Independently removable nucleic acid sequencing system and method

Patent metadata

Field	Value
Publication number	US-10053730-B2
Application number	US-201514817639-A
Country	US
Kind code	B2
Filing date	Aug 4, 2015
Priority date	Jan 26, 2007
Publication date	Aug 21, 2018
Grant date	Aug 21, 2018

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.

First claim

The invention claimed is:

1. A method for sequencing nucleic acids, comprising
(a) providing a sequencing system comprising
(i) a plurality of stations configured to carry out manipulations in a nucleic acid sequencing procedure,
(ii) a table having multiple sites configured to accept nucleic acid arrays, and
(iii) a first nucleic acid array at a first site on the table;
(b) causing relative movement between the table and the plurality of stations, wherein different stations of the plurality of stations carry out different steps of the sequencing procedure on the first nucleic acid array, thereby completing at least one cycle of the sequencing procedure on the first nucleic acid array;
(c) providing a second nucleic acid array to a second site on the table after completing the at least once cycle of the sequencing procedure for the first nucleic acid array;
(d) causing relative movement between the table and the plurality of stations, wherein different stations of the plurality of stations carry out different steps of the sequencing procedure on the first nucleic acid array and on the second nucleic acid array, thereby completing a further cycle of the sequencing procedure on the first nucleic acid array and completing at least one cycle of the sequencing procedure on the second nucleic acid array;
(e) replacing the first nucleic acid array with a third nucleic acid array at the first site;
(f) causing relative movement between the table and the plurality of stations, wherein different stations of the plurality of stations carry out different steps of the sequencing procedure on the second nucleic acid array and on the third nucleic acid array, thereby completing a further cycle of the sequencing procedure on the second nucleic acid array and completing at least one cycle of the sequencing procedure on the third nucleic acid array.

2. The method of claim 1 , wherein relative movement between the table and the plurality of stations is caused by an automated system controller interface.

3. The method of claim 1 , wherein sequencing data is obtained from the second nucleic acid array while reagents are being delivered to the first nucleic acid array.

4. The method of claim 1 , wherein each of the stations is configured to carry out a different step of the nucleic acid sequencing procedure.

5. The method of claim 4 , wherein the stations in the plurality of stations are in a fixed order and at fixed intervals relative to each other.

6. The method of claim 5 , wherein the sites of the multiple sites are in a fixed order and at fixed intervals relative to each other on the table.

7. The method of claim 6 , wherein the fixed order of the stations and the relative movement between the table and the plurality of stations correlates with the order and duration of reaction steps in the nucleic acid sequencing procedure.

8. The method of claim 4 , wherein each lap completed by a nucleic acid array through the sequencing system corresponds to determination of a single nucleotide for each target nucleic acid on the nucleic acid array.

9. The method of claim 1 , wherein the table is a circular table.

10. The method of claim 1 , wherein the relative movement comprises rotation of the table.

11. The method of claim 1 , wherein sequencing data is obtained from the second nucleic acid array while the first nucleic acid array is being replaced.

12. The method of claim 1 , wherein each cycle of the nucleic acid sequencing procedure comprises addition of a single nucleotide to target nucleic acids of a nucleic acid array, detection of the nucleic acid array and de-blocking of the nucleotide that was added to the nucleic acid.

13. The method of claim 1 , wherein the providing of the second nucleic acid array to the second site on the table, comprises placing a substrate at the second site and amplifying nucleic acids on the substrate to form the second nucleic acid array.

14. The method of claim 1 , wherein the first nucleic acid array comprises an array of nucleic acid clusters on a surface.

15. The method of claim 1 , wherein the first nucleic acid array comprises an array of beads attached to different nucleic acids.

16. The method of claim 1 , wherein the nucleic acid arrays are provided to the sites on the table when the sites are at an insertion or retrieval station.

17. The method of claim 16 , wherein the nucleic acid arrays are provided to the sites by robot.

18. The method of claim 1 , wherein fluids are removed from the multiple sites independent of the location of the sites in the system.

19. The method of claim 1 , wherein the plurality of stations comprises an optical detector, and the nucleic acid sequencing procedure comprises optical detection of the nucleic acid arrays.

20. The method of claim 19 , wherein the nucleic acid sequencing procedure comprises detecting fluorescent dyes that are added to nucleic acids on the nucleic acid arrays.

21. The method of claim 20 , wherein the nucleic acid sequencing procedure comprises removing the fluorescent dyes from nucleic acids on the nucleic acid arrays.

22. The method of claim 1 , wherein the nucleic acid sequencing procedure is selected from the group consisting of pyrosequencing, sequencing by synthesis, sequencing by ligation and sequencing by hybridization.

Assignees

• Illumina Inc

Inventors

• Kain Robert C
• Heiner David L
• Zhao Chanfeng
• Gunderson Kevin

Classifications

• C12Q1/6874 Primary

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title

• C12Q1/6869

  Methods for sequencing · CPC title

• C12Q2565/501

  being an array of oligonucleotides · CPC title

• C12Q1/686 Primary

  Polymerase chain reaction [PCR] · CPC title

• C12Q2537/143

  Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis · CPC title