• Assistant Examiner(s): Weiler, Karen S
• Application Number:
  US13/542,721
• Publication Number:
  US 20130178374A1
• Time in Patent Office: 879 Days
• Field of Search: None
• US Class Current: 506/7
• CPC Class Codes: C12N 15/1089 Design, preparation, screening or analysis of libraries using computer algorithms
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 1/701 Specific hybridization probes
• CPC Class Codes: C12Q 1/703 Viruses associated with AIDS
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR

Abstract

The systems and methods of the invention provide a guided approach to pyrosequencing (i.e., hybrid pyrosequencing). A de novo nucleic acid sequence may compared to a library of possible results and the next nucleotide to be dispensed is selected based on the comparison of the de novo sequence and the library of possible results. In another example, at least the first nucleotide to be dispensed is selected based on a query of a database(s) of non-sequence parameters (e.g., incidence of infection, diagnostic symptoms, sample source) and subsequent dispensations determined based on a comparison of the de novo sequence and the library of possible results (e.g., candidate sequences). The systems and methods of the invention may be performed using a droplet actuator.

Claims

1. A method for identifying a nucleic acid sequence in a sample by hybrid pyrosequencing, the method comprising:

(a) selecting a nucleotide to be dispensed to a sample comprising a primed DNA template and reagents sufficient for sequencing-by-synthesis of a de novo nucleic acid sequence to be identified, wherein selecting comprises querying a database of non-sequence parameters and/or comparing the de novo sequence to a library of candidate sequences, further wherein the query of the database of non-sequence parameters comprises using an algorithm to determine whether the non-sequence parameters comprising incidence of infection and organism type or diagnostic symptoms and organism type, or frequency of the nucleotide in the library of candidate sequences has the strongest predictive value, and selecting the nucleotide based on the strongest predictive value;

(b) controlling a dispenser to dispense the selected nucleotide to the sample;

(c) detecting a response signal to the dispensation;

(d) determining whether the dispensed nucleotide was incorporated or not incorporated;

(e) repeating steps (a)-(d) in response to determining that the dispensed nucleotide was not incorporated;

(f) in response to determining that the dispensed nucleotide was incorporated;

(i) comparing the de novo sequence to the library of candidate sequences; and

(ii) excluding candidate sequences that do not match the de novo sequence; and

(g) repeating steps (a)-(f) until the de novo sequence is uniquely identified, wherein a sequence and/or nonsequence parameter database is queried during each reaction cycle.

2. The method of claim 1, further comprising using a droplet actuator to implement steps (a)-(c),

(a) wherein step (b) further comprises controlling the dispenser to dispense:

(i) a first droplet comprising the primed DNA template immobilized on a bead;

(ii) a second droplet comprising the selected nucleotide and detection reagents; and

(iii) a third droplet comprising enzyme reagents;

(b) wherein the method further comprises on the droplet actuator;

(i) combining the first, second, and third droplets;

(ii) transporting the combined droplet to a detector location; and

(iii) transporting the droplets to a washing location for wash of the beads prior to returning to step (b).

3. The method of claim 2, wherein the detection reagents comprise adenosine 5′

phosphosulfate and luciferin, and the enzyme reagents comprise DNA polymerase, ATP sulfurylase, and luciferase.

4. The method of claim 2, wherein the bead is a magnetically responsive bead.

5. The method of claim 1, wherein identification of the nucleic acid sequence in the sample identifies one or more organisms in the sample.

6. The method of claim 5, wherein the organism is a bacteria, virus, or fungi.

7. The method of claim 1, wherein identification of the nucleic acid sequence in the sample rules out one or more organisms in the sample.

8. The method of claim 1, wherein identification of the nucleic acid sequence in the sample determines the nucleotide sequence of an unknown organism in the sample.

9. The method of claim 1, wherein the sample is a biological sample or an environmental sample.

10. The method of claim 1, wherein the nucleic acid sequence is a human immunodeficiency virus (HIV) sequence, a methicillin-resistant Staphylococcus aureus (MRSA) sequence, an influenza A sequence, or a 16S or 28S ribosomal DNA sequence of a known or an unknown organism.

11. The method of claim 1, wherein the database of non-sequence parameters comprises one or more of source of the sample, incidence of infection and organism type, or diagnostic symptoms and organism type.

12. The method of claim 1, wherein the selecting of a first nucleotide to be dispensed is based in part on the query of a database of non-sequence parameters and in part on frequency of the nucleotide in the library of candidate sequences.

13. The method of claim 1, wherein the selecting of the nucleotide to be dispensed, subsequent to a first nucleotide to be dispensed, is based on the comparison of the de novo sequence to the library of candidate sequences to select a most probable nucleotide for that position and to decrease the library of candidate sequences.

14. The method of claim 1, further comprising transitioning to a directed sequencing approach wherein the de novo sequence is uniquely identified to near 100% certainty, the direct sequencing approach comprising dispensing the nucleotide to the sample in an order dictated by the de novo sequence uniquely identified to near 100% certainty.

15. The method of claim 1, further comprising transitioning to a de novo sequencing approach in response to all the candidate sequences in the library of candidate sequences being excluded, the de novo sequencing approach comprising dispensing the nucleotides A, G, C, and T to the sample in a predetermined order to identify the nucleotide sequence.

16. The method of claim 1, further comprising querying an additional database of candidate sequences in response to all the candidate sequences in the library of candidate sequences being excluded.

17. The method of claim 1, further comprising:

(a) selecting multiple nucleotides; and

(b) dispensing the multiple nucleotides simultaneously to reduce the library of candidate sequences.

18. The method of claim 17, wherein multiple nucleotides are 2 or 3 nucleotides.

19. The method of claim 17, wherein step (a) further comprises distinguishing between a first similar sequence and a second similar sequence in the library of candidate sequences based on a determination of the most probable nucleotide to follow in each of the first similar sequence and the second similar sequence.