Automated method for determining the presence of a target nucleic acid in a sample

• US 20030027206A1
• Filed: 10/03/2002
• Published: 02/06/2003
• Est. Priority Date: 05/01/1998
• Status: Active Grant

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: Horner, Glenn A., Smith, Robert J., Burns, Ralph E., Schneider, Robert E., Ammann, Kelly G., Hansberry, Ernest V., Nieglos, Donald J., Kling, John E., Jakub, Cheryl A.
• Granted Patent: US 7,118,892 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01F 29/10 with receptacles rotated about two different axes, e.g. receptacles having planetary motion
• CPC Class Codes: B01F 29/30 Mixing the contents of individual packages or containers, e.g. by rotating tins or bottles
• CPC Class Codes: B01F 29/322 of two or more containers supported for simultaneous mixing, e.g. for bottles in crates
• CPC Class Codes: B01F 29/40354 arranged for planetary motion
• CPC Class Codes: B01L 2200/147 Employing temperature sensors
• CPC Class Codes: B01L 2300/1822 using Peltier elements
• CPC Class Codes: B01L 2300/1827 using resistive heater
• CPC Class Codes: B01L 7/52 with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• CPC Class Codes: B01L 7/5255 by moving sample containers
• CPC Class Codes: B01L 9/06 Test-tube stands; Test-tube holders
• CPC Class Codes: B03C 1/282 with associated accumulation indicator, e.g. Hall sensor
• CPC Class Codes: B03C 1/288 disposed at the outer circumference of a recipient
• CPC Class Codes: B03C 1/30 Combinations with other devices, not otherwise provided for
• CPC Class Codes: B03C 2201/26 for use in medical applications
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 1/6832 Enhancement of hybridisation reaction
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 2537/10 the purpose or use of
• CPC Class Codes: G01N 2035/00356 Holding samples at elevated temperature (incubation)
• CPC Class Codes: G01N 2035/00524 Mixing by agitating sample carrier
• CPC Class Codes: G01N 2035/0437 : Cleaning cuvettes or reaction vessels
• CPC Class Codes: G01N 2035/0455 : Coaxial carousels
• CPC Class Codes: G01N 2035/103 : using disposable tips
• CPC Class Codes: G01N 35/0098 : involving analyte bound to insoluble magnetic carrier, e.g. using magnetic separation magnetic particles used in immunoassays G01N33/54326; magnetic separation in general B03C
• CPC Class Codes: G01N 35/0099 : comprising robots or similar manipulators robots per se B25J
• CPC Class Codes: G01N 35/025 : having a carousel or turntable for reaction cells or cuvettes
• CPC Class Codes: G01N 35/1065 : Multiple transfer devices
• CPC Class Codes: Y10T 156/1105 : Delaminating process responsive to feed or shape at delamination
• CPC Class Codes: Y10T 156/1906 : Delaminating means responsive to feed or shape at delamination
• CPC Class Codes: Y10T 29/53657 : to apply or remove a resilient article [e.g., tube, sleeve, etc.]
• CPC Class Codes: Y10T 29/53683 : Spreading parts apart or separating them from face to face engagement
• CPC Class Codes: Y10T 29/53843 : Tube, sleeve, or ferrule inserting or removing
• CPC Class Codes: Y10T 436/11 : Automated chemical analysis
• CPC Class Codes: Y10T 436/111666 : Utilizing a centrifuge or compartmented rotor
• CPC Class Codes: Y10T 436/113332 : with conveyance of sample along a test line in a container or rack
• CPC Class Codes: Y10T 436/114998 : with treatment or replacement of aspirator element [e.g., cleaning, etc.]
• CPC Class Codes: Y10T 436/119163 : with aspirator of claimed structure
• CPC Class Codes: Y10T 436/2575 : Volumetric liquid transfer

Abstract

An automated analyzer for performing multiple diagnostic assays simultaneously includes multiple stations, or modules, in which discrete aspects of the assay are performed on fluid samples contained in reaction receptacles. The analyzer includes stations for automatically preparing a specimen sample, incubating the sample at prescribed temperatures for prescribed periods, preforming an analyte isolation procedure, and ascertaining the presence of a target analyte. An automated receptacle transporting system moves the reaction receptacles from one station to the next. The analyzer further includes devices for carrying a plurality of specimen tubes and disposable pipette tips in a machine-accessible manner, a device for agitating containers of target capture reagents comprising suspensions of solid support material and for presenting the containers for machine access thereto, and a device for holding containers of reagents in a temperature controlled environment and presenting the containers for machine access thereto. A method for performing an automated diagnostic assay includes an automated process for isolating and amplifying a target analyte. The process is performed by automatically moving each of a plurality of reaction receptacles containing a solid support material and a fluid sample between stations for incubating the contents of the reaction receptacle and for separating the target analyte bound to the solid support from the fluid sample. An amplification reagent is added to the separated analyte after the analyte separation step and before a final incubation step.

Claims

1. An automated method for determining whether a target nucleic acid is present in a sample contained by an open-ended receptacle vessel, said method comprising the steps of:

a) separating said target nucleic acid, if present in said sample, from non-target nucleic acid which may be present in said sample;

b) withdrawing at least a portion of said sample to remove non-target nucleic which may be present in said sample from said receptacle vessel;

c) exposing the contents of said receptacle vessel to reagents and conditions sufficient to amplify a target nucleic acid sequence contained within said target nucleic acid; and

d) determining whether said target nucleic acid sequence has been amplified as an indication of the presence or absence of said target nucleic acid in said sample,

wherein steps a)-d) are automated and performed on a single platform.

2. The method of claim 1, wherein said separating step includes providing to said sample a support material for immobilizing said target nucleic acid.

3. The method of claim 2, wherein said support material comprises magnetically-responsive particles.

4. The method of claim 3, wherein said separating step includes subjecting the contents of said receptacle vessel to a magnetic field, thereby isolating said magnetically-responsive particles within said receptacle vessel.

5. The method of claim 4, wherein said separating step further includes providing to said sample a capture probe having a first nucleotide base sequence region which hybridizes to said target nucleic acid under a first set of predetermined hybridization conditions.

6. The method of claim 5, wherein said capture probe has a second nucleotide base sequence region which hybridizes to a polynucleotide immobilized by said magnetically-responsive particles under a second set of predetermined hybridization conditions, said first and second sets of predetermined hybridization conditions being different.

7. The method of claim 4, wherein said withdrawing step includes aspirating at least a portion of said sample from said receptacle vessel after isolating said magnetically-responsive particles within said receptacle vessel.

8. The method of claim 7 further comprising the step of washing the contents of said receptacle vessel with a wash buffer between said withdrawing and exposing steps.

9. The method of claim 1, wherein said determining step includes providing a detection probe containing a nucleotide base sequence to the contents of said receptacle vessel under conditions such that said detection probe specifically hybridizes to nucleic acid in said receptacle vessel which contains said target sequence or the complement thereof.

10. The method of claim 9, wherein said detection probe includes a label.

11. The method of claim 10, wherein said label is selected from the group consisting of a radiolabel, a fluorescent dye, biotin, an enzyme and a chemiluminescent compound.

12. The method of claim 9, wherein said determining step provides an indication of the presence or absence of at least one member of a target group of organisms or viruses.

13. The method of claim 1, wherein said receptacle vessel is a component of an integral reaction receptacle comprising multiple receptacle vessels.

14. The method of claim 1, wherein said platform is contained within a housing of an analyzer.

15. The method of claim 14, wherein said analyzer is moveable.

16. An automated method for determining whether a target nucleic acid is present in a sample contained by an open-ended receptacle vessel, said method comprising the steps of:

a) providing a support material to said receptacle vessel, said support material comprising magnetically-responsive particles for immobilizing said target nucleic acid;

b) subjecting the contents of said receptacle vessel to a magnetic field, thereby isolating said magnetically-responsive particles within said receptacle vessel;

c) aspirating at least a portion of said sample from said receptacle vessel, thereby removing non-target nucleic acid present in said sample from said receptacle vessel;

d) washing the contents of said receptacle vessel with a wash buffer;

e) exposing the contents of said receptacle vessel to reagents and conditions sufficient to amplify a target nucleic acid sequence contained within said target nucleic acid; and

f) determining whether said target nucleic acid sequence has been amplified as an indication of the presence or absence of said target nucleic acid in said sample,

wherein steps a)-f) are automated and performed on a single platform.

17. The method of claim 16, wherein said separating step further includes providing to said sample a capture probe having a first nucleotide base sequence region which hybridizes to said target nucleic acid under a first set of predetermined hybridization conditions.

18. The method of claim 17, wherein said capture probe has a second nucleotide base sequence region which hybridizes to a polynucleotide immobilized by said magnetically-responsive particles under a second set of predetermined hybridization conditions, said first and second sets of predetermined hybridization conditions being different.

19. The method of claim 16, wherein said determining step includes providing a detection probe containing a nucleotide base sequence to the contents of said receptacle vessel under conditions such that said detection probe specifically hybridizes to nucleic acid in said receptacle vessel which contains said target sequence or the complement thereof.

20. The method of claim 19, wherein said detection probe includes a label.

21. The method of claim 20, wherein said label is selected from the group consisting of a radiolabel, a fluorescent dye, biotin, an enzyme and a chemiluminescent compound.

22. The method of claim 19, wherein said determining step provides an indication of the presence or absence of at least one member of a target group of organisms or viruses.

23. The method of claim 16, wherein said receptacle vessel is a component of an integral reaction receptacle comprising multiple receptacle vessels.

24. The method of claim 16, wherein said platform is contained within a housing of an analyzer.

25. The method of claim 24, wherein said analyzer is moveable.