CA2677953A1 - Composite arrays utilizing microspheres with a hybridization chamber - Google Patents

Composite arrays utilizing microspheres with a hybridization chamber Download PDF

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Publication number
CA2677953A1
CA2677953A1 CA002677953A CA2677953A CA2677953A1 CA 2677953 A1 CA2677953 A1 CA 2677953A1 CA 002677953 A CA002677953 A CA 002677953A CA 2677953 A CA2677953 A CA 2677953A CA 2677953 A1 CA2677953 A1 CA 2677953A1
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Prior art keywords
array system
array
nucleic acids
microspheres
binding ligands
Prior art date
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Granted
Application number
CA002677953A
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French (fr)
Other versions
CA2677953C (en
Inventor
John R. Stuelpnagel
Mark S. Chee
Steven R. Auger
Gan G. Wang
Laura S. Casas
Shawn Christopher Baker
Robert C. Kain
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Illumina Inc
Original Assignee
Illumina, Inc.
John R. Stuelpnagel
Mark S. Chee
Steven R. Auger
Gan G. Wang
Laura S. Casas
Shawn Christopher Baker
Robert C. Kain
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Application filed by Illumina, Inc., John R. Stuelpnagel, Mark S. Chee, Steven R. Auger, Gan G. Wang, Laura S. Casas, Shawn Christopher Baker, Robert C. Kain filed Critical Illumina, Inc.
Publication of CA2677953A1 publication Critical patent/CA2677953A1/en
Application granted granted Critical
Publication of CA2677953C publication Critical patent/CA2677953C/en
Anticipated expiration legal-status Critical
Expired - Lifetime legal-status Critical Current

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    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J19/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J19/0046—Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00306—Reactor vessels in a multiple arrangement
    • B01J2219/00313—Reactor vessels in a multiple arrangement the reactor vessels being formed by arrays of wells in blocks
    • B01J2219/00315—Microtiter plates
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00306—Reactor vessels in a multiple arrangement
    • B01J2219/00313—Reactor vessels in a multiple arrangement the reactor vessels being formed by arrays of wells in blocks
    • B01J2219/00315—Microtiter plates
    • B01J2219/00317—Microwell devices, i.e. having large numbers of wells
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00497—Features relating to the solid phase supports
    • B01J2219/005—Beads
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00497—Features relating to the solid phase supports
    • B01J2219/00511—Walls of reactor vessels
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00497—Features relating to the solid phase supports
    • B01J2219/00513—Essentially linear supports
    • B01J2219/00524—Essentially linear supports in the shape of fiber bundles
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
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    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00585—Parallel processes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
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    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00596—Solid-phase processes
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
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    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/0061—The surface being organic
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
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    • B01J2219/00583—Features relative to the processes being carried out
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    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00612—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports the surface being inorganic
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00614—Delimitation of the attachment areas
    • B01J2219/00621—Delimitation of the attachment areas by physical means, e.g. trenches, raised areas
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00623—Immobilisation or binding
    • B01J2219/00626—Covalent
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00632—Introduction of reactive groups to the surface
    • B01J2219/00637—Introduction of reactive groups to the surface by coating it with another layer
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00646—Making arrays on substantially continuous surfaces the compounds being bound to beads immobilised on the solid supports
    • B01J2219/00648—Making arrays on substantially continuous surfaces the compounds being bound to beads immobilised on the solid supports by the use of solid beads
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00659—Two-dimensional arrays
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/00702—Processes involving means for analysing and characterising the products
    • B01J2219/00704—Processes involving means for analysing and characterising the products integrated with the reactor apparatus
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B01J2219/00722—Nucleotides
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/02—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
    • G01N35/028—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations having reaction cells in the form of microtitration plates

Abstract

The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.

Claims (36)

1. An array system comprising:

a) a first array component comprising a plurality of wells; and b) a second array component comprising a plurality of projections, each projection having an end comprising a surface, said surface having a population of nucleic acids distributed thereon, wherein the plurality of projections is configured to be dipped into the plurality of wells.
2. The array system according to claim 1 further comprising a lid and a base plate, said base plate being configured to hold an array component.
3. The array system according to claim 2 further comprising a sealant disposed between the lid and the base plate.
4. The array system according to any one of claims 1 to 3, wherein said second array component comprises a fiber optic bundle.
5. The array system according to any one of claims 1 to 4, wherein the second array component comprises a plurality of fiber optic bundles comprising a plurality of individual fibers, each individual fiber comprising a bead well.
6. The array system according to any one of claims 1 to 5, wherein said first array component comprises a microtiter plate.
7. The array system according to any one of claims 1 to 6 further comprising at least one alignment feature.
8. The array system according to claim 7, wherein said at least one alignment feature is a male and female fitting.
9. The array system according to any one of claims 1 to 8 further comprising at least one fluid handling device.
10. The array system according to any one of claims 1 to 9, wherein said surface comprises depressions configured to contain one or more microspheres.
11. The array system according to any one of claims 1 to 10, wherein said nucleic acids are directly coupled to said surface.
12. The array system according to any one of claims 1 to 11 further comprising a population of microspheres distributed on said surface.
13. The array system according to claim 12, wherein said nucleic acids are associated with said microspheres.
14. The array system according to claim 13, wherein said microspheres further comprise an optical signature capable of identifying said nucleic acid.
15. The array system according to claim 13, wherein said microspheres comprise an identifier binding ligand that will bind a decoding binding ligand such that the identification of the nucleic acid can be elucidated.
16. The array system according to any one of claims 1 to 15, wherein said nucleic acids are selected from the group consisting of DNA and RNA.
17. The array system according to any one of claims 1 to 16, wherein said surface comprises from 10,000 to 2,000,000,000 different nucleic acids per square centimeter.
18. A method of decoding an array of nucleic acids, said method comprising:

a) providing an array system comprising:

i) a first array component comprising a plurality of wells; and ii) a second array component comprising a plurality of projections, each projection having an end comprising a surface, said surface having a population of nucleic acids distributed thereon, wherein the plurality of projections is configured to be dipped into the plurality of wells; and b) providing a plurality of decoding binding ligands to said surface to identify the location of at least one of said nucleic acids.
19. The method according to claim 18, wherein said decoding binding ligands bind to said nucleic acids.
20. The method according to claim 18, wherein said decoding binding ligands bind to identifier binding ligands present at said surface.
21. The method according to claim 18, wherein said array system further comprises a population of microspheres distributed on said surface.
22. The method according to claim 21, wherein said nucleic acids are associated with said microspheres.
23. The method according to claim 22, wherein said microspheres comprise identifier binding ligands.
24. The method according to claim 22 or claim 23, wherein said decoding binding ligands bind to said nucleic acids.
25. The method according to claim 23, wherein said decoding binding ligands bind to said identifier binding ligands.
26. The method according to any one of claims 18 to 25, wherein said decoding binding ligands are labeled.
27. A method of detecting the presence or absence of a target analyte in a sample, said method comprising:

a) providing an array system comprising:

i) a first array component comprising a plurality of wells; and ii) a second array component comprising a plurality of projections, each projection having an end comprising a surface, said surface having a population of nucleic acids distributed thereon, wherein the plurality of projections is configured to be dipped into the plurality of wells;

b) providing a sample to at least one well;

c) contacting said sample with at least one surface; and d) determining the presence or absence of said target analyte.
28. The method according to claim 27, wherein the array system further comprises a lid and a base plate, said base plate being configured to hold an array component.
29. The method according to claim 28, wherein the array system further comprises a sealant disposed between the lid and the base plate.
30. The method according to any one of claims 27 to 29, wherein said first array component comprises a microtiter plate.
31. The method according to any one of claims 27 to 30, wherein said array system further comprises at least one alignment feature.
32. The method according to claim 31, wherein said at least one alignment feature is a male and female fitting.
33. The method according to any one of claims 27 to 32, wherein said array system further comprises at least one fluid handling device.
34. The method according to any one of claims 27 to 33, wherein said nucleic acids are directly coupled to said surface.
35. The method according to any one of claims 27 to 33, wherein said nucleic acids are associated with microspheres distributed on said surface.
36. A kit comprising the array system according to any one of claims 1-17 and a decoding binding ligand.
CA2677953A 2000-06-28 2001-06-28 Composite arrays utilizing microspheres with a hybridization chamber Expired - Lifetime CA2677953C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US60636900A 2000-06-28 2000-06-28
US09/606,369 2000-06-28
CA002414618A CA2414618C (en) 2000-06-28 2001-06-28 Composite arrays utilizing microspheres with a hybridization chamber

Related Parent Applications (1)

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CA002414618A Division CA2414618C (en) 2000-06-28 2001-06-28 Composite arrays utilizing microspheres with a hybridization chamber

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CA2677953A1 true CA2677953A1 (en) 2002-01-03
CA2677953C CA2677953C (en) 2011-04-26

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EP (1) EP1307283A2 (en)
JP (2) JP2004502138A (en)
AU (2) AU7166201A (en)
CA (2) CA2677953C (en)
WO (1) WO2002000336A2 (en)

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CA2677953C (en) 2011-04-26
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WO2002000336A2 (en) 2002-01-03
JP2011221036A (en) 2011-11-04
JP2004502138A (en) 2004-01-22
CA2414618C (en) 2009-11-03
WO2002000336A9 (en) 2002-10-10
AU2001271662B2 (en) 2006-07-27
CA2414618A1 (en) 2002-01-03
EP1307283A2 (en) 2003-05-07

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