Method for simultaneously performing a plurality of different amplification reactions

1. A method of simultaneously performing a plurality of different amplification reactions, the method comprising performing within an instrument enclosure the steps of:

(a) depositing each receptacle of a first set of receptacles into a corresponding receptacle well of a first receptacle holder comprising a heat-conductive material, the first receptacle holder being in thermal communication with at least one associated thermal element, each receptacle well conforming to the dimensions of at least a bottom portion of the corresponding receptacle, thereby maximizing contact between each receptacle well of the first receptacle holder and an outer surface of the corresponding receptacle, and the contents each receptacle of the first set of receptacles including a first set of reagents for performing a first amplification reaction;

(b) subjecting the contents of each receptacle of the first set of receptacles to a first incubation process in the first receptacle holder, wherein the first incubation process results in the first amplification reaction in each receptacle of the first set of receptacles containing a first target nucleic acid;

(c) depositing each receptacle of a second set of receptacles into a corresponding receptacle well of a second receptacle holder comprising a heat-conductive material, wherein at least a portion of the second set of receptacles are deposited into the corresponding receptacle wells of the second receptacle holder during the first incubation process, the second receptacle holder being in thermal communication with at least one associated thermal element, each receptacle well conforming to the dimensions of at least a bottom portion of the corresponding receptacle, thereby maximizing contact between each receptacle well of the second receptacle holder and an outer surface of the corresponding receptacle, and the contents each receptacle of the second set of receptacles including a second set of reagents for performing a second amplification reaction;

(d) subjecting the contents of each receptacle of the second set of receptacles to a second incubation process in the second receptacle holder, wherein the second incubation process results in the second amplification reaction in each receptacle of the second set of receptacles containing a second target nucleic acid,

wherein the first and second incubation processes are different from each other,

wherein the at least one thermal element associated with each of the first and second receptacle holders is independently controllable, and

wherein no downward force is applied to the receptacles of the first and second sets of receptacles during the first and second incubation processes; and

(e) determining the presence or amount, if any, of the first or second target nucleic acid in each receptacle of the first and second sets of receptacles.

2. The method of claim 1 , wherein the first and second sets of receptacles each include a plurality of receptacles that are deposited into the corresponding receptacle wells of the first and second receptacle holders.

3. The method of claim 1 , wherein the determining step is performed during the first and second incubation processes.

4. The method of claim 1 , wherein each thermal element is positioned proximal to a side surface of one of the first and second receptacle holders.

5. The method of claim 4 , wherein each thermal element is a thermoelectric device.

6. The method of claim 5 , wherein the thermoelectric device is a Peltier device.

7. The method of claim 4 , further comprising the step of exerting a force against a front surface of each of the first and second receptacle holders opposite the thermal elements.

8. The method of claim 1 , wherein each of the first and second incubation processes comprises cycling the temperature of the corresponding receptacle wells of the first or second receptacle holders multiple times.

9. The method of claim 8 , wherein at least one of the cycling temperatures and the duration of the cycles differs between the first and second incubation processes.

10. The method of claim 1 , wherein at least one of the first and second incubation processes comprises cycling the temperature of the receptacle wells of the first or second receptacle holder multiple times.

11. The method of claim 10 , wherein a thermal melt analysis is performed during at least one of the first and second incubation processes.

12. The method of claim 10 , wherein one of the first and second incubation processes is performed under isothermal conditions.

13. The method of claim 1 , wherein each receptacle of the second set of receptacles is deposited into a corresponding receptacle well of the second receptacle holder during the first incubation process.

14. The method of claim 1 , further comprising the step of transporting the receptacles of the first and second sets of receptacles to the corresponding receptacle wells of the first and second receptacle holders with a receptacle transport mechanism.

15. The method of claim 14 , wherein the receptacles of the first set of receptacles are collectively transported to the corresponding receptacle wells of the first receptacle holder, and, separately, wherein the receptacles of the second set of receptacles are collectively transported to the corresponding receptacle wells of the second receptacle holder.

16. The method of claim 14 , wherein each of the receptacles of the first and second sets of receptacles is individually transported to the corresponding receptacle well of the first or second receptacle holder.

17. The method of claim 14 , further comprising the step of providing a plurality of samples to the instrument, wherein the first and second amplification reactions target different nucleic acids, wherein each sample is provided to one of the receptacles of the first and second sets of receptacles prior to the transporting step, and wherein the receptacles are transported to the receptacle wells of the first and second receptacle holders based on the targeted nucleic acid in each sample and independent of the order in which the samples are provided to the instrument.

18. The method of claim 14 , further comprising the step of removing each receptacle of the first set of receptacles with the receptacle transport mechanism during the second incubation process.

19. The method of claim 14 , wherein the receptacle transport mechanism is a pick-and-place mechanism.

20. The method of claim 14 , wherein the receptacle transport mechanism is a pipettor.

21. The method of claim 14 , further comprising the step of sealing each receptacle of the first and second sets of receptacles prior to transporting the receptacles to the first and second receptacle holders.

22. The method of claim 1 , wherein each receptacle well of the first and second receptacle holders has a through-hole extending through a bottom end thereof.

23. The method of claim 22 , wherein each receptacle well of the first and second receptacle holders has an associated optical fiber, a first end of the optical fiber being in optical communication with the receptacle well, and a second end of the optical fiber being in optical communication with at least one of an excitation signal source and an emission signal detector.

24. The method of claim 23 , wherein a single optical fiber is associated with each receptacle well of the first and second receptacle holders, the second end of the optical fiber being in optical communication with the excitation signal source and the emission signal detector.

25. The method of claim 24 , wherein the first end of the optical fiber is fixedly disposed within the corresponding through-hole of the associated receptacle well.