CA2928406A1

CA2928406A1 - Methods and apparatus for point-of-care nucleic acid amplification and detection

Info

Publication number: CA2928406A1
Application number: CA2928406A
Authority: CA
Inventors: Jane P. Bearinger; Scott Castanon; Kenneth J. Michlitsch
Original assignee: CORPOROS Inc
Current assignee: CORPOROS Inc
Priority date: 2013-10-22
Filing date: 2014-10-22
Publication date: 2015-04-30
Also published as: CN105874084A; WO2015061480A1; JP2016539633A; EP3060683A1; EP3060683A4

Abstract

Methods and apparatus are provided for point-of-care nucleic acid amplification and detection. One embodiment of the invention comprises a fully integrated, sample-to-answer molecular diagnostic instrument that optionally may be used in a multiplexed fashion to detect multiple target nucleic acid sequences of interest and that optionally may be configured for disposal after one-time use. The instrument preferable utilizes an isothermal nucleic acid amplification technique, such as loop-mediated isothermal amplification (LAMP), to reduce the instrumentation requirements associated with nucleic acid amplification. Detection of target amplification may be achieved, for example, via detection of a color shift or fluorescence in a dye added to the amplification reaction. Such detection may be performed visually by an operator or may be achieved utilizing an imaging technique, e.g., spectrophotometric imaging.

Description

METHODS AND APPARATUS FOR POINT-OF-CARE
NUCLEIC ACID AMPLIFICATION AND DETECTION
REFERENCE TO RELATED APPLICATIONS
[001] The present application claims priority and benefit of the filing date of U.S. Patent Application No. 61/894,392, filed October 22, 2013, and U.S. Patent Application No.
14/262,683, filed April 25, 2014, both of which are incorporated herein by reference in their entireties.
INCORPORATION BY REFERENCE

[002] All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
TECHNICAL FIELD

[003] The present invention relates to methods and apparatus for nucleic acid amplification and detection. More particularly, the present invention relates to methods and apparatus for point-of-care nucleic acid amplification and detection.
BACKGROUND

[004] Polymerase Chain Reaction (PCR) is considered the gold standard for nucleic acid amplification and detection because the specificity and sensitivity of PCR are considerably higher than that of analogous Enzyme-Linked Immuno-Sorbent Assay ("ELISA") tests. However, PCR systems typically are costly and require very clean samples. Point-Of-Care (POC) PCR systems generally are not fully disposable, are not appropriate for unskilled use, require substantial power and/or contain complicated processing and readout. Thus, PCR traditionally has been limited to high resource, centralized laboratory settings.

[005] In view of the foregoing, it would be desirable to provide methods and apparatus for point-of-care nucleic acid amplification and detection that overcome the drawbacks of previously known methods and apparatus.
BRIEF DESCRIPTION OF THE DRAWINGS

[006] Several embodiments of the present invention will be apparent upon consideration of the following detailed description, taken in conjunction with the accompanying drawings, in which like reference characters refer to like parts throughout, and in which:

[007] Figure 1 is a schematic view of one embodiment of a sample collector;

[008] Figures 2A-2C are isometric and side views of apparatus and methods for preparing and transferring sample from the sample collector of Figure 1 to point-of-care nucleic acid amplification and detection apparatus;

[009] Figures 3A and 3B are side and isometric views of alternative apparatus and methods for preparing and transferring sample from the sample collector of Figure 1 to point-of-care nucleic acid amplification and detection apparatus;

[0010] Figures 4A-4D are side-sectional and isometric views of additional alternative apparatus and methods for preparing and transferring sample from the sample collector of Figure 1 to point-of-care nucleic acid amplification and detection apparatus;

[0011] Figure 5 is an exploded assembly view of the point-of-care nucleic acid amplification and detection apparatus of Figures 2-4;

[0012] Figure 6 is a bottom view of a channel and chamber element of the point-of-care nucleic acid amplification and detection apparatus of Figure 2-5;

[0013] Figure 7A is an isometric view of the point-of-care nucleic acid amplification and detection apparatus of Figures 2-6 in thermal communication with a heating element, while Figure 7B is an isometric view of an optional detection sensor for use with the apparatus and method of Figure 7A;

[0014] Figures 8A-8E are isometric, top, bottom and side-sectional views of an alternative embodiment of the methods and apparatus for point-of-care nucleic acid amplification and detection of Figures 2-7;

[0015] Figures 9A-9J are isometric, top, bottom, assembly, side-sectional detail, and translucent isometric views of another alternative embodiment of methods and apparatus for point-of-care nucleic acid amplification and detection;

[0016] Figures 10A-10G are isometric top, isometric bottom, isometric detail, translucent detail and side-sectional detail views of another alternative embodiment of methods and apparatus for point-of-care nucleic acid amplification and detection; and

[0017] Figures 11A-11J are side, side-sectional, isometric, and translucent isometric views of yet another alternative embodiment of methods and apparatus for point-of-care nucleic acid amplification and detection.
DETAILED DESCRIPTION

[0018] Although this disclosure is detailed and exact to enable those skilled in the art to practice the disclosed technologies, the physical embodiments herein disclosed merely exemplify the various aspects of the invention, which may be embodied in other specific structures. While the preferred embodiments are described, the details may be changed without departing from the invention, which is defined by the claims.

[0019] The present invention relates to methods and apparatus for nucleic acid amplification and detection. More particularly, the present invention relates to methods and apparatus for point-of-care nucleic acid amplification and detection. The apparatus and methods optionally may be used in a multiplexed fashion to detect multiple target nucleic acid sequences of interest (e.g., to detect at least two target nucleic acid sequences of interest), and the apparatus optionally may be configured for disposal after one-time use.

[0020] The apparatus preferable utilizes an isothermal nucleic acid amplification technique, e.g., loop-mediated isothermal amplification ("LAMP)", to reduce the instrumentation requirements associated with nucleic acid amplification.
Detection of target amplification may be achieved, for example, via detection of a color shift and/or fluorescence in one or more dyes, such as hydroxynaphthol blue, picogreen, and/or SYBR
green, added to the amplification reaction, or via a change in turbidity. Such colorimetric, fluorescent and/or turbidity detection may be performed visually by an operator and/or may be achieved utilizing an imaging technique, such as spectrophotometric and/or fluorescence imaging, as described below.

[0021] Figure 1 illustrates one embodiment of sample collector 10, per se known, for collecting a nucleic acid sample S. Sample collector 10 may, for example, comprise a sponge, foam or swab. Sample collector 10 may, for example, be fabricated from an inert polymer. Various sample matrices - including, but not limited to, food, urine, saliva, mucous, feces, blood, semen, tissue, cells, DNA, RNA, protein, plant matter, animal matter, liquids, solutions, solids, gases, and other sample matrices - may be deposited onto sample collector 10 as sample S.

[0022] In order to collect sample S with sample collector 10, the sample collector may, for example, be dipped or placed into one or more sample matrices of interest. In one method of using sample collector 10, the sample collector may be placed in a person's mouth for a period of time in order to collect a saliva sample S. Additionally or alternatively, one or more drops of one or more sample matrices of interest may, for example, be placed or deposited onto the sample collector. As yet another alternative, sample collector 10 may, for example, be swabbed or wiped across one or more sample matrices or surfaces of interest.

[0023] After collection of sample S, the sample may be transferred from sample collector 10 to point-of-care nucleic acid amplification and detection apparatus 100.
Optionally, the sample may be prepared before, during or after transfer, e.g., via placement of sample S in fluid communication with lysis chemicals. Sample collector 10 optionally may comprise lysis chemicals that prepare sample S. Additionally or alternatively, sample S may be prepared via heat treatment. For example, sample S may be heated to a temperature higher than that required for isothermal amplification, e.g., higher than that required for loop-mediated isothermal amplification ("LAMP").
In some embodiments, sample S may comprise whole blood, which may, for example, be heat treated at about 99 C, e.g., for about 10 minutes, to achieve sample preparation. Other preparation methods, per se known, additionally or alternatively may be used.
In some embodiments, sample S may not require preparation. In some embodiments, mixing of sample S with water, buffer and/ or dye solution may be sufficient to prepare the sample for nucleic acid amplification.

[0024] Figures 2 illustrate one embodiment of methods and apparatus for transferring sample S from sample collector 10 to point-of-care nucleic acid amplification and detection apparatus 100. As seen in Figure 2A, sample collector 10 may be placed within sample collector containment element 20 having luer lock 22. Containment element 20 comprises a lumen or compartment in which sample collector 10 may be placed. As seen in Figure 2B, cap 24 having luer lock 26 may be attached to sample collector containment element 20 after placement of sample collector 10 within the containment element 20.
Containment element 20 and sample collector 10 then may be attached to syringe 30 via mating of (male or female) luer lock 26 of cap 24 with (female or male) luer lock 32 of syringe 30.

[0025] As seen in Figure 2C, syringe 30 and containment element 20 with sample collector 10 may be coupled to point-of-care nucleic acid amplification and detection apparatus 100 by mating of (male or female) luer lock 22 of containment element 20 with (female or male) luer lock 102 of apparatus 100. Syringe 30 may contain liquid L (e.g., water, buffer and/or colorimetric or other dye solution) for eluting sample S
from sample collector 10 into apparatus 100 via depression of plunger 34. Luer lock 102 of apparatus 100 (and/or the syringe or other alternative delivery device for delivering sample S) optionally may comprise a one-way valve that prevents backflow during nucleic acid amplification and detection.

[0026] Figures 3 illustrate alternative methods and apparatus for transferring sample S from sample collector 10 to apparatus 100. As seen in Figure 3A, luer lock 22 of containment element 20 may be coupled to luer lock 42 of second syringe 40.
Plunger 34 of syringe 30 may be depressed to elute liquid L and sample S from sample collector 10 into second syringe 40. Elution of liquid L and sample S into second syringe 40 before transfer of the sample to apparatus 100 may enhance mixing of the liquid and the sample before transfer to apparatus 100. Furthermore, sample S optionally may be collected and/or eluted multiple times into second syringe 40 before transfer to apparatus 100.

[0027] As seen in Figure 3B, after collection of sample S and liquid L
within second syringe 40, second syringe 40 may be detached from syringe 30, containment element 20 and sample collector 10. Second syringe 30 then may be coupled to apparatus 100 by mating of luer lock 42 to luer lock 102. Depression of plunger 44 forces sample S and liquid L into apparatus 100.

[0028] Figures 4 illustrate additional alternative methods and apparatus for transferring sample S from sample collector 10 to apparatus 100. As seen in Figure 4A, sample collector 10 having sample S may be placed directly within syringe 30 by temporarily detaching plunger 34 from the syringe. Optionally, liquid L may be placed within syringe 30 along with sample collector 10 having sample S, though it should be understood that liquid L alternatively may be omitted. After placement of sample collector within syringe 30, plunger 34 may be reattached to the syringe, as in Figure 4B.
Syringe 30 then may be coupled to apparatus 100 by mating of luer lock 32 with luer lock 102, as in Figure 4C. Depression of plunger 34, as in Figure 4D, compresses sample collector 10 and expresses sample S into apparatus 100.

[0029] With reference now to Figure 5, a first embodiment of fully integrated sample-to-answer molecular diagnostic apparatus 100 for point-of-care nucleic acid amplification and detection is described. Apparatus 100 comprises luer lock 102 that is connected to channel and chamber element 110. Element 110 may, for example, be fabricated from polypropylene.

[0030] Channel cover 104 connects to the bottom of element 110, e.g., via adhesive or screws, while chamber cover 106 connects to the top of element 110, e.g., via adhesive or screws. Covers 104 and 106 may, for example, comprise an adhesive film or tape.
Chamber cover 106 (and, optionally, channel cover 104) preferably is translucent or transparent to facilitate visual inspection of the contents of reaction chambers 112 of element 110. Apparatus 100 also may comprise top cover 120 with air filter 122, as well as chamber windows 124 that align with chambers 112 of element 110. In some embodiments, each chamber 112 may have a volume less than about 100 microliters, e.g., a volume on the order of about 30 microliters.

[0031] As seen in Figures 5 and 6, reaction chambers 112 of element 110 are connected to inlet 116 via (preferably equal length) microfluidic channels 114. Sample S is collected and expressed into apparatus 100 through luer lock 102, e.g., via depression of a syringe plunger as described previously with respect to Figures 2-4. Continued expression of samples S, e.g., via continued depression of the syringe plunger, forces sample S from inlet 116 through microfluidic channels 114 into chambers 112. Each chamber contains reagents 130 for conducting nucleic acid amplification. Reagents 130 may, for example, comprise enzyme and master mix. When conducting nucleic acid amplification via LAMP, the enzyme may, for example, comprise Bst DNA polymerase, Bst 2.0 WarmStart DNA Polymerase, and/or Bsm DNA polymerase (and, optionally, a reverse transcriptase). The master mix may, for example, comprise primers, dNTPs, Mg504, betaine and/or excipients (e.g., mannitol, trehalose and/or dextrin). Reagents 130 also may comprise water, TE buffer, isothermal buffer and/or other buffers, which optionally may be delivered to chambers 112 via microfluidic channels 114, e.g., before, during and/or after delivery of sample S, e.g., as liquid L.

[0032] Reagents 130 also may comprise one or more dyes to facilitate detection of nucleic acid amplification, such as hydroxynaphthol ("HNB") blue. Detection of target amplification may be achieved, for example, via detection of a color shift in the colorimetric dye in the presence of amplicon, e.g., due to a shift in free magnesium (Mg2+) concentration during LAMP amplification. Such colorimetric detection may be performed visually by an operator or may be achieved utilizing spectrophotometric imaging, as described below. In addition or as an alternative to colorimetric amplification detection with a colorimetric dye, a fluorescent dye, such as picogreen or SYBR green, may be utilized to detect amplification via fluorescence.

[0033] One or more of the reagents 130 preferably are lyophilized, e.g., to facilitate long-term storage. Additionally or alternatively, one or more of the reagents temporarily may be sequestered from one or more of the other reagents prior to nucleic acid amplification. Such temporary reagent sequestration may facilitate long-term storage of the reagents and/or may forestall reagent mixing (and, thereby, nucleic acid amplification) until desired, e.g., until the reagents have been exposed to sample S. For example, the enzyme may be sequestered from the master mix.

[0034] In some embodiments, one or more of the reagents 130 may be temporarily sequestered within one or more temporary sequestration vessels. In some embodiments, the temporary sequestration vessel(s) may, for example, comprise one or more thermal encasement materials that are configured to melt, become porous or otherwise release the sequestered reagent(s) 130 upon heating, e.g., during nucleic acid amplification. The thermal encasement material(s) may, for example, comprise polycaprolactone, and/or phase change materials such as paraffin or wax. In some embodiments, the temporary sequestration vessel(s) may comprise one or more blister packs or other containers such as gel caps that may be punctured or otherwise opened to release the sequestered reagent(s) 130. When the temporary sequestration vessel(s) comprise gel caps, they optionally may be opened via hydrolysis in addition or as an alternative to puncturing.

[0035] Upon delivery of sample S to chambers 112 through microfluidic channels 114, each reagent-containing chamber 112 is configured to amplify a nucleic acid target sequence of interest, if contained in the sample S. Different chambers 112 optionally may utilize different primers to facilitate amplification and detection of different target sequences of interest (i.e., to facilitate multiplexed nucleic acid amplification and detection) in different chambers. A fraction of the chambers 112 may serve as positive controls (e.g., may be preloaded with one or more target nucleic acid sequences of interest that are expected to amplify during nucleic acid amplification). Additionally or alternatively, a fraction of the chambers 112 may serve as negative controls (e.g., may comprise reagents 130 but may not be connected to microfluidic channels 114 such that they do not contain sample S).

[0036] After delivery of sample S to chambers 112, the chambers may be heated, e.g., isothermally heated, to amplify the one or more target nucleic acid sequences of interest. When conducting isothermal nucleic acid amplification via LAMP, the contents of chambers 112 may be heated in the range of about 60 C-65 C for about 5-70 minutes. As seen in Figure 7A, the contents of chambers 112 may be heated via a heating element 200 that is thermally coupled to apparatus 100. Such heating may be achieved utilizing any of variety of techniques, including (but not limited to) electrical, chemical and/or electrochemical techniques. Heating element 200 may, for example, comprise a resistive heater connected to a power supply, such as one or more batteries or a wall outlet connection, and an optional temperature controller for resistively heating the contents of chambers 112. Additionally or alternatively, heating element 200 may comprise a diamond/tungsten heater, an inductive heater, a chemical heater (e.g., an exothermic chemical heater, such as a supersaturated sodium acetate heater, a cellulose/iron/water/activated carbon/vermiculite/salt heater, an iron oxide heater, an iron/magnesium salt heater, a catalytic burner, a fuel cell heater, etc.).
Heating element 200 may be reusable or may be configured for disposal after one-time use.
Optionally, heating element 200 may be integrally connected to apparatus 100. Heating element 200 may be fully automated or may comprise controls that, e.g, allow the user to set a target temperature and duration of heating. Optionally, heating element 200 may comprise a phase change material, such as paraffin, for maintaining a desired temperature for an extended period of time.

[0037] As discussed previously, detection of target amplification optionally may be achieved via detection of a color shift (i.e. a wavelength shift) and/or fluorescence (i.e., an intensity shift) in one or more dyes in the presence of amplicon. Such colorimetric and/or fluorescence detection may be performed visually by an operator and/or may be achieved utilizing an imaging technique, such as spectrophotometric and/or fluorescence imaging.
In the embodiment of Figure 7B, sensor 300, such as spectrophotometric CMOS or CCD
imaging sensor 300, is in proximity to chambers 112 for detection of a color shift, fluorescence, turbidity or some other change indicative of target nucleic acid sequence amplification. Chamber cover 106 (see Figure 5) preferably is transparent to facilitate detection of changes within the reaction chambers. In some embodiments, sensor may be integrally connected to element 110 and may cover chambers 112, obviating chamber cover 106.

[0038] Sensor 300 optionally may comprise a coating, such as an Indium Tin Oxide ("ITO") coating, which may be utilized in addition or as an alternative to heating element 200 to resistively heat the contents of each chamber 112 to achieve target nucleic acid amplification. The coating may be placed in proximity to chambers 112. As discussed previously, when conducting isothermal amplification via LAMP, the contents of chambers 112 may be heated in the range of about 60 C-65 C for about 5-70 minutes.

[0039] Imaging sensor 300 may measure a baseline color of reagents 130 and sample S prior to isothermal heating, and a final color of the reagents after isothermal heating (e.g., after isothermal heating). Since the reagents 130 within each reaction chamber 112 may, for example, include a colorimetric (or fluorescent) dye that shifts in color, e.g., from purple to blue, upon amplification of a target nucleic acid sequence, any such shift in color within the chambers may be detected by the imaging sensor 300 as a differential between the baseline and final color, and this differential may be indicative of target amplification. As seen in Figure 7B, optional digital readout or display 310 may output detection results (and/or instructions) to the user, removing any risk of detection ambiguity. While the embodiment of Figure 7B illustratively achieves colorimetric or fluorescence detection via spectrophotometric imaging, it should be understood that such colorimetric or fluorescence detection additionally or alternatively may be performed visually by an operator.

[0040] Heating element 200 and/or sensor 300 may comprise a logic chip for controlling operation of the heating element and/or the sensor, for controlling nucleic acid amplification via heating of chambers 112, for comparing baseline and final color measurements taken with sensor 300 to determine whether amplification has occurred, and/or for controlling the display of instructions or detection results via display 310. Wires and/or a circuit board may connect the logic chip to heating element 200, sensor 300 and/or a power supply. The power supply may, for example, comprise one or more batteries or a wall outlet connection.

[0041] With reference now to Figure 8, an alternative embodiment of apparatus 100 is described. In the embodiment of Figure 8, element 110' comprises four chambers rather than sixteen (as will be apparent to those of skill in the art, any number of chambers 112 may be provided). Element 110' comprises vent channels 118 in fluid communication with the top of each chamber 112 for venting air from the chambers to the atmosphere.
Microfluidic channels 114 deliver sample S to the bottom of each chamber 112, and vent channels 118 vent overflow from the top of each chamber out of apparatus 100 through breathable membrane or one-way valve 119. Figure 8A is an isometric view of apparatus 100. In the top view of element 110' seen in Figure 8B, the fluid communication of vent channels 118 with the tops of chambers 112 is visible. In the bottom view of element 110' seen in Figure 8C, the extension of microfluidic channels 114 from inlet 116 to chambers 112 is visible, as is membrane or valve 119. The side-sectional view of Fig 8D
is taken through luer lock 102 and the outlet of vent channels 118. The side-sectional view of Figure 8E is taken through a chamber 112 and shows the fluid communication of microfluidic channels 114 with the bottom of the chamber and of vent channels 118 with the top of the chamber.

[0042] Figures 9 provide another alternative embodiment of apparatus 100 comprising element 110". Figure 9A provides an isometric view of apparatus 100, Figure 9B shows a top view of element 110" of the apparatus with chamber cover 106 removed, and Figure 9C shows a bottom view of the element 110" with channel cover 104' removed.
While the embodiment of apparatus 100 shown in Figures 8 comprises venting of air from chambers 112 to the atmosphere via vent channels 118 and membrane or valve 119 of element 110', the embodiment of apparatus 100 shown in Figures 9 vents air from chambers 112 through vent channels 118' to one or more overflow chamber(s) 125 of element 110" (see Figure 9C), rather than venting to the atmosphere. Thus, apparatus 100 of Figures 9 is fully contained. Overflow chamber(s) 125 preferably are sized to limit a pressure increase in the overflow chamber(s) during nucleic acid amplification to less than about 5-10 psi.

[0043] As best seen in Figure 9C, element 110" also comprises anti-backflow valves 140 that prevent cross-contamination between chambers 112 via backflow across microfluidic channels 114'. Furthermore, as best seen in Figure 9B, element 110"
comprises flow control media 150 positioned along vent channels 118 between chambers 112 and overflow chamber(s) 125 that allow venting of air or other gases from the chambers 112 but not fluid, thereby ensuring equal fill of sample S in all chambers 112 while releasing excess pressure.

[0044] Element 110" of Figures 9 has shorter microfluidic channels 114' as compared to microfluidic channels 114 of element 110' of Figures 8. Shorter microfluidic channels reduce the priming volume over which sample S must travel to reach chambers 112.
Element 110" may have a priming volume on the order of 20-50 microliters. In contrast to previously described microfluidic channels 114, microfluidic channels 114' extend along both the top and the bottom of element 110", as well as through the element 110". The circuitous path of microfluidic channels 114' is described in more detail below.

[0045] In the embodiment of Figures 9, channel cover 104' comprises laminate 160 that, in addition to covering the portion of microfluidic channels 114' positioned on the bottom of element 110", works in conjunction with anti-backflow valves 140 to prevent cross-contamination between chambers 112. In one embodiment seen in the exploded assembly view of Figure 9D, laminate 160 comprises double-sided adhesive layer 162, elastomer layer 166 and optional single-sided adhesive backing layer 168.
Element 110"
comprises optional registration posts 111 for aligning the layers of laminate 160 during attachment of the laminate to element 110". Layer 162 comprises optional registration cutouts 163 that align with registration posts 111. Similarly, layer 166 comprises optional registration cutouts 167, while layer 168 comprises optional registration cutouts 169.
Layer 162 also comprises valve cutouts 164 that encircle anti-backflow valves 140, while layer 168 comprises valve cutouts 170. Double-sided adhesive layer 162 is attached to element 110" and to elastomer layer 166. Optionally, single-sided adhesive backing layer 168 may be connected to elastomer layer 166 to reduce a risk of laminate 160 delaminating. Figure 9E is a bottom view of apparatus 100 with channel cover 104' attached.

[0046] With reference now to Figures 9F and 9G in conjunction with Figures 9A-9E, a method of using the embodiment of apparatus 100 shown in Figures 9 is described. As seen in Figure 9F, syringe 30 (or any other sample transfer device, e.g., previously described syringe 40 or previously described syringe 30 with containment element 20) is coupled to apparatus 100 via mating of luer lock 32 with luer lock 102.
Syringe 30 expresses sample S (and, optionally, liquid L) into apparatus 100 through inlet 116.
Sample S travels along the bottom of element 110" within microfluidic channel 114' (see Figure 9F in conjunction with Figure 9C). The microfluidic channel then passes through element 110" and takes sample S to the top of the element 110" before branching into multiple microfluidic channels 114' (see Figure 9F in conjunction with Figure 9B). The microfluidic channels 114' then travel back through element 110" and deliver sample S to anti-backflow valves 140. Pressure applied via syringe 30 causes elastomer layer 166 of laminate 160 to locally and temporarily deflect in the immediate vicinity of valves 140, thereby allowing passage of sample S (see Figure 9G in conjunction with Figure 9C). After passage of sample S, anti-backflow valves 140 reseal to prevent backflow of sample S
and, thereby, cross-contamination of chambers 112. As best seen in Figure 9G
in conjunction with Figure 9C, microfluidic channels 114' take sample S that has passed through valves 140 back to the top of element 110" and into chambers 112.
Chambers 112 comprise reagents 130, e.g., lyophilized reagents 130.

[0047] Vent channels 118' extend from chambers 112 for venting of air A
from chambers 112 to overflow chamber(s) 125 (see Figure 9G in conjunction with Figures 9B
and 9C). Flow control media 150 are positioned within channels 118' between chambers 112 and overflow chamber(s) 125. Flow control media 150 may, for example, comprise a small pore hydrophobic material that allows passage of air but not fluid.
After air passes through flow control media 150, it travels within vent channels 118' from the top of element 110" through the element to overflow chamber(s) 125.

[0048] As with all other embodiments of apparatus 100, the embodiment of apparatus 100 shown in Figures 9 may comprise or be coupled to a heating element (e.g., heating element 200 of Figures 7) for amplifying one or more target nucleic acid sequence(s) of interest, when present in sample S, via reagents 130. Target sequence amplification may be detected visually by an operator, e.g. by visual detection of a visual indicator such as a color shift in a colorimetric dye or a turbidity change, or automatically, e.g. via a sensor (such as sensor 300 of Figure 7B) that detects amplification by detection of a visual indicator (color shift, fluorescence, turbidity change, etc.). The embodiment of apparatus 100 shown in Figures 9 illustratively comprises both air overflow chambers 125 and anti-backflow valves 140. It should be understood that apparatus alternatively may comprise only the anti-backflow valves or only the overflow chambers.

[0049] Referring now to Figures 9H-9J, apparatus 100 optionally may comprise case 180 that contains apparatus 100. Case 180 may comprise cavity 182 with indentations 184 configured to receive anti-backflow valves 140 of element 110". Heating element 200 also may be positioned within cavity 182 in the vicinity of chambers 112 for heating the contents of chambers 112. Case 180 further comprises cover 186 with chamber cutout 188 to facilitate visualization of chambers 112, and with luer lock cutout 190 to provide access to luer lock 102. Cover 186 firmly attaches to cavity 182, e.g., via screws or a press fit, to form case 180 with the other components of apparatus 100 disposed therein.

[0050] Figures 10 provide another alternative embodiment of apparatus 100 comprising element 110¨. The embodiment of apparatus 100 shown in Figures 10 comprises anti-backflow locking valve 200 that is configured to lock microfluidic channels 114" of element 110" in either an open position that allows flow through the channels 114"
or a closed position that prevents backflow and cross-contamination between chambers 112 via channels 114". Such locking of the channels may be made reversible or irreversible, as desired. Figure 10A provides an isometric top view of apparatus 100, while Figure 10B provides an isometric bottom view of the apparatus. Figure 10C
provides an isometric detail view of anti-backflow locking valve 200. For the sake of clarity, chamber cover 106 and channel cover 104 are not shown in Figures 10. However, it should be understood that they may be provided as described with respect to prior embodiments of the apparatus.

[0051] As seen in Figures 10A and 10B, anti-backflow locking valve 200 is configured for placement inside void 202 of element 110¨ in order to lock channels 114"
in the open (i.e. flow-enabled) or closed (i.e., flow-blocked) position, as desired, by sliding the locking valve 200 within void 202 relative to the element 110¨. As seen in Figure 10C, lumens 230 pass through anti-backflow locking valve 200 and may be selectively aligned and unaligned with channels 114" to unlock and lock the channels, respectively.
Locking valve 200 may, for example, comprise relatively stiff or rigid substrate 210 with elastomeric overmold 220. Elastomeric overmold 220 may comprise 0-ring elements 222a and 222b that are configured to create a fluid-tight seal against element 110". 0-ring elements 222a are associated with the locked configuration of anti-backflow lock 200 that prevents cross-contamination between chambers 112 by blocking channels 114". 0-ring elements 222b are concentrically aligned with lumens 230 and are associated with the unlocked configuration of anti-backflow locking valve 200 that allows fluid flow through channels 114". In an alternative embodiment of locking valve 200 (not shown), elastomeric overmold 220 may be omitted, and 0-ring elements 222a and/or 222b may be formed or attached directly to substrate 210. Locking valve 200 preferably comprises enlarged end 240 that facilitates manipulation of the locking valve during use (i.e., that may be grasped by the user for sliding the locking valve from the unlocked to the locked configuration, or vice versa).

[0052] Figures 10D and 10E are translucent detail views that illustrate actuation of locking valve 200. As seen in Figure 10D, channels 114" may be placed in the unlocked configuration by positioning locking valve 200 within void 202 of element 110"
such that lumens 230 are aligned with microfluidic channels 114". Optionally, locking valve 200 and/or void 202 may be lubricated to facilitate sliding of the lock relative to the void. In this unlocked configuration, 0-ring elements 222b create fluid seals around the perimeters of channels 114" such that sample may flow from a sample transfer device (e.g., a syringe) through the first section of channels 114", through lumens 230 and through the second section of the channels 114" to chambers 112. As seen in Figure 10E, locking valve 200 then may be slid within void 202 to place channels 114" in the locked configuration such that lumens 230 are out of alignment with the microfluidic channels. In this locked configuration, 0-ring elements 222a create fluid seals around the perimeters of channels 114", thereby isolating and blocking each channel 114" from the others and preventing cross-contamination between chambers 112 via backflow through the channels.

[0053] In one embodiment, enlarged end 240 of locking valve 200 may sit flush with element 110" in the locked configuration of Figure 10E, such that the user is unable to grasp end 240 and unlock channels 114" once locking valve 200 has blocked the channels. Such an irreversible locking valve may reduce a risk of backflow contamination or of accidental venting of sample to the environment. In an alternative embodiment, enlarged end 240 of locking valve 200 may protrude from element 110¨ in the locked configuration, such that the user may grasp end 240 for reversible locking and unlocking of channels 114" with locking valve 200.

[0054] With reference now to Figures 10F and 10G in conjunction with Figures 10A-10E, a method of using the embodiment of apparatus 100 shown in Figures 10 is described. In Figure 10F, locking valve 200 positions channels 114" in the unlocked configuration shown in Figure 10D. A syringe or other sample transfer device is coupled to apparatus 100 via mating with luer lock 102. The syringe or other sample transfer device expresses sample S (and, optionally, liquid L) into apparatus 100 through inlet 116.
Sample S travels along the bottom of element 110" within microfluidic channel 114", which branches into multiple microfluidic channels 114" (see Figure 1OF in conjunction with Figures 10B and 10D). Each microfluidic channel then passes through element 110"
via a lumen 230 of locking valve 200, thereby taking sample S to the top of the element 110¨ and into chambers 112 having reagents 130 (e.g., lyophilized reagents 130). As seen in Figure 10G, locking valve 200 then may be slid within void 202 relative to element 110" in order to position channels 114" in the locked configuration of Figure 10E wherein the channels are blocked. Sample S cannot flow back through locking valve 200 when channels 114" are in the locked configuration, which prevents cross-contamination of chambers 112 via backflow through the channels.

[0055] Element 110¨ comprises previously described vent channels 118' that extend from chambers 112 for venting of air A (but not sample S) from the chambers 112 to overflow chamber(s) 125 (see Figure 10G in conjunction with Figures 10A and 10B). Flow control media 150 are positioned within channels 118' between chambers 112 and overflow chamber(s) 125. Flow control media 150 may, for example, comprise a small pore hydrophobic material that allows passage of air but not fluid. After air passes through flow control media 150, it travels within vent channels 118' from the top of element 110"
through the element 110¨ to overflow chamber(s) 125. The embodiment of apparatus 100 shown in Figures 10 illustratively comprises both air overflow chambers 125 and anti-backflow locking valve 200. It should be understood that the apparatus alternatively may comprise only the anti-backflow lock or only the overflow chambers.

[0056] As with all other embodiments of apparatus 100, the embodiment of apparatus 100 shown in Figures 10 may comprise or be coupled to a heating element (e.g., heating element 200 of Figures 7) for amplifying one or more target nucleic acid sequence(s) of interest, when present in sample S, via reagents 130. Target sequence amplification may be detected visually by an operator, e.g. by visual detection of a visual indicator such as a color shift in a colorimetric dye or a turbidity change, or automatically, e.g. via a sensor (such as sensor 300 of Figure 7B) that detects amplification by detection of a visual indicator (color shift, fluorescence, turbidity change, etc.). Optionally, the heating element, element 110¨ and/or some other aspect of apparatus 100 may comprise a geometric or other constraint that precludes coupling of element 110¨ to the heating element when locking valve 200 is positioned in the open configuration allowing flow through channels 114". Such a constraint may reduce a risk of sample amplification before locking of channels 114" in the closed configuration, thereby reducing a risk of backflow-induced cross-contamination of chambers 112.

[0057] Embodiments of apparatus 100 described thus far have delivered sample S to reaction chambers 112 via microfluidic channels that distribute the sample S
across the chambers. In the embodiment of apparatus 100 shown in Figures 11, sample S is delivered to a reaction chamber without microfluidics. The embodiment of apparatus 100 shown in Figures 11 illustratively comprises a single reaction chamber, but it should be understood that apparatus 100 may comprise any desired number of reaction chambers.

[0058] With reference to Figure 11A, apparatus 100 comprises reaction chamber 400 and punch element 500. Punch element 500 comprises male element 502, which is configured to press fit into female element 402 of reaction chamber 400 and seal the reaction chamber 400 in advance of nucleic acid amplification and detection.

[0059] As seen in Figures 11B and 11 D, female element 402 of reaction chamber 400 comprises reagent insert 410 that may be press fit therein. Reagent insert 410 comprises cutting element 412 and reagent chamber 414. Reagents 130 are positioned within reagent chamber 414. The reagents 130 may, for example, be in solution or liquid form.
Alternatively, the reagents 130 may be lyophilized, as in Figures 10.

[0060] Reagent insert 410 is sealed within female element 402 of reaction chamber 400 via seal 404 (see, e.g., Figure 11C). Seal 404 may, for example, comprise a metal foil or plastic film. Sealing of reaction chamber 400 may facilitate long-term storage of reagents 130 prior to use and/or may ensure that lyophilized reagents 130 remain dry prior to use.

[0061] As seen in Figures 11B, 11E and 11F, male element 502 of punch element 500 comprises liquid insert 510 that may be press fit therein. Liquid insert 510 comprises cutting element 512 and liquid chamber 514. Liquid chamber 514 is sealed with seal 516.
Seal 516 may, for example, comprise a metal foil or plastic film. Liquid L, such as water and/or TE buffer, is sealed within liquid chamber 514. Dye, Mg504, betaine and/or isothermal buffer additionally or alternatively may be sealed within chamber 514.

[0062] Apparatus 100 further comprises heating element 200, which is in thermal communication with the reaction chamber 400. Heating element 200, which optionally may be disposed of after single use along with the rest of apparatus 100, is configured to heat the contents of reaction chamber 400 to achieve nucleic acid amplification, e.g., isothermal nucleic acid amplification such as LAMP. Heating element 200 may comprise, for example, a resistive heater comprising an etched foil element encapsulated between two layers of polyimide film. The heating element further may comprise a power supply, such as batteries or connection to a standard wall outlet, as well as a thermocouple for temperature monitoring in a feedback loop with a temperature controller for adjusting the monitored temperature as desired to achieve nucleic acid amplification.

[0063] Reaction chamber 400 preferably is transparent or translucent to facilitate visualization of the reaction chamber in order to detect amplification of a target nucleic acid sequence of interest. Nucleic acid amplification may be detected via a color shift in a colorimetric dye, via an increase in turbidity, via fluorescence, etc.
Detection may be achieved with the naked eye and/or via optional sensor 300, which may be disposable.
Detection results may be shown on a display, which may be disposable.

[0064] Sample S may be placed directly into reaction chamber 400 and/or punch element 500 prior to sealing of the reaction chamber with the punch element.
Alternatively, sample collector 10 comprising sample S may be positioned between the reaction chamber 400 and the punch element 500 such that mating of male element 502 with female element 402 places sample S within the reaction chamber 400, as shown in Figures 11. In the embodiment of Figures 11, sample collector 10 may, for example, comprise a filter paper, such as a chemically treated filter paper, e.g., Flinders Technology Associates ("FTA") cards available from Whatman (part of GE Healthcare).
Various sample matrices - including, but not limited to, food, urine, saliva, mucous, feces, blood, semen, tissue, cells, DNA, RNA, protein, plant matter, animal matter, solutions, solids, and other sample matrices - may be deposited onto sample collector 10 (additional sample matrices will be apparent). In this manner, sample collector 10 may collect sample S via the filter paper.

[0065] In order to collect sample S with sample collector 10, the filter paper may, for example, be dipped or placed into one or more sample matrices of interest.
Additionally or alternatively, one or more drops of one or more sample matrices of interest may, for example, be placed or deposited onto the filter paper. Additionally or alternatively, the filter paper may, for example, be swabbed or wiped across one or more sample matrices or surfaces of interest.

[0066] Referring now to Figures 11G-11J, a method of using the embodiment of apparatus 100 seen in Figures 11 is described. As seen in Figure 11G, reaction chamber 400 and punch element 500 are approximated, such that male element 502 of the punch element mates with female element 402 of the reaction chamber to seal the reaction chamber. Cutting element 512 of liquid insert 510 pierces sample collector 10, and male element 502 removes a punch of sample S from sample collector 10, thereby placing sample S within reaction chamber 400.

[0067] As seen in Figure 11H, continued approximation of reaction chamber 400 and punch element 500 causes cutting element 512 of liquid insert 510 to puncture seal 404 of reaction chamber 400, thereby providing access to reagent insert 410. As seen in Figure 111, still further approximation causes cutting element 412 of reagent insert 410 to puncture seal 516 of liquid insert 510, thereby causing liquid L to flow out of liquid chamber 514 into reagent chamber 414. As seen in Figure 11J, full approximation of reaction chamber 400 with punch element 500 positions all materials necessary for nucleic acid amplification and detection (sample S, reagents 130 and optional liquid L) within reagent chamber 414.

[0068] After approximating the reaction chamber and punch element, heating element 200 heats the contents of reagent chamber 414 to achieve nucleic acid amplification of a target nucleic acid sequence of interest when present in sample S. Detection may be achieved via the naked eye and/or via sensor 300.

[0069] Apparatus 100 of Figures 11 optionally may be used as part of instrument 40 previously described in co-pending U.S. patent application Serial No.
13/447,218, filed April 14, 2012, which is incorporated herein by reference in its entirety.
Specifically, reaction chambers 400 and punch elements 500 of apparatus 100 in Figures 10 may be substituted for punch elements 90 and chambers 70 of instrument 40 shown in the '218 application.

[0070] The methods and apparatus of Figures 1-11 provide fully contained, sample-to-answer, nucleic acid sample preparation, (optionally multiplexed) target amplification and detection in (optionally disposable, e.g., single-use disposable) apparatus that is appropriate for use in limited resource settings at the point of care by relatively unskilled users.
Conclusion

[0071] Although preferred illustrative embodiments of the present invention are described above, it will be apparent to those skilled in the art that various changes and modifications may be made thereto without departing from the invention. For example, while mating of various components of the apparatus has been described as mating via luer lock connections, it should be understood that luer slip, press fit or other mating connectors, per se known, may be utilized. Furthermore, while some of the described embodiments of the apparatus illustratively have utilized one or more syringes to transfer sample S to the nucleic acid amplification and detection apparatus, it should be understood that any alternative sample transfer device may be utilized, including purpose-built transfer devices.

[0072] Further still, although apparatus 100 and associated methods have been described with respect to nucleic acid amplification and detection, it should be understood that the apparatus and associated methods alternatively may comprise and/or be used for holding and analyzing a sample without necessarily amplifying and/or detecting nucleic acid in the sample. In such an embodiment, apparatus 100 may comprise sample holder 100 that maintains a nucleic acid or other sample for analysis within the reaction chamber(s), which may serve as observation and/or analysis chamber(s).
Analysis may comprise, for example, one or more techniques such as microscopy, hybridization and/or protein analysis ¨ in addition, or as an alternative, to nucleic acid amplification and detection.

[0073] When apparatus 100 comprises a sample holder, a method of holding a sample for analysis may comprise collecting a sample matrix, transferring the sample matrix through at least one microfluidic channel to at least one reaction/observation/analysis chamber, optionally heating the sample matrix as part of an analytical technique, and preventing backflow of the sample matrix from the at least one chamber through the at least one microfluidic channel (e.g., during heating).
Backflow prevention may prevent cross-contamination when multiple chambers are provided.
Backflow prevention may be achieved via a one-way valve into the reaction/observation/analysis chamber(s) and/or via blocking of the microfluidic channel(s) after transferring of the sample matrix to the chamber(s).

[0074] It is intended in the appended claims to cover all such changes and modifications that fall within the true spirit and scope of the invention.

Claims

What Is Claimed Is:

1. A method for point-of-care amplification and detection of a target nucleic acid sequence, the method comprising:
collecting a sample matrix;
transferring the sample matrix through at least one microfluidic channel to at least one reaction chamber having nucleic acid amplification reagents;
heating the nucleic acid amplification reagents in order to amplify the target nucleic acid sequence when contained within the sample matrix;
preventing backflow of the sample matrix from the at least one reaction chamber through the at least one microfluidic channel during heating; and detecting amplification of the target nucleic acid sequence when present in the sample matrix.

2. The method of claim 1, wherein preventing backflow further comprises passing the sample matrix through at least one one-way valve while transferring the sample matrix to the at least one reaction chamber.

3. The method of claim 1, wherein preventing backflow further comprises blocking the at least one microfluidic channel after transferring the sample matrix to the at least one reaction chamber.

4. The method of claim 1 further comprising venting overflow from the at least one reaction chamber.

5. The method of claim 1 further comprising disposing of the sample matrix, at least one microfluidic channel, at least one reaction chamber and nucleic acid amplification reagents after one-time use.

6. The method of claim 1 wherein heating further comprises:
heating the nucleic acid amplification reagents with a heating element; and disposing of the heating element after one-time use.

7. The method of claim 1, wherein detecting amplification further comprises detecting a color shift in a colorimetric dye, detecting an increase in turbidity, or detecting fluorescence.

8. The method of claim 1, wherein transferring further comprises transferring the sample matrix through at least one branching microfluidic channel that distributes the sample matrix across multiple reaction chambers.

9. The method of claim 8, wherein preventing backflow further comprises preventing cross-contamination between the multiple reaction chambers.

10. The method of claim 8 further comprising amplifying and detecting different target nucleic acid sequences in different reaction chambers.

11. A method for point-of-care amplification and detection of a target nucleic acid sequence, the method comprising:
collecting a sample matrix;
transferring the sample matrix from the sample collector to at least one reaction chamber having nucleic acid amplification reagents;
heating the nucleic acid amplification reagents in order to amplify the target nucleic acid sequence when contained within the sample matrix;
venting overflow from the at least one reaction chamber during heating; and detecting amplification of the target nucleic acid sequence.

12. The method of claim 11, wherein transferring further comprises transferring the sample matrix through at least one microfluidic channel.

13. The method of claim 11, wherein collecting further comprises collecting the sample matrix with a sample collector, and wherein transferring further comprises placing at least one punch of the sample collector in the at least one reaction chamber.

14. The method of claim 11, wherein venting overflow further comprises venting to at least one sequestered overflow chamber.

15. The method of claim 11, wherein venting overflow further comprises venting gases through flow control media while precluding venting of fluids.

16. The method of claim 11 further comprising preventing backflow of the sample matrix from the at least one reaction chamber through the at least one microfluidic channel during heating.

17. Apparatus for point-of-care amplification and detection of a target nucleic acid sequence, the apparatus comprising:
a sample collector configured to collect a sample matrix;
a device having at least one microfluidic channel, at least one reaction chamber with nucleic acid amplification reagents, and at least one valve; and a heating element, wherein the at least one microfluidic channel is configured to transport the sample matrix from the sample collector to the at least one reaction chamber, wherein the heating element is configured to heat the nucleic acid amplification reagents after transport of the sample matrix to the at least one reaction chamber in order to amplify the target nucleic acid sequence when contained in the sample matrix, and wherein the at least one valve is configured to prevent backflow of the sample matrix from the at least one reaction chamber through the at least one microfluidic channel during heating.

18. The apparatus of claim 17, wherein the device further comprises at least one sequestered chamber for venting of overflow from the at least one reaction chamber.

19. The apparatus of claim 18, wherein the device further comprises flow control media for venting of gases but not liquids from the at least one reaction chamber.

20. The apparatus of claim 17, wherein the valve is chosen from the group consisting of one-way valves, locking valves, reversible valves, irreversible valves and combinations thereof.

21. The apparatus of any of claims 17-19, wherein the valve includes a sliding bar valve that can selectably be slid into a closed position that prevents fluid communication between the at least one reaction chamber and the at least one microfluidic channel or into an open position that allows fluid communication between the at least one reaction chamber and the at least one microfluidic channel.

22. The apparatus of claim 21, wherein there are a plurality of reaction chambers and a plurality of microfluidic channels and the sliding bar valve in the closed position prevents fluid communication between a plurality of respective reaction chambers and microfluidic channels.

23. Apparatus for point-of-care analysis of a fluid sample, the apparatus comprising:
a sample collector configured to collect a fluid sample; and a device having at least one microfluidic channel, at least one analysis chamber, and a sliding bar valve, wherein the at least one microfluidic channel is configured to transport the fluid sample from the sample collector to the at least one analysis chamber, and wherein the sliding bar valve is configured to selectably allow or prevent fluid communication between the at least one microfluidic channel and the at least one analysis chamber.

24. The apparatus of claim 23, wherein there are a plurality of reaction chambers and a plurality of microfluidic channels and the sliding bar valve is configured to selectably allow or prevent fluid communication between a plurality of respective reaction chambers and microfluidic channels.

25. The apparatus of any of claim 23-24, wherein the sliding bar valve can selectably be slid between an open position to allow the fluid communication and a closed position to prevent the fluid communication.

26. The apparatus of any of claims 23-25, wherein the analysis chamber is a reaction chamber.

27. The apparatus of any of claims 23-26, wherein the analysis includes amplification and detection of a target nucleic acid sequence.

28. The apparatus of any of claims 23-27, further including a heating element to heat the fluid sample.

29. The apparatus of any of claims 23-28, wherein the analysis chamber includes reagents that combine with the fluid sample when the fluid sample is provided to the analysis chamber.

30. The apparatus of any of claims 23-29, further including an imaging sensor to capture an image of at least a portion of the fluid sample in the analysis chamber.