Automated method for direct sampling of immune cells from whole blood or other biological samples in microwell plates

Abstract

A method for automatic sampling of immune cells from a biological fluid sample, e.g., whole blood, deposited in a well of a microwell plate. The sample contains red blood cells (RBCs) and magnetic beads which are designed to bind to the RBCs. The microwell plate is placed on a shaker having a magnetic adapter including at least one magnet. The magnet causes the RBCs bound to the magnetic beads to be attracted to and migrate to a wall of the well (e.g., the bottom or side wall) and be held against the wall. The shaker is then operated to shake the microwell plate in a manner and for a time period so as to suspend substantially evenly or homogeneously the immune cells in the biological fluid sample within a region of the well but still retain the holding of the RBCs to the wall of the well such that the immune cells are substantially isolated from the RBCs in the region of the well. During or after shaking, a sample probe is then lowered into the region of the well to withdraw a portion of the sample containing the immune cells.

Claims

1. A method for automatic sampling of immune cells from a biological fluid sample deposited in a well of a microwell plate, the well having a wall, the biological fluid sample containing (1) red blood cells (RBCs) and (2) magnetic beads which are designed to bind to the RBCs in the sample, comprising the steps of: a) placing the microwell plate on a shaker having a magnetic adapter including at least one magnet, wherein the magnet causes the RBCs bound to the magnetic beads to be held against the wall of the well; b) shaking with the shaker the microwell plate in a manner and for a time period so as to suspend substantially evenly the immune cells in the biological fluid sample within a region of the well such that the immune cells are substantially isolated from the RBCs held against the wall of the well; and c) lowering a sample probe into the well in the region of the well and withdrawing a portion of the sample containing the immune cells from the region.

2. The method of claim 1, wherein the magnetic adapter comprises a structure holding individual magnets, one for each well of the microwell plate, wherein the magnetic adapter is configured to fit onto an upper surface of the shaker and be sandwiched between the upper surface and the microwell plate, and wherein the magnets cause the RBCs to be held to a bottom wall or a side wall of the well.

3. The method of claim 1, wherein the biological fluid comprises whole blood.

4. The method of claim 1, wherein the biological fluid comprises a cyst fluid sample, amniotic fluid, a bone marrow sample, a cerebrospinal fluid sample, a liquid biopsy, or a chorionic villus sample.

5. The method of claim 1, wherein the sample probe is part of a flow cytometer, and wherein the method includes step d) of introducing the portion of the sample containing the immune cells into the flow cytometer.

6. The method of claim 1, wherein the shaker further comprises a home position sensor, and wherein the method further comprises the step of shielding the home position sensor from a magnetic field created by the magnet.

7. The method of claim 1, wherein the shaking step comprises the step of operating the shaker in an eccentric rotation at a speed of between 100 rpm and 1500 rpm.

8. The method of claim 1, wherein the magnetic beads comprise magnetic or paramagnetic beads with an estimated size between 1 nm-50 um, conjugated with a specific molecule that binds to a molecule expressed on the RBCs but not on the immune cells.

9. The method of claim 1, wherein in step a) and c) the shaker is in a non-shaking condition.

10. The method of claim 1, wherein the magnetic adapter including the at least one magnet is integrated into the shaker.

11. A shaker system, comprising, in combination: a shaker configured for shaking in a controlled and programmable manner a plate containing a multitude of wells, the shaker having a top surface; and a magnetic adapter cooperating with structures on the shaker so as to be removably fitted to the top surface of the shaker, the magnetic adapter comprising a structure holding an array of one or more magnets, and wherein the magnetic adapter is configured to fit onto the upper surface of the shaker and be sandwiched between the upper surface of the shaker and the plate.

12. The system of claim 11, wherein the magnets are arranged in the magnetic adapter so as to be in registry with a bottom portion of the wells when the plate is placed on a top surface of the magnetic adapter.

13. The system of claim 11, further comprising a control system for the shaker, wherein the control system operates the shaker such that the shaker shakes the plate in a manner and for a time period so as to suspend substantially evenly immune cells in a biological fluid sample within a region of the well.

14. The system of claim 13, wherein the control system is configured to operate the shaker in an eccentric rotation at a speed of between 100 rpm and 1500 rpm.

15. The system of claim 11, further comprising a sampling probe robotically controlled to move in X, Y and Z directions relative to the plate, the sampling probe withdrawing a sample containing immune cells from the well and introducing the immune cells into an analytical instrument.

16. The system of claim 15, wherein the analytical instrument comprises a flow cytometer.

17. The system of claim 11, further comprising a ferromagnetic shield positioned between the top surface of the shaker and the magnetic adapter.

18. The system of claim 11, wherein the magnetic adapter includes an array of individual magnets, one for each well of the plate.

19. A flow cytometer, comprising: a robotic sampling probe; a shaker having a top surface; a magnetic adapter configured to be placed on the top surface of the shaker, the magnetic adapter having one or more features for holding a microwell plate placed thereon, the microwell plate having a plurality of wells with biological fluid sample, wherein the magnetic adapter cooperates with structures on the shaker so as to be removably fitted to the top surface of the shaker, wherein the magnetic adapter comprises a structure holding one or more magnets, and wherein the magnetic adapter is configured to be sandwiched between the shaker and the microwell plate; a control system configured for shaking the shaker with the microwell plate in a manner and for a time period so as to suspend substantially evenly immune cells within a region of the well of the microwell plate, wherein the immune cells in the region of the well are substantially isolated from red blood cells magnetically bound to a wall of the well; and analytical instrumentation for conducting one or more measurements on immune cells withdrawn from the well of the microwell plate, wherein the probe withdraws the immune cells from the well and introduces the immune cells into the instrumentation.

20. The flow cytometer of claim 19, wherein the biological fluid sample comprises whole blood.

21. The flow cytometer of claim 19, wherein the biological fluid sample comprises a cyst fluid sample, amniotic fluid, a bone marrow sample, a cerebrospinal fluid sample, a liquid biopsy, or a chorionic villus sample.

22. The flow cytometer of claim 19, wherein the shaker further comprises a home position sensor, and wherein the shaker further comprises a shield positioned between the shaker and the magnetic adapter shielding the home position sensor from a magnetic field created by the magnets.

23. The flow cytometer of claim 19, wherein the control system operates the shaker in an eccentric rotation at a speed of between 100 rpm and 1500 rpm.

24. The flow cytometer of claim 23, wherein the red blood cells are bound to magnetic beads with an estimated size between 1 nm-50 um, conjugated with a specific molecule that binds to a molecule expressed on a cell surface of the red blood cells but not a cell surface of the immune cells.

25. The flow cytometer of claim 19, wherein the sampling probe withdraws a sample from the well of the microwell plate after the shaking of the microwell plate and while the immune cells are suspended substantially evenly in the region of the well.

26. The flow cytometer of claim 25, wherein the withdrawal of the sample from the well occurs at a sampling time of between 0.5 second and 5 minutes per well.

27. The flow cytometer of claim 19, further comprising one or more reagents for the biological fluid sample, wherein the one or more reagents include magnetic beads conjugated to an antibody designed to bind selectively to the surface of RBCs.

28. The system of claim 11, wherein the magnetic adapter is configured to position the magnets in a space proximate to a side wall of the wells of the microwell plate.

29.-32. (canceled)

33. The method of claim 1, further comprising the step of placing a pierceable seal over the microwell plate prior to performing step A).

34. The method of claim 1, wherein the sample further includes in-well marker beads or in-well counting beads.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0012] FIGS. 1A-1E are an illustration of a workflow or method for automatically sampling cells, such as immune cells, from a biological fluid sample containing red blood cells, e.g., a whole blood sample, in a microwell plate format, consisting of preliminary steps shown in FIGS. 1A and 1B, and then steps shown in FIGS. 10, 1D and 1E.

[0013] FIG. 2 is an illustration of a microwell plate positioned over a shaker in accordance with FIG. 1 and showing a magnetic adapter secured to the shaker and positioned between the shaker and the microwell plate.

[0014] FIG. 3 is an exploded view of the assembly of FIG. 2.

[0015] FIG. 4 is a top view of the magnetic adapter of FIGS. 2 and 3.

[0016] FIG. 5 is a side view of the magnetic adapter of FIG. 4.

[0017] FIG. 6 is an illustration of a sampling probe inserted into one of the wells of the microwell plate of FIG. 2 withdrawing a sample from the well, in accordance with step E of FIG. 1E.

[0018] FIG. 7 is an exploded view of the magnetic adapter of FIG. 4 showing an optional ferromagnetic shield placed below and immediately adjacent to the lower surface of the magnetic adapter.

[0019] FIG. 8 is a partial cross-sectional view of the assembly of FIG. 7.

[0020] FIG. 9 is an illustration of a flow cytometer adapted for processing samples, including whole blood samples, in microwell plate format, which includes the shaker and magnetic assembly of FIG. 2; FIG. 9 also shows an associated workstation which is used for displaying analytical results from the flow cytometer.

[0021] FIG. 10 is a perspective view of the flow cytometer of FIG. 9, with the shaker moved into the interior of the flow cytometer in position for various processing steps to be performed on the microwell plate; FIG. 10 also shows a sampling probe connected to a three-axis robotic movement system which enables all the wells to be sampled.

[0022] FIG. 11 is another perspective view of the flow cytometer of FIG. 9 with the sample probe in position for withdrawing a sample from one of the wells in accordance with step E of FIG. 1E.

DETAILED DESCRIPTION

[0023] Overview

[0024] In one aspect of this disclosure, a method is provided for automatic sampling of cells, such as immune cells, from a biological fluid sample containing red blood cells (RBCs) deposited in a well of a microwell plate. In the following description, the fluid sample is described as whole blood, but as stated previously, the sample can be other biological fluids containing mixed particle populations, such as red blood cells, other cell types, or particles of noninterest, and so on. These fluids can be, for example, amniotic fluid, cerebrospinal fluid, etc.

[0025] The methodology is shown in FIGS. 1A-1E, consisting of preliminary steps shown in FIGS. 1A and 1B, and then steps 10, 1D and 1E. The process will further be explained in conjunction with FIGS. 2 and 3. It will be appreciated from the following description that the process shown for a single well 10 of a microwell plate 100 (FIG. 2) is performed for all the wells which have been loaded with the sample 12 (e.g., whole blood).

[0026] At step A (FIG. 1A), user-specified treatment and/or staining cocktails (reagents) are added to the sample 12. Such reagents could include marker beads for well identification (well-ID) for samples with few white blood cells (WBCs), in-well counting beads to facilitate WBCs counting, staining agents, or possibly others.

[0027] At step B (FIG. 1B), magnetic beads 14 which are conjugated to antibodies or otherwise designed to bind to RBCs 15 in the sample are added to the sample 12. An example of such beads are anti-human CD235 antibody-coated magnetic beads. The antibodies coated on the magnetic beads are not limited to the antibodies against a CD235 molecule but can also be other antibodies against a molecule specifically expressed on RBCs but not on the WBCs. Further, the moiety molecules coated on the beads are not limited to antibodies, but could be other molecules such as antibody fragments, affimers, and antigens that can specifically bind to the molecules only expressed on RBCs but not on the WBCs.

[0028] Steps A and B can be performed on the laboratory bench, prior to insertion of a microwell plate 100 (FIG. 2) into an analytical instrument. After step B, the microwell plate 100 can be incubated for some period of time to allow the magnetic beads 14 to be conjugated to the RBCs 15, for example between one minute and two hours; the duration for incubation is flexible and the user can optimize.

[0029] At step C (FIG. 10), a magnetic separation of the RBCs 15 from the WBCs 17 in the sample 12 is performed. In particular, the microwell plate 100 is placed on top of a microtiter plate shaker 104, such as the BioShake 3000, with the shaker 104 having a magnetic adapter 102 including a magnet 120 fitted or placed on top of the shaker 104. The magnet 120 attracts the magnetic beads 14 and causes the RBCs 15, bound to the magnetic beads 14, to be attracted to and migrate to a bottom wall 16 or a side wall 19 of the well 10 and be held against the wall 16 (or 19, depending on the location of the magnets). This action separates WBCs 17 into a layer above the RBCs 15, which are bound to the bottom wall 16 of the well 10. The magnetic adapter 102 is placed on top of the microtiter plate shaker and is designed to be removed from or inserted onto the top surface of the shaker 104 by a user without the use of special tools. The adapter 102 is thus sandwiched between the top of the shaker 104 and the microwell plate 100. Shaking is not performed at step C or, optionally, only very gentle shaking can be performed at step C, which allows the magnetic beads 14 to bind to the RBCs 15 and still be pulled down the RBCs 15 to the side wall 19 and/or the bottom wall 16 of the well 10, depending on the location of the magnets. In the embodiment where the magnets are positioned below the microwell plate the RBCs are pulled down to the bottom wall 16 as show in FIG. 10.

[0030] In step D (FIG. 1D), after the RBCs 15 settle down at the well bottom 16 as shown in FIG. 1D, the shaker 104 is turned on and shakes at a designated speed (revolutions per minute, rpm) within a certain range so as to only resuspend substantially evenly or homogenously the WBCs 17 in the top liquid layer (mostly serum and plasma), while the RBCs 15 will remain tightly attached at the well bottom 16 by virtue of the attraction of the conjugated magnetic beads 14 to the magnet. In other words, in this step the shaker 104 shakes the microwell plate 100 in a manner and for a time period so as to suspend and distribute substantially evenly or homogeneously the immune cells 17 (WBCs) in the biological fluid sample within a region of the well (indicated at 18) but still retain the holding of the RBCs to the bottom wall 16 and/or side wall 19 (FIG. 10) of the well 10 such that the immune cells 17 (WBCs) are substantially isolated from the RBCs in the region 18. The manner of performing the shaking (i.e., speed) is described in some detail below, the particulars of which may vary depending on the strength of the binding of the beads 14 to the RBCs 15, the design of the shaker 104 itself, the microwell plate 100 design, the liquid volume in each well, and may be experimentally determined for particular magnetic beads and a given shaker. After some predetermined time period, e.g., 10 seconds, the shaker 104 is turned off.

[0031] In step E (FIG. 1E), immediately after the shaking is concluded, or optionally while the shaking is ongoing, software with a specific sampling protocol governing operation of a sampling probe 200 automatically guides the sample probe 200 to insert the tip thereof into the top liquid layer (region 18) and to acquire a certain volume of WBCs 17 without contamination of RBCs 15 still magnetically held at the bottom of the well 16. This acquisition is performed by controlling a sampling height position of the sample probe 200. Thus, in this step the sample probe 200 is lowered into the well 10 in the region 18 of the well where the WBCs 17 are substantially evenly or homogenously suspended. A portion of the sample containing the immune cells is then withdrawn from the region 18. This is shown in FIG. 6.

[0032] After withdrawal of the WBC sample 17, the sample can be processed in an analytical instrument to which the probe 200 belongs, such as a flow cytometer. The sample is introduced into the analytical instrument, such as a sample introduction port, which conveys the sample to further analytical instrumentation which conducts measurements on the sample.

[0033] Shaker and Magnetic Adapter Design

[0034] Referring now to FIGS. 2-5, the shaker 104 can take the form of any of the commercially available devices designed to shake or agitate a microwell plate, such as the shaker mentioned previously, shakers from such companies as QInstruments, ThermoFisher, SigmaAldrich, Southwest Science, and others. The shaker 104 typically is designed with an eccentric or orbital rotation to induce vortex action within the well and is programmably controlled to rotate at a predetermined or user-specified speed. For example, the eccentric offset may be 2 mm, and the optimal speed of rotation and duration is determined such that the desired even distribution of the WBCs 17 is achieved in the upper region 18 of the well without release of the RBCs 15 from the bottom of the well, for example 250 rpm for 10 seconds. Referring to FIG. 3, the magnetic adapter 102 can take the form of a substantially flat structure as shown holding individual magnets 120, one for each well 10 of the microwell plate 100. As an alternative, the magnets 120 on the adapter plate 102 can be configured as two or more magnets per well, or even two or more wells per magnet or a group of magnets. A configuration having exactly one magnet-per-well is not required, only that the magnets produce a substantially uniform magnetic field. The magnetic adapter 102 is configured to fit onto an upper surface 106 of the shaker 104 and be sandwiched between the upper surface 106 and the microwell plate 100 as shown in FIG. 2, wherein the magnets 120 cause the RBCs 15 to be held to the bottom wall of the well. The adapter plate 102 includes corner features 114 which are designed to hold the corners 116 of the microwell plate 100 and prevent the plate from being dislocated from the shaker 104 during shaking. In addition, the corner features 114 can be designed to guide the microwell plate 100 into the correct location when the user is placing it onto the adapter 102. The adapter 102 is designed to be readily attached to and removed from the shaker 104 manually without the use of tools. This can be achieved by resilient gripping skirts 110, for example, that descends from the adapter 102 which fit against a recess 112 provided in the front and rear sides of the shaker 104. Locating pins 108 project from the upper surface of the shaker 104, which serve to fit in corresponding recesses provided in the adapter plate 102 and snugly grip the adapter plate as shown in FIG. 2. Depending on the embodiment, the locating pins 108 can grip and hold the adapter plate 102 in place, or the microwell plate 100, or both.

[0035] The locating pins 108 can be computer-controlled to move into and out of a gripping position to grip the adapter plate 102. This feature can be important when the shaker 104 is used in an automation mode. In this mode, the software can automatically loosen or tighten the locating pins 108 when a robotic arm removes a microwell plate 100 from the shaker 104 and/or puts a new microwell plate on the shaker. When the magnetic adapter design includes a magnetic shield 302 (see the discussion of FIGS. 7 and 8), the existing grippers/locating pins 108 on some shakers (such as the BioShake 3000) are not long enough to reach the microwell plate and hold it in place. One solution to this is to add further compliant gripping features (not shown) to the magnetic adapter. These compliant gripping features interact with the existing grippers/locating pins 108 on the BioShake 3000 so that when the BioShake 3000's locating pins 108 close, the compliant gripping features push to grip the microwell plate. Then, when the BioShake 3000 locating pins 108 relax, the compliant gripping features on the magnetic adapter also relax and the microwell plate is released. Of course, these solutions can be applied to other shaker designs; indeed, the particular form factor and design of the magnetic adapter 102 of FIG. 3 can change in order to be compatible with the surface geometry, locating pins and grippers of any shaker in question, as well as the particular configuration of the microwell plate 100.

[0036] One possible configuration of the adapter plate 102 and magnets 120 is shown in an exploded view in FIG. 7. The adapter plate 102 has an array of recessed pockets 300, each of which receive and hold one of the magnets 120. The layout of the array of pockets 300 (and thus the magnets 120) is such that each magnet is designed to be positioned directly below a sample well in a standard format microwell plate. While FIG. 7 shows a 96 well plate, the same design consideration will apply to microwell plates with different numbers of wells, such as a 384 well plate. As an alternative, the magnets 120 on the adapter plate 102 can be configured as two or more magnets per well, or even two or more wells per magnet or a group of magnets. A configuration having exactly one magnet-per-well is not required, only that the magnets produce a substantially uniform magnetic field.

[0037] The shaker 104 typically is configured with a home position sensor, which can take the form of, for example, a hall-effect sensor. The presence of the magnets on the adapter plate 102 immediately above the shaker 104 produces a magnetic field which can interfere with the operation of the home position sensor in the shaker. To ameliorate this, in one optional embodiment, a ferromagnetic shield 302 (FIGS. 7, 8) in the form of a thin, flat plate of ferromagnetic material, such as stainless steel or mu-metal, is positioned below the adaptor plate 102 as shown in FIGS. 7 and 8 such that when the adapter plate 102 and shield 302 are placed on the shaker 104, the home position sensor operation is not adversely affected. The shield 302 can be mounted or affixed to the bottom surface of the magnetic adapter plate 102 in any suitable manner. The shield 302 redirects the magnetic field lines and reduces the field strength at the location of the home position sensor. Shield thickness and material is not especially critical provided it is made from a ferromagnetic material. However, increasing the separation distance between the shaker 104 and the magnets 120 and adding the shield 302 below the magnets 120 allows the shaker to operate correctly.

EXAMPLE

[0038] Flow Cytometer with Direct Sampling of Immune Cells from Whole Blood Samples in Microwell Plate (FIGS. 1, 9-11)

[0039] An example of a system in which the present method can be performed is shown in FIGS. 9-11. FIG. 9 is an illustration of a flow cytometer 400 adapted for processing samples, including whole blood samples, in a microwell plate format 100, which includes the shaker 104 and the magnetic adapter 102 assembly of FIG. 2. The instrument shown is the iQue® 3 flow cytometer of the assignee of this invention, however the principles discussed in this example would apply to other analytical devices or flow cytometers. FIG. 9 also shows an associated workstation 410 which is used for displaying analytical results from the flow cytometer. The workstation 410 can include an interface to allow the user to designate certain workflow and processing steps to be performed for a given microwell plate, and associated samples loaded into the microwell plate 100, such as initiate a “whole blood sample module” described below. The flow cytometer can also include a supply of reagents, buffers, cleaning solutions, etc. 402. The flow cytometer 400 includes a loading station 404 where the microwell plate 100 is placed on the shaker 104, a clear plastic partition 412 mounted on hinges which opens to allow access to the interior of the flow cytometer, and a rinse station 406 (FIG. 10).

[0040] FIG. 10 is a perspective view of the flow cytometer 400 of FIG. 9, showing the clear partition 412 moved to an open position, showing the shaker 104 moved into the interior of the flow cytometer 400 adjacent to the rinse station 406 where various processing steps can be performed on the microwell plate 100. FIG. 10 also shows a sampling probe 200 connected to a three-axis robotic movement system 414. The movement system 414 is under program control to move in X, Y and Z directions and thus enables all the wells on the microwell plate 100 to be sampled by the sampling probe 200.

[0041] The flow cytometer 400 also includes analytical instrumentation for conducting flow cytometry on the immune cells withdrawn from a well of the microwell plate 100, located behind the panels of the flow cytometer shown in FIG. 10, which is conventional and therefore not described in detail in this document for the sake of brevity. The probe 200 withdraws the immune cells from the well and introduces the immune cells into the analytical instrumentation.

[0042] FIG. 11 is another perspective view of the flow cytometer of FIG. 9 with the sample probe 200 in position for withdrawing a sample from one of the wells in the microwell plate 100 in accordance with step E of FIG. 1E and FIG. 6.

[0043] The flow cytometer 400 includes a loading station 404 (FIG. 9) which is the location where the user places the microwell plate 100 onto the shaker 104 (with the magnetic adapter 102 positioned on the upper surface of the shaker 104 as shown in FIG. 2). The shaker 104 is connected to a motor-driven electro-mechanical system which then moves the shaker 104 from the loading station 404 (FIG. 9) into the interior of the flow cytometer through an opening in the clear partition 412, see FIG. 10.

[0044] In accordance with the method of FIG. 1, the steps A and B of FIGS. 1A and 1B, respectively, are typically performed off-line, e.g., on a laboratory bench. After step B, the microwell plate 100 is then placed on the shaker 104 at the loading station 404, see FIG. 9. By virtue of the magnetic adapter 102 sandwiched between the shaker 104 and the microwell plate 100, the RBCs are pulled down to the bottom of the wells of the microwell plate in accordance with step C of FIG. 10 when the microwell plate is placed on the magnetic adapter. During or immediately after performing step C, the duration of which may for example be 30, 60 or 90 seconds, the shaker is moved from the loading station 404 of FIG. 9 to the interior of the flow cytometer in the position shown in FIGS. 10 and 11.

[0045] At step D of FIG. 1D, the shaker 104 is activated for a period of time while the RBCs remain held against the bottom and/or side wall to suspend substantially evenly or homogeneously the immune cells in the sample at the top of the wells in the region 18 (FIG. 1D). This shaking step can be done with the shaker 104 in the loading station 404 of FIG. 9 or in the sample acquisition position shown in FIG. 10.

[0046] In step E of FIG. 1E, the shaker 104 is stopped and immediately thereafter the sample probe 200 is lowered, as shown in FIG. 11, into the first well of the microwell plate to withdraw a sample containing substantially only the immune cells in accordance with FIG. 6. The sample probe is operated by the robotic movement system in X, Y and Z directions to sample in the same manner any and/or all of the wells of the microwell plate 100 which hold a sample. After the sample is acquired by the probe 200 using the force from a peristaltic pump or a vacuum pump (not shown), it is delivered to analytical instrumentation (not shown) within the flow cytometer 400, which conducts flow cytometry in a conventional manner. For example, the flow cytometer 400 of FIG. 9 is configured in the manner described in U.S. Pat. Nos. 10,048,191; 9,897,531; 9,797,917; and 6,890,487.

[0047] Software Operations

[0048] The operation of the shaking and sampling modes of FIGS. 1D and 1E in the flow cytometer of FIGS. 9-11 is governed by software operations and a processor within the flow cytometer 400, which control the operation of the shaker 104, the sample probe 200, and associated 3-axis robotic movement system 414. These operations are within a mode or module of the flow cytometer which is designed to process whole blood samples and is referred to as a “whole blood sample module” or “whole blood sample mode” in the following description. The parameters of this mode can be accessed by the workstation 410 of FIG. 9 and configured by a user, or can be pre-set instructions which are automatically performed when the user selects the whole blood sample module for processing of a given microwell plate.

[0049] Module Detection and RBC Pull Down

[0050] In FIG. 10, prior to sampling, a probe (FIG. 10, 200) extending from the sampling head 411 (FIG. 10) is lowered until it makes contact with the magnetic adapter 102. Once the probe 200 senses a deck height difference (due to the presence of the magnetic adapter 102 on top of the shaker), the software in the flow cytometer is triggered to alert the user that the system is operating in a whole blood sample module or mode. A predefined waiting period for RBCs pulldown is automatically included in this mode, step C of FIG. 10. If the user selects the whole blood sample module and the probe does not detect the magnetic adapter 102, the run will stop with a warning notifying the user of an error condition.

[0051] Automated Optimal Shaking

[0052] The software for the flow cytometer automatically adopts a specific whole blood sample module (operating mode) with a specific sample acquisition template. The software then sets a specific shaking speed to suspend the WBCs only, but not the RBCs which remain bound to the bottom or side wall of the well.

[0053] For the shaking speed range, in order to maintain the intact layer of RBCs pulled down by magnetic beads while keeping the WBCs homogenously distributed in the top clear liquid within the sample well, the shaking speed range on a BioShake 3000 is between 100 rpm and 1500 rpm. Above 1500 rpm, the RBCs attached with magnetic beads start to get lifted into the top clear liquid containing WBCs. This maximum speed can be experimentally determined, for example, by observation of the top liquid color and when it changes color from yellow to reddish as the speed is increased. For example, once above 1500 rpm, the top liquid color starts to change from yellowish to reddish or fully red.

[0054] Further, the shaking speed range is related to the magnetic or paramagnetic beads materials placed in the biological fluid sample and the magnetic field strength. The reagent with magnetic beads used for proof-of-concept in the present disclosure was the EasySep RBC depletion reagent (StemCell Tech, Cat. #18170) which has nano-magnetic beads (Iron oxide, Fe.sub.3O.sub.4) with estimated size between 20-500 nm (diameter). The magnetic beads were conjugated with anti-human CD235 antibody in order to bind to the CD235 molecule expressed on the cell surface of the human RBCs only. Once the magnetic field was present below the well (due to the magnets of the adapter plate), the RBCs bound with the magnetic beads were pulled down to the well bottom.

[0055] In general, the optimal shaking speed may also be determined by the eccentricity or amplitude of the shaker itself, and thus the optimal speed of rotation of the shaker may depend on this factor as well.

[0056] Automated Acquisition

[0057] The software of the flow cytometer operating in the whole blood sample mode will guide the sampling probe to descend such that the tip of the probe is into the top liquid layer of the well with WBCs suspended substantially evenly or homogeneously therein, without touching or disturbing the RBCs at the bottom of the well. See FIG. 6 and FIG. 1E. The sampling time and speed is limited to a certain range to avoid RBCs contamination into the probe. Sampling occurs immediately after shaking stops or during the shaking, with sampling time ranging between 0.5 seconds and 5 minutes per well.

[0058] Automated Analysis

[0059] After the sample probe 200 has sampled the wells of the microwell plate the sample is introduced into flow cytometer instrumentation per se, which is part of the instrument 400 of FIG. 9. After passage of the WBC sample into the flow cytometer instrumentation, the analytical software for the instrument will perform an automatic data analysis. In one possible configuration this analysis includes automated bead-based sample well identification and immune cell count normalization. The details of the data analysis are not particularly pertinent to this disclosure and can make use of algorithms which are known in the art and described in the patent and technical literature.

[0060] Further details on the flow cytometer and sampling arrangement of FIGS. 9-11 is set forth in U.S. Pat. Nos. 10,048,191; 9,897,531; 9,797,917; and 6,890,487, the contents of which is incorporation by reference herein.

[0061] Additional Optional Features

[0062] The whole blood sample module software ensures that the magnetic adapter 102 is installed correctly on the shaker 104, and when that is verified, locks down the shaking and sampling protocol to appropriate values. Additional cleaning can be automated in the software sampling protocol. The module can also enable specific and automated analysis if marker or counting beads are present. Further, the module can also detect RBCs contamination in the sample, indicating a potential problem with the assay.

[0063] In one configuration it is possible to provide a pierceable seal or membrane covering the wells of the microwell plate (e.g., Excel Scientific X-Pierce plate seal) that increases biosafety by preventing contamination and spillover in accidents. This is especially important for blood samples which may potentially carry unknown pathogen(s). The seal is applied to the microwell plate after the reagents, such as dyes, and magnetic beads are added to the sample and before the plate is placed on the shaker and magnetic adapter.

[0064] In another configuration it is possible to provide in-well marker beads. Such beads can be used for sample well identification (well-ID) for samples with few WBCs due to specific conditions. It is also possible to provide in-well counting beads. Such beads allow for accurately calculating WBC concentration based on the counts of in-well counting beads. Such beads can be added in preliminary step A, off-line on a table top; or they can be part of the reagents which are present in the rinse station 406 of FIG. 10 and introduced immediately prior to shaking operation (step D, FIG. 1D).

[0065] Specific assay microwell plates are contemplated for use with whole blood samples, and particularly those that have smaller volumes that is typical for a 96 well plate. For example, the plate from Greiner, Cat #675101 of 96-well format with the well area about half of a normal well area, can be used. This well geometry increases the top layer height with the same volume of sample for easy probe access, minimizes the use of sample/reagent, and reduces the risk of RBC contamination in the sample.

ALTERNATIVE EMBODIMENTS

[0066] 1. As explained in conjunction with FIG. 1, the principal method for separating immune cells is negative selection of RBCs by the magnetic pulling of magnetic bead-bound RBCs to the well bottom, and the magnet is positioned proximate to the well bottom of the assay plate. An alternative location for the magnet is the gap in-between the adjacent wells so the magnetic field can pull the magnetic bead-bound cells to the side wall of the assay well (19 in FIG. 10). In this configuration, the form factor and design of the magnetic adapter 102 is such that the magnetic adapter includes features which project into spaces formed in the bottom of the microwell plate 100 such that the magnets incorporated therein are proximate to the side walls of the well instead of the bottom of the well.

[0067] 2. A second alternative method to separate cells is by using hollow or buoyant particles conjugated with interest molecules, such as antibodies or affimers which can bind to and float any specific cell population to a top surface of the liquid sample in the assay well. For example, it can be possible to float the RBCs to the top of the well, and sample from the lower or middle regions of the well to draw WBCs into the probe. In accordance with this design, a method of sampling immune cells in a liquid sample containing a mixture of red blood cells and immune cells can comprise the steps of: (A) introducing into the sample hollow or buoyant particles designed to bind RBCs, (B) either before or after step (A), introducing the liquid sample into an assay well of a microwell plate; (C) allowing the RBCs to float to a top surface of the liquid sample in the assay by virtue of the binding of the RBCs to the hollow or buoyant particles, the top surface lying above lower and middle regions of the assay well containing the WBCs; and (D) withdrawing with a sampling probe WBCs from the lower or middle regions of the assay well.

[0068] 3. A third alternative method to separate cells in the microwell plate is to use gradient centrifugation to force multiple liquid layers to form in the sample in the microwells, with each layer containing different cell populations.

[0069] 4. For all of the above different cell separation methods, after cell separation, the sampling probe descends to a specific layer containing cell/particle population(s) of interest and acquires the sample. The sampling probe can descend to a specific location of the well to sample only one layer or descend to multiple locations in the same well to sample different layers.

[0070] 5. The sample probe can be just one single probe that descends to one or more locations to acquire one or more layers. An alternative way is to use multiple probes which descend to one or more locations to acquire samples from one or more layers.

[0071] 6. The methods of this disclosure can be applied to any detection system, e.g. hematology analyzers, cell sorters, mass spectrometers, DNA/RNA analyzer, etc. The methodology of FIG. 1A-1E is accordingly not limited to flow cytometers. Hence the instrument shown in FIGS. 9-11 is offered by way of example and not limitation.

[0072] Further considerations One of the applications of the method of this disclosure is a miniaturized “clinical-trial-in-a-dish” application and expands a flow cytometer's capability to directly acquire/analyze a whole blood sample in a miniaturized format for immunology, immuno-oncology, immuno-toxicity, drug profiling studies, and similar research efforts. The method of this disclosure can be applied to any sampling of one or more particles of interest from a mixed sample in liquid containing RBCs or other uninteresting particles, such as liquid biopsy, cerebrospinal fluid (CSF), chorionic villus sample (CVS), amniotic fluid (AF), cyst fluid sample, bone marrow sample, etc. The mixed sample may be pre-stained with antibodies and other dyes and pre-mixed with different functional beads, such as Sartorius/Intellicyt QBeads, for simultaneous measurement of cytokines, growth factors, chemokines, hormones, and other biological factors or particles.