Method for sequential sequencing nucleic acids

• US 8,728,729 B2
• Filed: 12/04/2012
• Issued: 05/20/2014
• Est. Priority Date: 05/23/1997
• Status: Expired due to Fees

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Bridgham, John, Corcoran, Kevin, Golda, George, Pallas, Michael C., Brenner, Sydney
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US13/693,658
• Publication Number:
  US 20130184162A1
• Time in Patent Office: 532 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00274 Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01L 2200/0647 Handling flowable solids, e.g. microscopic beads, cells, particles
• CPC Class Codes: B01L 2200/10 Integrating sample preparation and analysis in single entity, e.g. lab-on-a-chip concept
• CPC Class Codes: B01L 2300/0877 Flow chambers
• CPC Class Codes: B01L 2400/0403 specific forces
• CPC Class Codes: B01L 2400/0475 specific mechanical means and fluid pressure
• CPC Class Codes: B01L 2400/0622 distribution valves, valves having multiple inlets and/or outlets, e.g. metering valves, multi-way valves
• CPC Class Codes: B01L 2400/0644 rotary valves
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: G01N 15/1433 : using image recognition
• CPC Class Codes: G01N 15/1456 : without spatial resolution of the texture or inner structure of the particle, e.g. processing of pulse signals
• CPC Class Codes: G01N 15/1484 : microstructural devices
• CPC Class Codes: G01N 15/149 : specially adapted for sorting particles, e.g. by their size or optical properties
• CPC Class Codes: G01N 2015/0015 : in solids
• CPC Class Codes: G01N 21/253 : for batch operation, i.e. multisample apparatus analytical automats G01N35/00

Abstract

An apparatus and system are provided for simultaneously analyzing a plurality of analytes anchored to microparticles. Microparticles each having a uniform population of a single kind of analyte attached are disposed as a substantially immobilized planar array inside of a flow chamber where steps of an analytical process are carried out by delivering a sequence of processing reagents to the microparticles by a fluidic system under microprocessor control. In response to such process steps, an optical signal is generated at the surface of each microparticle which is characteristic of the interaction between the analyte carried by the microparticle and the delivered processing reagent. The plurality of analytes are simultaneously analyzed by collecting and recording images of the optical signals generated by all the microparticles in the planar array. A key feature of the invention is the correlation of the sequence of optical signals generated by each microparticle in the planar array during the analytical process.

Claims

1. A method of sequencing multiple target polynucleotides in parallel using a sequencing system, comprising:

providing a flow chamber comprising a plurality of ridges within the flow chamber, the flow chamber comprising multiple microparticles immobilized between the ridges, each microparticle of the multiple microparticles including a target polynucleotide to be sequenced immobilized on the microparticle, the average distance between centers of adjacent microparticles being less than two microparticle diameters, and the ridges being of a height less than a diameter of a microparticle and of a length greater than a plurality of said diameters;

performing successive cycles of a base-by-base sequencing for the target polynucleotides immobilized on the microparticles in the flow cell; and

obtaining data that provides sequence information about the plurality of target polynucleotides based on the successive cycles of the base-by-base sequencing.

2. The method of claim 1, wherein the plurality of ridges within the flow chamber run parallel to the axis of the flow chamber.

3. The method of claim 1, wherein the successive cycles of a base-by-base sequencing comprise:

providing an oligonucleotide through an inlet of the flow chamber;

ligating the oligonucleotide to a strand hybridized to a polynucleotide of the plurality of target polynucleotides when the oligonucleotide is complementary to a single-stranded portion of the polynucleotide; and

cleaving at least a portion of the oligonucleotide that was ligated.

4. The method of claim 3, further comprising:

providing a second oligonucleotide through the inlet of a flow chamber after the cleaving of the at least a portion of the oligonucleotide that was ligated;

ligating the second oligonucleotide to the strand hybridized to a polynucleotide of the plurality of target polynucleotides when the oligonucleotide is complementary to a second single-stranded portion of the polynucleotide; and

obtaining data that provides information about the plurality of target polynucleotides based on the ligation of the second oligonucleotide.

5. The method of claim 1, wherein said obtaining data comprises using a data processor configured to receive data from the successive cycles of the base-by-base sequencing to provide sequence data for the polynucleotides immobilized on the multiple microparticles.

6. The method of claim 5, wherein the data processor is further configured to track each microparticle through multiple rounds of label identification.

7. The method of claim 5, wherein the data processor is configured to receive data corresponding to the polynucleotides as they are processed in parallel.

8. The method of claim 1, wherein the number of microparticles per unit area in the planar array is at least eighty percent of the number of microparticles in a hexagonal array of equal area.

9. The method of claim 1, wherein the ridges are spaced such that the microparticles are arranged single-file between the ridges.

10. The method of claim 1, wherein multiple ridges in the flow chamber are parallel to each other.

11. The method of claim 1, wherein a distance between ridges is configured to allow for maximal packing of microparticles.

12. The method of claim 1, wherein a diameter of each of the multiple microparticles is approximately a same diameter.

13. The method of claim 1, wherein the multiple microparticles are chemically constrained in the flow chamber.

14. The method of claim 13, wherein the multiple microparticles are constrained by a crosslinked chemical attachment.

15. The method of claim 1, wherein said obtaining data comprises using a light source configured to provide an excitation beam and an optics system configured to receive light produced in response to the excitation beam.

16. The method of claim 1, wherein the sequencing system comprises a body attached to a plate to form the flow chamber.

17. The method of claim 1, wherein the multiple microparticles are connected to the flow chamber in a monolayer between the ridges, said monolayer comprising multiple tiles and a detector is configured to separately generate data based on a first subset of the multiple microparticles and a second subset of the multiple microparticles physically separate from the first subset of the multiple microparticles.

18. The method of claim 1, wherein at least 500,000 microparticles are immobilized in the flow chamber, each of the 500,000 microparticles comprising an analyte to be sequenced immobilized on the microparticle.

19. The method of claim 1, wherein the distance between the elongated ridges having multiple microparticles immobilized therebetween is greater than the diameter of a microparticle.

20. The method of claim 1, wherein the microparticles comprise a hexagonal array.