NUCLEIC ACID SEQUENCING SYSTEM AND METHOD

• US 20080262747A1
• Filed: 01/28/2008
• Published: 10/23/2008
• Est. Priority Date: 01/26/2007
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Kain, Robert C., Zhao, Chanfeng, Gunderson, Kevin, Heiner, David L.
• Granted Patent: US 7,835,871 B2
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.

Claims

1. A method for sequencing a plurality of nucleic acids comprising:

(a) beginning a cycle of a sequencing procedure for an array comprising a plurality of nucleic acids via a system capable of determining nucleotide sequence of the array;

(b) evaluating a parameter of the system, wherein the parameter relates to a decay in signal-to-noise ratio over a plurality of sequencing cycles;

(c) altering the sequencing procedure for the array based on the parameter; and

(d) performing another cycle of the sequencing procedure for the array.

2. The method of claim 1, wherein the parameter relates to phasing between sample sites of the array.

3. The method of claim 1, wherein the parameter relates to a quality of a control cluster of the array.

4. The method of claim 1, wherein the parameter relates to a reagent used to sequence the array.

5. The method of claim 4, wherein the parameter includes a volume of the reagent.

6. The method of claim 1, wherein the parameter includes a parameter of an optical imaging system used to sequence the array.

7. The method of claim 1, wherein step (c) includes repeating introduction of nucleotides to the array.

8. The method of claim 1, wherein step (c) includes evaluating operation of a reagent delivery system.

9. The method of claim 1, wherein step (c) includes re-imaging the array.

10. The method of claim 9, wherein the array is re-imaged with a longer exposure or a greater imaging system sensitivity.

11. The method of claim 1, wherein step (c) includes selecting certain areas of the array for which imaging data will be used for sequencing.

12. The method of claim 11, wherein step (d) includes collecting imaging data for only the selected areas of the array.

13. The method of claim 11, wherein step (d) includes collecting imaging data for all areas of the array.

14. The method of claim 13, wherein the imaging data for areas of the array not selected to be used for sequencing is stored.

15. The method of claim 1, wherein step (c) includes interrupting the sequencing procedure and step (d) is not performed.

16. The method of claim 1, wherein steps (b) and (c) are performed by a human operator based on analysis generated by a computer system.

17. The method of claim 1, wherein steps (b) and (c) are performed by a computer system.

18. A method for sequencing a plurality of nucleic acids, comprising:

(a) performing an automated nucleic acid sequencing operation;

(b) generating data based upon the operation; and

(c) evaluating a quality of the sample based upon the data.

19. A method for sequencing a plurality of nucleic acids, comprising:

(a) performing a cycle of a sequencing procedure for an array comprising a plurality of nucleic acids via a system capable of determining nucleotide sequence of the array;

(b) detecting a plurality of signals indicative of nucleotides present at sites of the array;

(c) evaluating the signals to determine quality of the array; and

(d) altering the sequencing procedure for the array based on the quality.

20. A system for sequencing a plurality of nucleic acids, comprising:

a fluidics handling system for facilitating assay reaction protocols;

an imaging system for acquiring sequencing data;

diagnostic components configured to measure system parameters during operation of the sequencing system;

quality evaluation circuitry configured to assess a quality of the sequencing system based upon a multiple step analysis; and

control circuitry configured to alter operating conditions of the sequencing system based upon data collected by the diagnostic components or the quality evaluation circuitry.