WO2022035382A1

WO2022035382A1 - Automated sample pre-processing system and method

Info

Publication number: WO2022035382A1
Application number: PCT/SG2021/050476
Authority: WO
Inventors: Min-Han Tan; Geok Soon LIM
Original assignee: Lucence Life Sciences Pte. Ltd.
Priority date: 2020-08-14
Filing date: 2021-08-16
Publication date: 2022-02-17

Abstract

An automated sample pre-processing system includes a first liquid handling module and a first mixing module. The first liquid handling module is configured to uncap a sample tube containing a biological sample, dispense a predefined volume of a solubilization reagent into the uncapped sample tube, and cap the uncapped sample tube, the uncapped sample tube containing the biological sample and the solubilization reagent. The first mixing module is configured to mix the biological sample and the solubilization reagent in the capped sample tube received from the first liquid handling module to obtain a first mixed sample.

Description

AUTOMATED SAMPLE PRE-PROCESSING SYSTEM AND METHOD

TECHNICAL FIELD

[0001] The present disclosure relates broadly, but not exclusively, to automated systems and methods for pre-processing biological samples such as saliva/ sputum.

BACKGROUND

[0002] Saliva may be a preferred sample for mass testing of respiratory diseases such as COVID-19, MERS, etc. as compared to invasive swabs because it is accurate, easier to collect, and the risks of infection through aerosol are reduced for healthcare workers during specimen collection. Presently, in the laboratory, saliva and sputum solubilization is manual, gives rise to heterogeneous samples if not properly mixed, and can even be physically painful or injurious for medical laboratory staff because of repeated stress injury from sample shaking/mixing requirements. Diverse laboratory practices to solubilize saliva samples, or even worse, the omission of this step, can lead to reduced test accuracy.

[0003] It has also been noted that sample pooling procedures allow for mass screening and surveillance testing to monitor for a community- or population-level occurrence, such as an infectious disease outbreak. Sample pooling has several advantages including improved sample throughput and reduced cost per test. However, sample pooling of during testing for respiratory infections are typically performed on nasopharyngeal or oropharyngeal swabs, nasal swabs, or midturbinate swabs but not on saliva / sputum samples due to the effects of sample dilution which can result in reduced test sensitivities.

[0004] It may be desirable to provide systems, methods and devices for preprocessing of saliva / sputum samples that can address at least some of the above problems. SUMMARY

[0005] An aspect of the present disclosure provides an automated sample preprocessing system, comprising: a first liquid handling module configured to:

(i) uncap a sample tube, wherein the sample tube contains a biological sample;

(ii) dispense a predefined volume of a solubilization reagent into the uncapped sample tube; and

(iii) cap the uncapped sample tube, wherein the uncapped sample tube contains the biological sample and the solubilization reagent; and a first mixing module configured to mix the biological sample and the solubilization reagent in the capped sample tube received from the first liquid handling module to obtain a first mixed sample.

[0006] Another aspect of the present disclosure provides an automated sample preprocessing method, comprising:

(a) uncapping a sample tube, wherein the sample tube contains a biological sample;

(b) dispensing a predefined volume of a solubilization reagent into the uncapped sample tube;

(c) capping the uncapped sample tube, wherein the uncapped sample tube contains the biological sample and the solubilization reagent;

(d) mixing the biological sample and the solubilization reagent in the capped sample tube to obtain a first mixed sample; and

(e) incubating the first mixed sample based on a predefined parameter to obtain a pre-processed sample.

BRIEF DESCRIPTION OF THE DRAWINGS

[0007] Embodiments of the disclosure will be better understood and readily apparent to one of ordinary skill in the art from the following written description, by way of example only, and in conjunction with the drawings, in which:

[0008] Figure 1 A shows a perspective view of an automated sample pre-processing system according to an example embodiment. [0009] Figure 1 B shows a plan view of the system of Figure 1 A.

[0010] Figure 2 shows a simplified diagram of the system of Figure 1 A during sample tray loading.

[0011] Figure 3 shows a partial view of the system of Figure 1 A during bar code scanning.

[0012] Figure 4 shows a partial view of the system of Figure 1 A during uncapping of a sample tube.

[0013] Figure 5 shows a partial view of the system of Figure 1 A during dispensing of a reagent into the sample tube.

[0014] Figure 6 shows a partial view of the system of Figure 1A during capping of the sample tube.

[0015] Figure 7 shows a partial view of the system of Figure 1 A during mixing.

[0016] Figure 8 shows a partial view of the system of Figure 1A during transferring from mixer to output tray.

[0017] Figure 9 shows a plan view of an automated sample pre-processing system according to an alternate embodiment.

[0018] Figure 10 shows a perspective view of an implementation to fully enclose an automated sample pre-processing system according to an example embodiment.

[0019] Figure 1 1 shows a flow chart illustrating an automated sample pre-processing method according to an example embodiment.

[0020] Skilled artisans will appreciate that elements in the figures are illustrated for simplicity and clarity and have not necessarily been depicted to scale. For example, the dimensions of some of the elements in the illustrations, block diagrams or flowcharts may be exaggerated in respect to other elements to help to improve understanding of the present embodiments. DETAILED DESCRIPTION

[0021] The present disclosure provides an automated saliva / sputum solubilization, pooling and pre-concentration workflow and system that may allow a robust, standardized, and repeatable process to pre-process heterogenous and nonNewtonian saliva / sputum samples into a more homogenous and less viscous sample for enhanced downstream molecular testing.

[0022] In example implementations, the automated workflow comprises some or all of the following:

1 ) Loading of the primary sample tubes onto a tube holder tray (i.e. input tray)

2) Sequential pick up of individual primary sample tubes into a barcode scanner to read a 1 -dimensional/2-dimensional (1 D/2D) barcode. Sample ID will then be entered through a software into a database or sample list file

3) Sequential (i.e. single channel) uncapping of primary sample tubes

4) Dispensing of a solubilization reagent (e.g. dithiothreitol (DTT), or proteinase K) into the saliva and sputum sample for pre-processing

5) Sequential (i.e. single channel) recapping of primary sample tubes

6) Mixing of the primary sample tubes to ensure homogenization of the sample with solubilization reagent

7) Loading of the primary sample tubes onto another tube holder tray (i.e. output tray), in a complementary orientation or layout to that of the input tray

8) Incubation of the pre-processed samples while still stored in the output tray at a particular temperature for a period of time (e.g. 15 minutes)

9) Pooling of multiple pre-processed samples into 1 tube or reservoir via robotic liquid handling

10) Nucleic acid virus pre-concentration based on membranes or filters used in conjunction with suction pumps or centrifuges to increase viral load in the pooled sample.

[0023] Embodiments will be described, by way of example only, with reference to the drawings. Like reference numerals and characters in the drawings refer to like elements or equivalents.

[0024] Figure 1 A shows a perspective view of an automated sample pre-processing system 100 according to an example embodiment. Figure 1 B shows a plan view of the system 100 of Figure 1 A. Briefly, the system 100 includes a plurality of sensors, actuators, timers, etc. and a control circuit arranged to activate components of the system 100 to perform relevant actions. In addition to sensors directly used in the workflow, other sensors to detect whether a disposal bin needs to be emptied, whether consumables need to be topped up, etc. may be incorporated, together with displays providing outputs (e.g. error messages) from such sensors. As described in further detail below, some of such actions may be carried out sequentially, while some actions may be carried out concurrently thereby improving system throughput. For example, the system 100 includes a first robotic liquid handling module 102, a mixing module 104 and an incubation module 108. The liquid handling module 102 is configured to uncap a sample tube 104, which initially contains a biological sample, dispense a predefined volume of a solubilization reagent into the uncapped sample tube 104, and cap the uncapped sample tube 104, which then contains the biological sample and the solubilization reagent. The mixing module 106 is configured to mix the biological sample and the solubilization reagent in the capped sample tube 104 received from the liquid handling module 102 to obtain a mixed sample, and the incubation module 108 is configured to incubate the mixed sample received from the mixing module based on a predefined parameter to obtain a pre- processed sample. Further actions can be performed with respect to the pre- processed sample depending on practical requirements.

[0025] An example implementation of the system 100 is now described with reference to Figures 2-8.

[0026] In an initial step of the workflow, the primary saliva/sputum sample tubes 104 are labelled with respective optically-readable identifiers (e.g. barcodes or QR codes) and placed in a first tube holder tray (herein termed as input tray 202). The input tray 202 comprises an array/grid and typically organizes the primary sample tubes 104 in a 24-tube (i.e. 4x6), 48-tube (i.e. 6x8), or 96-tube (i.e. 8x12) format. Other formats are possible, as will be appreciated by a person skilled in the art. As shown in Figure 2, the input tray 202 may subsequently be loaded or inserted by an operator into a designated loading position of the system 100 for sample preprocessing.

[0027] In the next step, as shown in Figure 3, the input tray 202 is transported to the next station or module of the system 100, for example, by means of a motorized axis, conveyor belt system or robotic gripper. This brings the input tray 202 into close proximity to first robotic tube transfer module (e.g. a robotic gripper 302) which then holds onto individual primary sample tubes 104 and transports them in front of a reader (e.g. a barcode scanner 304). The barcode scanner 304 subsequently reads the 1 D/2D barcodes on the labelled sample tubes 104, and stores the sample IDs in a database or readable sample list file (e.g. .txt, .csv, .dat, .xml). Such recording of sample IDs is consistent or compatible with standard testing protocols, as will be appreciated by a person skilled in the art.

[0028] Next, as shown in Figure 4, the sample tubes 104 are uncapped sequentially in a single-channel format (i.e. one at a time) using a uncapping/capping mechanism 402. The uncapping/capping mechanism 402 has swappable adaptors 404 to permit compatibility with a wide range of sample tubes from different manufacturers. In other words, the adaptors 404 can work with sample tubes of different heights and/or diameters, thereby improving versatility of the system 100. The single-channel uncapping format also can minimize sample cross-contamination via aerosol generation and release during the uncapping process. An example suitable uncapping/capping mechanism is the rotary gripper module EHMD from Festo Group.

[0029] Then, as shown in Figure 5, a fixed volume of a solubilization reagent (e.g. DTT or proteinase K) is dispensed from a dispenser 502 into the sample tube 104 for pre-processing. The addition of a solubilization reagent helps to reduce the viscosity of the saliva / sputum samples, in order to enhance downstream molecular testing. In a non-limiting example, 250pl_ of 500 mM DTT solution (Promega, Ref V3151 ) is dispensed into each sample tube 104 containing 4ml_ of saliva sample and the SAFER™ Sample Stabilization Fluid to aid in the solubilization of the viscous samples.

[0030] After the reagent has been dispensed, the sample tubes 104 are recapped sequentially in a single-channel format (i.e. one at a time) as shown in Figure 6, using the same uncapping/capping mechanism 402 as described above with reference to Figure 4.

[0031] In example embodiments, the uncapping/capping mechanism 402 and dispenser 502 can be collectively considered a liquid handling module in which successive actions are coordinated. For example, as shown in Figures 4-6, after uncapping the sample tube 104, the uncapping/capping mechanism 402 moves upward, allowing a swing arm 504 of the dispenser 502 to move into position to dispense the reagent. Once the dispensing is completed, the swing arm 504 swivels back and the uncapping/capping mechanism 402 moves downward to re-cap the sample tube 104.

[0032] In the next step, as shown in Figure 7, the sample tubes 104 are mixed to ensure homogenization of the sample with the solubilization reagent. In one example implementation, a robotic gripper transfers the sample tubes 104 onto a vortex mixer 702 which oscillates at a sufficiently high speed (rpm) for a period of time to result in sample fluids circulating and undergoing turbulent flow for effective mixing. For example, the vortex mixer may operate at a speed between 500 and 3000 rpm for a duration between 1 to 10 seconds, or longer, based on practical requirements.

[0033] Thereafter, in one embodiment, the sample tubes 104 are loaded by the first robotic tube transfer module, e.g. using similar mechanism as the robotic gripper 302 in Figure 3, back to the input tray 202 at the respective positions where they are initially placed. This can both reduce the number of items required to run the system and ensure that each sample tube 104 is consistently associated with a position on the input tray 202.

[0034] Alternatively, the sample tubes 104 may be loaded onto a second tube holder tray (herein termed as output tray 802), in a complementary orientation or layout to that of the input tray 202. Such arrangement can similarly ensure that the sample ID sequence list is maintained such that the sample layout in the input tray 202 is complementary to that in the output tray 802. Figure 8 shows one sample tube 104 stored on the output tray 802. In some embodiments, once the output tray 802 has been filled with sample tubes, it is transported to a designated unloading position by means of a motorized axis, conveyor belt system or robotic gripper before further steps are taken. In alternate embodiments, the further steps may take place in a continuous sequence without the output tray 802 being unloaded.

[0035] In embodiments in which the output tray 802 is transported to the designated unloading position, an operator or a robot may remove the output tray 802 and incubate the sample tubes 104 at a particular temperature and for a period of time for completion of the solubilization process. In a non-limiting example, the sample tubes 104 are incubated at room temperature for at least 15 minutes. If a higher or lower incubation temperature is desired, the output tray may be placed in an incubator. In alternate embodiments, the sample tubes 104 may be incubated without the output tray 802 being removed. Following incubation, the pre-processed samples may be used directly for downstream molecular testing or may undergo additional treatments as described below.

[0036] In some embodiments which make use of sample pooling, multiple pre- processed samples in the primary sample tubes 104 are pooled together into a single tube. For example, a robotic handler may transfer either a portion or an entirety of the pre-processed sample volume from each sample tube 104 in a sequential order into a common single tube (herein termed as the pre-concentration tube). Example ratios for pooling maybe 2:1 , 3:1 , 4:1 , 5:1 , 6:1 , 7:1 , 8:1 , 9:1 , 10:1 , etc. depending on practical requirements. An optional general filter (e.g. micron-scale filter membranes) or medium speed centrifugation step may be included to remove any particulates or residues that may otherwise adversely clog or hinder downstream processes.

[0037] Then, a robotic tube transfer system may transfer the pre-concentration tube onto a vacuum / suction pump module, or a centrifuge module to perform nucleic acid virus pre-concentration based on membranes or filters. This step may significantly reduce the initial pooled sample volume to a working volume range of, for example, 100pl_ to 500pl_ depending on the viscosity of the pooled sample. This additional step may also increase viral load in the pooled sample to increase test sensitivities. This concentrated pooled sample may subsequently be transferred into a clean / sterile tube for downstream processing (e.g. ribonucleic acid (RNA) extraction, polymerase chain reaction (PCR) plate setup). The transfer step may be specially calibrated to avoid transfer of any particulates or residues resulting from the previous upstream pre-concentration process.

[0038] Figure 9 shows a plan view of an automated sample pre-processing system 900 according to an alternate embodiment. System 900 is similar to system 100 in several aspects. For example, system 900 also includes a turntable 901 for performing sequential steps. In addition to the modules as described above with reference to Figures 1 -8, system 900 also includes a labelling module 902 and a second robotic liquid handling module 904.

[0039] During operation of system 900, a plurality of primary sample tubes 906, each containing a respective sample, as well as a plurality of empty and unlabelled secondary tubes 908 are loaded onto the system 900. For example, the primary sample tubes 906 are placed in a primary tray 907, and the secondary tubes 908 are placed in a secondary tray 909. While the optically-readable identifiers (e.g. barcodes or QR codes) of the primary sample tubes 906 are being read at station 2 of the turntable 901 , a robotic arm picks up an empty secondary tube 908 from the secondary tray 909, and the labelling module 902 labels the empty secondary tube 908 based on at least one identifier, such that the labelled empty tube corresponds to at least one sample tube. For example, one secondary tube may correspond to one primary tube when a direct sample transfer is desired, while one secondary tube may correspond to multiple primary tubes when sample pooling is desired. In one example implementation, the labelling module 902 may employ a thermal printer to perform the concurrent labelling. In one example, primary tray 907 and secondary tray 909 are affixed with optically-readable identifiers (e.g. barcodes or QR codes) that are scanned when the trays are placed in the system 900.

[0040] Thereafter, the at least one primary sample tube 906 undergoes uncapping, dispensing, capping, mixing and incubation in the same manner as described above with reference to Figures 4-8. For example, the uncapping, dispensing and capping may be performed at station 4 of the turntable 901 , while the mixing is performed at station 5 of the turntable 901. At the end of this pre-processing, the at least one primary sample tube 906 is returned to the primary tray 907 at the position where it was originally taken from, while the labelled secondary tube 908 is stored in the secondary tray 909.

[0041] In this embodiment, after the incubation period is completed, the primary sample tube 906 containing the pre-processed sample is transferred from the primary tray 907 to the second robotic liquid handling module 904, for example, by means of a robotic tube transfer module (e.g. a robotic arm). In other words, a primary sample tube which is ready for transfer or further treatments can be transferred from the primary tray 907 without having to wait for all the samples to be incubated. Such arrangement may improve the throughput of the system.

[0042] For example, the primary sample tube 906 may be picked from the primary tray 907 and placed at station 1 of the turntable 901. The primary sample tube 906 then undergoes mixing, e.g. using a vortex mixer, to ensure that sample molecules are evenly distributed. Following that, the identifier of the sample tube 906 is read at station 2 of the turntable 901 and the sample tube 906 is moved on to the liquid handling module 904 at station 4 of the turntable 901 .

[0043] At the liquid handling module 904, the primary sample tube 906 is uncapped, a predefined volume of the pre-processed sample is withdrawn from the uncapped primary sample tube 906, and the primary sample tube 906 is then recapped. The withdrawn pre-processed sample is transferred to the corresponding labelled secondary tube 908 on the secondary tray 909. In one example implementation, a pipette arm may be used to withdraw the sample from the primary sample tube 906 and transfer the withdrawn sample to the labelled secondary tube 908. In such implementation, after the sample has been transferred, the used pipette tip is automatically discarded and replaced by a fresh pipette tip to avoid crosscontamination. The steps performed by the liquid handling module 904 may be repeated with other primary sample tubes in the output tray.

[0044] In other words, the example embodiment as shown in Figure 9 integrate additional modules to further improve the workflow, by ensuring that the empty secondary tubes are labelled correctly based on desired corresponding primary sample tubes and by minimising idle time. The second liquid handling module 904 can help to perform sample pooling or sample transfer for downstream molecular testing, as described above, in a continuous workflow.

[0045] Figure 10 shows a perspective view of an implementation to fully enclose a sample pre-processing system, such as system 100 of Figure 1A or system 900 of Figure 9 according to an example embodiment. In order to provide an engineering control to protect laboratory workers, laboratory environment and work materials from exposure to infectious or biohazardous aerosols and splashes, the automated workflow may be performed in a fully or partially-enclosed environment with accompanying HEPA filters and/or laminar airflow systems. For example, in the implementation shown in Figure 10, HEPA filters 1002, 1004 may be disposed at air inlets while HEPA filter 1006 is disposed at air outlet. A dedicated exhaust system exterior to the automated instrument, in the form of fan unit 1008, can keep the interior under negative pressure. Additional airflow sensors and alarms may allow the operator to monitor the internal negative pressure at all times. Further, an ultraviolet (UV) lamp allows the interior to be sterilized during regular maintenance.

[0046] In an alternate embodiment (not shown), the sample pre-processing system may be disposed in a biosafety cabinet hood, such as one manufactured by ESCO Lifesciences Group, which can function with the cabinet door open. Such cabinet may include open fronts for operator access, and utilise vertical laminar airflow where external air is run through a filter before it gets inside the cabinet and internal air is HEPA-filtered before it is released outside. [0047] Figure 11 shows a flow chart 1100 illustrating an automated sample preprocessing method according to an example embodiment. At step 1102, a sample tube containing a biological sample is uncapped. At step 1104, a predefined volume of a solubilization reagent is dispensed into the uncapped sample tube. At step 1106, the uncapped sample tube containing the biological sample and the solubilization reagent is capped. At step 1108, the biological sample and the solubilization reagent in the capped sample tube are mixed to obtain a mixed sample. At step 1110, the mixed sample is incubated based on a predefined parameter to obtain a pre- processed sample.

[0048] As described, the system and method according to the present disclosure can reduce operators’ hands-on-time, thereby reducing manual labour and repeated stress injuries, reduce sample pre-processing time, allowing for ease of scaling up for mass testing and screening of large populations. Further, the system and method according to the present disclosure can improve sample testing throughput, making it more amenable to mass population-wide screening applications, and increase nucleic acid virus concentrations which would otherwise be diluted during the sample pooling process.

[0049] Table 1 shows an example comparing the time spent between a manual approach and the automated processing according to the present disclosure. It can be seen from Table 1 that there is a significant reduction of operator hands-on time through use of the system and method as disclosed, improving throughput of 1 Medical Lab Technologist (MLT) by 582%, and increasing testing capacity to 3000 samples/day/machine.

Table 1

[0050] It will be appreciated by a person skilled in the art that numerous variations and/or modifications may be made to the present disclosure as shown in the specific embodiments without departing from the scope of the disclosure as broadly described. For example, different solubilization reagents may be used in alternate embodiments. Further, the present system and method are not limited to saliva / sputum sample preprocessing, but rather, can be used for general laboratory’s sample processing workflows that works with collection tubes and requires addition of a particular reagent or solution followed by homogenization. The present embodiments are, therefore, to be considered in all respects to be illustrative and not restrictive.

Claims

1 . An automated sample pre-processing system, comprising: a first liquid handling module configured to:

(i) uncap a sample tube, wherein the sample tube contains a biological sample;

2. The system as claimed in claim 1 , further comprising an incubation module configured to incubate the first mixed sample received from the first mixing module based on a predefined parameter to obtain a pre-processed sample.

3. The system as claimed in claim 1 or 2, wherein the biological sample comprises a biofluid, the biofluid including saliva and/or sputum, and viral and/or bacterial matter contained therein.

4. The system as claimed in claim 2, wherein the sample tube containing the biological sample comprises one of a plurality of sample tubes disposed on an input tray, and wherein the system further comprises a tube transfer module configured to sequentially provide each of the sample tubes from the input tray to the first liquid handling module.

5. The system as claimed in claim 4, wherein each of the sample tubes comprises a respective optically-readable identifier, and wherein the system further comprises a reader configured to read the identifier of each sample tube.

6. The system as claimed in claim 5, wherein the tube transfer module is further configured to sequentially provide each capped sample tube containing a respective first mixed sample to an output tray associated with the incubation module such that positions of the plurality of sample tubes on the output tray correspond to positions of the plurality of sample tubes on the input tray.

7. The system as claimed in claim 6, wherein the output tray is the same as the input tray.

8. The system as claimed in any one of claims 4 to 7, wherein the first liquid handling module is further configured to uncap the plurality of sample tubes individually and to cap the plurality of sample tubes individually.

9. The system as claimed in any one of the preceding claims, wherein the solubilization reagent comprises a mucolytic agent, the mucolytic agent comprising dithiothreitol (DTT) or proteinase K.

10. The system as claimed in any one of the preceding claims, wherein the first mixing module comprises a vortex mixer.

11. The system as claimed in any one of the preceding claims, wherein the predefined parameter comprises a predefined temperature and/or a predefined duration.

12. The system as claimed in any one of the preceding claims, further comprising a pooling module configured to receive a plurality of pre-processed samples to form a pooled sample in a single container.

13. The system as claimed in claim 12, further comprising a filter module positioned downstream of the pooling module and configured to remove particulates or residues from the pooled sample.

14. The system as claimed in claim 13, further comprising a pre-concentration module positioned downstream of the filter module and configured to reduce a volume of the pooled sample to a predefined volume.

15. The system as claimed in claim 6 or 7, further comprising a labelling module configured to concurrently label an empty tube based on at least one identifier read by the reader, such that the labelled empty tube corresponds to at least one sample tube.

16. The system as claimed in claim 15, further comprising a second mixing module configured to: receive from the output tray containing a plurality of capped sample tubes, a capped sample tube corresponding to the labelled tube, wherein the capped sample tube contains a respective incubated pre-processed sample; and mix the incubated pre-processed sample to obtain a second mixed sample.

17. The system as claimed in claim 16, further comprising a second liquid handling module configured to:

(a) receive the capped sample tube containing the second mixed sample;

(b) uncap the capped sample tube;

(c) withdraw a predefined volume of the second mixed sample from the uncapped sample tube;

(d) transfer the withdrawn second mixed sample to the labelled tube on a secondary tray; and

(e) re-cap the sample tube.

18. The system as claimed in claim 17, wherein the second liquid handling module comprises a pipette arm configured to withdraw and transfer the predefined volume of the second mixed sample, and wherein the pipette arm is configured to automatically replace a used pipette tip with a new pipette tip after transferring the predefined volume.

19. An automated sample pre-processing method, comprising:

20. The method as claimed in claim 19, wherein the biological sample comprises a biofluid, the biofluid including saliva and/or sputum, and viral and/or bacterial matter contained therein.

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21 . The method as claimed in claim 19 or 20, wherein the sample tube containing the biological sample comprises one of a plurality of sample tubes disposed on an input tray, and wherein the method further comprises sequentially transferring each of the sample tubes from the input tray for uncapping.

22. The method as claimed in claim 21 , wherein each of the sample tubes comprises a respective optically-readable identifier, and wherein the method further comprises reading the identifier of each sample tube.

23. The method as claimed in claim 22, further comprising sequentially transferring each capped sample tube containing a respective first mixed sample to an output tray for incubating such that positions of the plurality of sample tubes on the output tray correspond to positions of the plurality of sample tubes on the input tray.

24. The method as claimed in claim 23, wherein the output tray is the same as the input tray.

25. The method as claimed in any one of claims 21 to 24, further comprising uncapping the plurality of sample tubes individually and capping the plurality of sample tubes individually.

26. The method as claimed in any one of claims 19 to 25, wherein the solubilization reagent comprises a mucolytic agent, the mucolytic agent comprising dithiothreitol (DTT) or proteinase K.

27. The method as claimed in any one of claims 19 to 26, wherein mixing comprises using a vortex mixer.

28. The method as claimed in any one of claims 19 to 27, wherein the predefined parameter comprises a predefined temperature and/or a predefined duration.

29. The method as claimed in any one of claims 19 to 28, further comprising pooling a plurality of pre-processed samples into a pooled sample.

30. The method as claimed in claim 29, further comprising removing particulates or residues from the pooled sample.

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31. The method as claimed in claim 30, further comprising reducing a volume of the pooled sample to a predefined volume.

32. The method as claimed in claim 23 or 24, further comprising concurrently labelling an empty tube based on at least one identifier read by the reader, such that the labelled empty tube corresponds to at least one sample tube.

33. The method as claimed in claim 32, further comprising: receiving a capped sample tube corresponding to the labelled tube from the output tray containing a plurality of capped sample tubes, wherein the capped sample tube contains a respective incubated pre-processed sample; and mixing the incubated pre-processed sample to obtain a second mixed sample.

34. The method as claimed in claim 33, further comprising:

(a) receiving the capped sample tube containing the second mixed sample;

(b) uncapping the capped sample tube;

(c) withdrawing a predefined volume of the second mixed sample from the uncapped sample tube;

(d) transferring the withdrawn second mixed sample to the labelled tube on a secondary tray; and

(e) re-capping the sample tube.

35. The method as claimed in claim 34, further comprising replacing a used pipette tip with a new pipette tip after transferring the predefined volume to the labelled tube.

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