# Patent

## Title
Unitized reagent strip

## Abstract

The embodiments disclosed herein relate to unitized reagent strips for holding and transporting reagents and materials used in automated sample preparation and/or processing for biological and or chemical assays.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
The present application is a continuation of International Application No. PCT/US2012/058102, filed Sep. 28, 2012, which claims priority to U.S. Provisional Application Ser. No. 61/541,991, entitled “UNITIZED REAGENT STRIP,” filed Sep. 30, 2011. Each of the above applications is hereby incorporated by reference in its entirety.


BACKGROUND
1. Technical Field
The technology described herein generally relates to holders for reagents and disposables, such as may be used for transporting the reagents and for carrying out processing operations with the reagents. e.g., in automated sample preparation/processing devices.
2. Background
Automation of diagnostic assays and high throughput screening has become more prevalent, and several devices have been developed to meet the growing need for quick, sensitive, and consistent analysis of multiple samples. For example, in recent years, integrated devices in which sample preparation and processing, e.g., for nucleic acid assays, have been developed.
Many important assays require the isolation of various components, such as nucleic acids, proteins, or the like, from clinical and/or environmental samples. Isolating nucleic acids, proteins, or other analytes of interest from clinical or environmental samples can be time consuming and labor intensive. Manual preparation of samples is also subject to more variation due to human error and inaccuracies. Several variables that affect the consistency and accuracy of sample preparation, which typically involves several reagents and the need for multiple transfer (e.g., pipetting) operations. Often, required reagents are of sufficient variety that they typically require different handling from one another and are available from different vendors. As such, the variation between different vendors and lots of a particular reagent, and different handling of various reagents by one or many individuals, can lead to assay variability. Second, multiple pipetting operations introduces the possibility of cross-contamination, e.g., inter-sample and intra-sample, (e.g., the reagents used during different preparation and/or processing steps of a single sample).
There is a need for methods and devices of carrying out preparation and processing of large numbers of samples in parallel, and that minimize inter-assay variability. Desirably, the methods and devices would minimize user manipulation of reagents and/or disposables used in the preparation and processing procedures, to enable efficient sample processing and minimize both contamination and imprecision, and that would maintain flexibility.
The discussion of the background herein is included to explain the context of the inventions described herein. This is not to be taken as an admission that any of the material referred to was published, known, or part of the common general knowledge as at the priority date of any of the claims.
BACKGROUND
Provided herein are unitized reagent strips, and methods of using the same. In one aspect, provided is a unitized reagent strip, comprising: a strip with a top side and a bottom side, comprising: a first and a second pipette sheath comprising a opposing sides, said first and second pipette sheaths comprising a first and second pipette tip aperture, respectively, each of which comprises a separate opening on the top side of the strip, and wherein said first and second pipette tip apertures are configured for insertion of a first and second pipette tip into said first and second pipette sheaths, respectively, and wherein each of said first and second pipette sheaths is configured to substantially surround the length of a first and second pipette tip, respectively; a process tube; and a receptacle, comprising an opening through the reagent strip, wherein said receptacle is configured to receive a reagent tube.
In another aspect, provided herein is a method of detecting the presence or absence of a pipette tip within a pipette sheath of a unitized reagent strip, comprising: a strip with a top side and a bottom side, comprising: a first and a second pipette sheath comprising a opposing sides, said first and second pipette sheaths comprising a first and second pipette tip aperture, respectively, each of which comprises a separate opening on the top side of the strip, and wherein said first and second pipette tip apertures are configured for insertion of a first and second pipette tip into said first and second pipette sheaths, respectively, and wherein each of said first and second pipette sheaths is configured to substantially surround the length of a first and second pipette tip, respectively; a process tube; and a receptacle, comprising an opening through the reagent strip, wherein said receptacle is configured to receive a reagent tube, wherein said first pipette sheath comprises an aperture pair, said aperture pair comprising the first cored hole and a second cored hole extending through the sidewall of the first pipette sheath, wherein the first and second cored holes are located on opposing sides of the sidewall of the first pipette sheath, and are positioned at the same distance along the length of the first pipette sheath from the first pipette tip aperture; providing an optical beam through the first cored hole of said pipette sheath aperture pair; and detecting whether said optical beam exits unobstructed through said second cored hole of said first pipette sheath aperture pair, wherein the unobstructed exit of said optical beam through said second cored hole of said first pipette sheath is indicative of the absence of the pipette tip within the pipette sheath, and wherein obstructed exit of said optical beam though said second cored hole indicates the presence of the pipette tip within said first pipette sheath.
In another aspect, provided herein is a method of determining the length of a pipette tip within a pipette sheath of a unitized reagent strip, comprising: providing a unitized reagent strip comprising: a strip with a top side and a bottom side, said strip comprising: a process tube; a receptacle, comprising an opening through the reagent strip, wherein said receptacle is configured to receive a reagent tube; a first and a second pipette sheath, each of said pipette sheaths comprising: a first and second pipette tip aperture, respectively, each of which comprises a separate opening on the top side of the strip, and wherein said first and second pipette tip apertures are configured for insertion of a first and second pipette tip into said first and second pipette sheaths, respectively, and wherein each of said first and second pipette sheaths is configured to substantially surround the length of a first and second pipette tip, respectively; a top pipette sheath aperture pair and a bottom pipette sheath aperture pair within said first pipette sheath, said top and bottom aperture pairs each comprising a first and a second cored hole extending through a sidewall of the first pipette sheath, wherein the first and second cored holes of said top and bottom pipette sheath aperture pairs are located on opposite sides of the first pipette sheath, and positioned at the same distance along the length of the first pipette sheath from the first pipette tip aperture, and wherein said top pipette sheath aperture pair is located more proximal to the first pipette tip aperture than said bottom pipette sheath aperture pair; providing an optical beam through said first cored hole of said top pipette sheath aperture pair; providing an optical beam through said first cored hole of said bottom pipette sheath aperture pair; detecting whether said optical beam is obstructed from passing through said second cored hole of said top pipette sheath aperture pair; and detecting whether said optical beam is obstructed from passing through said bottom cored hole of said first pipette sheath aperture pair, wherein obstruction of said optical beam through the second cored hole of the top aperture pair and passage of said optical beam through said second cored hole of said bottom pipette sheath aperture pair indicates that the pipette tip within said first pipette sheath has a length that does not extend down to the bottom pipette sheath aperture pair when inserted into the first pipette sheath.
In yet another aspect, provided is a method of determining the length of a pipette tip within a pipette sheath of a unitized reagent strip, comprising: providing a unitized reagent strip comprising: a strip with a top side and a bottom side, said strip comprising: a process tube; a receptacle, comprising an opening through the reagent strip, wherein said receptacle is configured to receive a reagent tube; a first and a second pipette sheath, each pipette sheath comprising: a first and second pipette tip aperture, respectively, each of which comprises a separate opening on the top side of the strip, and wherein said first and second pipette tip apertures are configured for insertion of a first and second pipette tip into said first and second pipette sheaths, respectively, and wherein each of said first and second pipette sheaths is configured to substantially surround the length of a first and second pipette tip, respectively; a top pipette sheath aperture pair and a bottom pipette sheath aperture pair within said first pipette sheath, said top and bottom aperture pairs each comprising a first and a second cored hole extending through a sidewall of the first pipette sheath, wherein the first and second cored holes of said top and bottom pipette sheath aperture pairs are located on opposite sides of the first pipette sheath, and positioned at the same distance along the length of the pipette sheath from the pipette tip aperture, and wherein said top pipette sheath aperture pair is located more proximal to the first pipette tip aperture than said bottom pipette sheath aperture pair; providing an optical beam through said first cored hole of said top pipette sheath aperture pair; providing an optical beam through said first cored hole of said bottom pipette sheath aperture pair; detecting whether said optical beam is obstructed from passing through said second cored hole of said top pipette sheath aperture pair; and detecting whether said optical beam is obstructed from passing through said bottom cored hole of said first pipette sheath aperture pair, wherein obstruction of said optical beam through the second cored hole of the top aperture pair and passage of said optical beam through said second cored hole of said bottom pipette sheath aperture pair indicates that the pipette tip within said pipette sheath has a length that does not extend down to the bottom pipette sheath aperture pair when inserted into the pipette sheath.
In still another aspect, provided herein is a method of determining the length of a pipette tip within a pipette sheath of a unitized reagent strip, comprising: providing a unitized reagent strip comprising: a strip with a top side and a bottom side, said strip comprising: a process tube; a receptacle, comprising an opening through the reagent strip, wherein said receptacle is configured to receive a reagent tube; a first and a second pipette sheath, each comprising: a first and second pipette tip aperture, respectively, each of which comprises a separate opening on the top side of the strip, and wherein said first and second pipette tip apertures are configured for insertion of a first and second pipette tip into said first and second pipette sheaths, respectively, and wherein each of said first and second pipette sheaths is configured to substantially surround the length of a first and second pipette tip, respectively; a top cored hole and a bottom cored within said first pipette sheath, said top and bottom cored holes each extending through a sidewall of the pipette sheath, wherein said top cored hole is located more proximal to the first pipette tip aperture than said bottom cored hole; determining whether a pipette tip extends within said first pipette sheath from the first pipette tip aperture to the distance of the first cored hole; and determining whether a pipette tip extends within said first pipette sheath from the first pipette tip aperture to the distance of the second cored hole.



BRIEF DESCRIPTION OF THE DRAWINGS
One or more various embodiments provided herein is described in detail with reference to the following figures. The drawings are provided for purposes of illustration only and merely depict typical or example embodiments of the invention. These drawings are provided to facilitate the reader's understanding of the invention and shall not be considered limiting of the breadth, scope, or applicability of the invention. It should be noted that for clarity and ease of illustration these drawings are not necessarily made to scale.
Some of the figures included herein illustrate various embodiments of the invention from different viewing angles. Although the accompanying descriptive text may refer to such views as “top,” “bottom” or “side” views, such references are merely descriptive and do not imply or require that the invention be implemented or used in a particular spatial orientation unless explicitly stated otherwise.
These and other features and advantages of the various embodiments disclosed herein will be better understood with respect to the following description and drawings, in which like numbers refer to like parts throughout, and in which:
FIG. 1A is a perspective view of a reagent strip as described herein.
FIG. 1B is a perspective view of the reagent strip as described herein, with reagent tube (160) shown separate from and inserted in the strip.
FIG. 1C is a cutaway view of the process tube in section A-A from FIG. 1A.
FIG. 1D is a cutaway view of the reagent tube. 140 in section B-B from FIG. 1A.
FIG. 1E is a cutaway view of the pipette sheath in section C-C from FIG. 1A.
FIG. 1F is a top view of the reagent strip of FIG. 1A.
FIG. 1G is a bottom view of the reagent strip of FIG. 1A.
FIG. 1H is a cutaway view of one embodiment of the reagent strip of FIG. 1A.
FIG. 2A is a perspective view of a reagent strip as described herein.
FIG. 2B is a top view of the reagent strip of FIG. 2A.
FIG. 2C is a bottom view of the reagent strip of FIG. 2A.
FIG. 3 is a plan view of a reagent strip as described herein.
FIGS. 4A-4E show a sequence of pipetting operations in conjunction with a laminated layer.
FIGS. 5A and 5B show embodiments of a laminated layer.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT
The embodiments described herein provide reagent holders that are configured to hold, transport, and store a plurality of reagents and materials used in the preparation and processing of samples, e.g., clinical and/or environmental samples. The reagent holders provided herein provide several advantages in the preparation and processing of samples, such as clinical and/or environmental samples, and are suitable for use with automated sample processing devices. By way of example, some of the advantages provided by the reagent holders disclosed herein include, but are not limited to a design that (1) minimizes of cross-contamination of reagents and samples; (2) facilitates quality control of the strips/disposables; (3) simplifies manufacture; and (4) provides versatility useful for different molecular platforms and automated devices.
The holders herein are also configured for use by an apparatus that carries out automated sample preparation, for example, on multiple samples simultaneously. An exemplary form of such an apparatus is described, e.g., in International Patent Application Publication. No. WO 09/054870, incorporated herein by reference in its entirety.
Preparation of a sample for use in assays, such as nucleic acid testing (“NAT”), e.g., by PCR or the like, can include one or more of the following steps: contacting a polynucleotide sample with a nucleic acid testing NAT reagent mixture, e.g., in the case of PCR or other amplification, which comprises a polymerase enzyme and a plurality of nucleotides. In some embodiments, the reagent mixtures can further comprise hybridization probes with detectable moieties, wherein the probes specifically hybridize to target nucleic acids (and/or positive control target nucleic acid sequences).
In some embodiments, the reagent mixture can be in the form of one or more lyophilized pellets, as stored in a reagent tube on the holder, and the method can further include reconstituting the reagent pellet with liquid to create a PCR reagent mixture solution. The holder herein provides in a self-contained manner, all of the reagents required to prepare a nucleic acid testing-ready sample, or, when delivered to a user in kit form, contains in conjunction with other packages all of the required reagents. Suitable reagents, and protocols for using the same in DNA and RNA extractions can be found in, respectively, U.S. Patent Application Publication Nos. US 2010-0009351, and US 2009-0131650, each of which is herein incorporated by reference.
Several features of the reagent holders described herein are described with reference to the drawings provided herein. The exemplary holders shown in FIGS. 1A-H, 2A-C, and 3, can each be referred to as a “unitized disposable strip”, or a “unitized strip”, because they are intended to be used as a single unit that is configured to hold all of the reagents and receptacles necessary to perform a sample preparation, and because they are laid out in a strip format. It is consistent with the description herein, though, that other geometric arrangements of the various receptacles are contemplated, so that the description is not limited to a linear, or strip, arrangement, but can include a circular or grid arrangement.
Turning to FIGS. 1-3, shown are exemplary reagent strips 100. Reagent strip 100 comprises a strip 110, that has both a top side 310 and a bottom side 320, and that houses various components used in sample preparation and/or processing, including one or more pipette sheaths 120, one or more process tubes 130, and which also houses one or more integral reagent tubes 140 having reagent tube apertures 330. In some embodiments, the reagent tubes 140 are integral/unitary with the strip 110. In some embodiments, the process tubes 130 are integral with the strip 110. In some embodiments, the process tubes 130 are separate from the unitized strip. In some embodiments, the reagent strip comprises one or more tube receptacles 150. The tube receptacles 150 can be integral/unitary with the strip 110, and are configured to receive one or more reagent tubes 160 that are not integral/unitary with the strip 110. In some embodiments, reagent tubes 160 can be integral with the strip, as shown in FIG. 2A.
By way of example, unitized reagent strips as described herein can include, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more pipette sheaths, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more process tubes, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more receptacles, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more integral reagent tubes, 1, 2, 3, 4, 5, or more waste containers, or the like, organized in any configuration on the strip.
In preferred embodiments, the reagent strip comprises one or more pipette sheaths 120 that are substantially separated from adjacent pipette sheaths and/or adjacent reagent tubes 140, process tubes 130, or tube receptacles 150. Preferably, the pipette sheaths 120 are integral with the strip 110, and thus do not require manual assembly onto the strip 110. Individual pipette tips can be inserted into individual pipette sheaths 120, by virtue of individual pipette tip apertures 170 that are present in the strip 110. The pipette sheaths 120 substantially surround the sides and bottoms of individual pipette tips. The term “substantially surrounding”, when used in reference to the pipette sheaths, means that the sheath surrounds at least the main body of the pipette tip. That is, the top of the pipette tip may comprise a lip, or the like, at the top portion of the pipette tip (through which the pipettor is inserted), that extends past (and possibly rests on top of), the top portion of the strip 110. In some embodiments, the pipette sheath surrounds, e.g., 70%, 80%, 85%, 80%, 90%, 95%, or more, of the length of a pipette tip. By substantially surrounding individual pipette tips, the pipette sheaths prevent contact between each pipette tip and other pipette tips, reagent tubes, process tubes, waste containers, or the like, present in the strip. Specifically, each pipette sheath is configured to have material surrounding, or forming a barrier or wall 290 that isolates the body of a pipette tip inserted therein, from other reagents/holders or disposables (e.g., other pipette tips) within the unitized strip. Thus, the individual pipette sheaths prevent any cross-contamination between reagents and/or samples that are manipulated during preparation and/or processing by pipetting. For example, the pipette sheaths 120 prevent contamination between adjacent pipette tips on the same strip, as well as between pipette tips housed in reagent strips held in adjacent position, e.g., within an automated sample preparation/processing device.
In some embodiments, the pipette sheaths contain one or more sheath apertures, or cored holes 180. In some embodiments, the cored holes 180 are present as pairs of sheath apertures. whereas in other embodiments, the cored holes are not part of an aperture pair. In some embodiments, the pipette sheaths comprise one, two, three, four, five, six, seven, eight, nine, ten, or more, unpaired cored holes 180. In some embodiments, the pipette sheaths comprise a plurality of aperture pairs, wherein each pipette sheath aperture pair comprises two cored holes 180. For example, a pipette sheath can include e.g., one pair, two pairs, three pairs, four pairs, five pairs, six pairs, seven pairs, eight pairs, nine pairs, ten pairs, or more, of sheath aperture pairs. Pipette sheath aperture pairs comprise a first cored hole 180a and a second cored hole 180b, which are present on opposing sides of, and equidistant from the top of, the pipette sheath 120, as shown e.g., in FIG. 1D. In some embodiments, unpaired cored holes 180 can be present on opposing sides of, and at various distances from the top of, the pipette sheath 120.
The cored holes 180, whether present unpaired, or as an aperture pair(s), can advantageously be used to determine the presence or absence of a pipette tip within a pipette sheath 120, either manually (by visual inspection), or automatically (e.g., by an optical sensor). The cored holes 180 thereby provide an additional quality control checkpoint prior to use of the unitized reagent strip. For example, in the context of automated detection of pipette tips, when cored holes 180 are present as a pipette sheath aperture pair, one can pass light through the first cored hole of the pair. When the pipette sheath 120 is not housing a pipette tip, light can pass through the first and second cored holes of the aperture pair aligned on opposing sides of the sheath. When a pipette tip is present within the sheath, the pipette tip blocks or obstructs visible pathway between the first and second cored holes of each aperture pair. In this manner, the sheath aperture pairs 180 can be readily used to determine whether or not a pipette tip is present in each sheath 120. When cored holes 180 are present, but not part of a pipette sheath aperture pair, one can determine the presence or absence of a pipette tip within the sheath by calculating, e.g., the reflection or obstruction of light passed through the unpaired cored hole, as the reflection or obstruction will differ depending upon whether a pipette tip is present within the pipette sheath or is absent. For example, in some embodiments, detection of light reflection may be determined using art recognized means and devices such as retro-reflective detectors. In some embodiments, the presence or absence of a pipette tip in a sheath is determined by measuring the obstruction of light, for example by using art-recognized means and devices such as through-beam sensors.
As mentioned above, in some embodiments more than one pipette sheath aperture pair 180 is present within the sheath, as shown e.g., in FIGS. 1B and 1E. When multiple cored holes 180 are present within the pipette sheath (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more), each cored hole can be present at a different position or distance along the length of pipette sheath relative to the top side of the strip 110, that defines the pipette tip aperture. By the same token, multiple sheath aperture pairs 180 can be present along the length of a single pipette sheath, wherein each sheath aperture pair 180 can be located at a different position or distance along the length of the pipette sheath 120, with respect to the top side of the strip 110, which defines the pipette tip aperture. The arrangement of a plurality of cored holes 180 along the length of the pipette sheath (whether unpaired or as part of a pipette sheath aperture pair) offers the ability to not only determine whether or not a pipette tip is present within a sheath, but further provides the capability of determining the length (size) of the pipette tip inserted within the sheath. For example, as when a shorter pipette tip is present in sheath 120, the tip may alter the reflection or the obstruction of light directed through cored hole 180a, but may be too short to alter the reflection or obstruction of light directed through cored hole 180d. By the same token, when multiple sheath aperture pairs are present, a tip present in the pipette sheath may obstruct the passage of light directed through cored hole 180a as it exits cored hole 180b, but may be too short to obstruct light passing through sheath aperture pair 180c, 180d, or 180e, 180f. The pipette sheath aperture pairs 180 thus offer advantages for quality control of the reagent strips, by enabling the rapid determination of the presence or absence of tips, which can be performed manually (e.g., visible inspection by an individual), or which can be readily automated during the manufacturing process or assembly process for the reagent strips. For example, optical sensors can be used to transmit and detect light entering or exiting the first or second cored holes of aperture pairs 180, in order to detect the presence or absence (and, e.g., length) of pipette tips within each individual sheath 120.
In addition to providing advantages for quality control, the cored holes 180 can facilitate manufacture of the reagent strips 100. Specifically, manufacture of long, relatively narrow sheaths, such as pipette sheaths 120 by injection molding poses significant challenges. The pipette sheaths typically are a long, narrow shape with low draft angle vessels. Long core pins that are conventionally used in injection molding of structures such as the pipette tip sheaths as described herein, would tend to shift under the high pressure injection of e.g., thermoplastic material or thermosetting material from which the reagent strips are made. The presence of the cored holes 180, whether present unpaired or as part of the sheath aperture pairs, enables the use of stabilizing pins, created with mold action, to be used to stabilize the long core pins that are used for the molding of the pipette sheaths 120. Accordingly, cored holes 180 make feasible the manufacture of adjoined pipette sheaths by injection molding, thereby simplifying and reducing the cost of manufacture.
In some embodiments, the reagent strip comprises pipette sheaths having the same length. In some embodiments, the reagent strip can comprise pipette sheaths having different lengths. For example, as shown in FIG. 2A, the reagent strip 100 can comprise one or more pipette sheaths 180 having a first length 230, and one or more pipette sheaths having a second length 240, as shown, for example in FIG. 2A. Thus, pipette sheaths having the first, longer length 230 can house longer pipette tips than the pipette sheaths having the second, shorter length 240. As discussed above, in some embodiments, the pipette sheaths can comprise one or more unpaired cored holes 180, or cored holes present as pipette sheath aperture pairs. In some embodiments, however, the pipette sheaths do not comprise any cored holes 180. In some embodiments, for example, a reagent strip is provided, wherein the reagent strip comprises one or more pipette sheaths having a first, longer length and having pipette sheath aperture pairs along the longer length of the sheath; and one or more pipette sheaths having a second, shorter, length and no cored holes or pipette sheath aperture pairs. In some embodiments, however, both the longer and the shorter pipette sheaths can comprise at least one unpaired cored hole 180, or at least one pipette sheath aperture pair. In some embodiments, the longer pipette sheath can comprise more unpaired cored holes 180 or pipette sheath aperture pairs than the shorter pipette sheath. By way of example, a shorter pipette sheath can contain one or two cored holes 180, or one or two pipette sheath aperture pairs, and a longer pipette sheath can contain three or four unpaired cored holes 180, or three or four pipette sheath aperture pairs.
As shown in FIG. 3, the pipette sheaths 120 are closed at their base, which provides room to collect any liquids or drippings from the pipette tips following use. The individual pipette sheaths are substantially separated, e.g., by a wall.
As discussed above, the reagent strips disclosed herein preferably comprise one or more receptacles 150. Receptacles 150 of the reagent strip can be configured to accept reagent tubes that contain, respectively, sufficient quantities of one or more reagents used to prepare and/or process the biological and/or environmental samples. In some embodiments, the reagents may be in solid form, such as in lyophilized form, for carrying out sample preparation and/or processing, e.g., isolation of nucleic acids from a sample to create a sample suitable for nucleic acid testing (“NAT”) that is associated with the holder. In some embodiments, the reagents can be in liquid form.
The one or more receptacles 150 can be the same size and shape, or may be of different sizes and shapes from one another. Receptacles 150 are shown as having open bottoms, but are not limited to such topologies, and may be closed other than the inlet 220 in the upper side of the strip 110. Preferably the receptacles 150 are configured to accept commonly used containers, vessels or tubes in the field of laboratory analysis, or containers suitably configured for use with the holder herein. Reagent tubes 160 that are not integrated with strip 110 can thus be stored separately from the reagent strips, and can be snapped in just prior to use. This is advantageous as different reagents (e.g., nucleic acid extraction versus PCR reagents) may require different storage conditions. For example, lyophilized reagents can be moisture sensitive, and require different storage conditions that, e.g., a lysis buffer. The snap-in design of reagent tubes also affords versatility as tubes containing different reagents can be loaded into reagent strip 100, depending upon the different type of preparation/processing that the user wishes to perform on the sample
The strips disclosed herein can include a leading edge 190. Leading edge 190 can be configured to facilitate handling by the user. Leading edge 190 can also be configured to facilitate to proper insertion and/or position of the reagent strip 100, in e.g., an automated preparation and processing device. The leading edge 190 can comprise certain identifying features, such as a color, barcode, RFID, or the like to facilitate identification and/or tracking of individual reagent strips 100.
In some embodiments, reagent strip 100 comprises a registration member such as a mechanical key 250. Typically such a key is part of the strip 110, e.g., part of the leading edge 190 or the like. A mechanical key ensures that the holder is accepted by a complementary member in, for example, a supporting rack or a receiving bay of an apparatus that controls pipetting operations on reagents in the holder. A mechanical key 250 is normally a particular-shaped cut-out that matches a corresponding cutout or protrusion in a receiving apparatus. Thus, reagent strip 100 can comprise a mechanical key 250 that comprises a pair of rectangular-shaped cut-outs on one end of the strip 110. This feature as shown additionally provides for a tab by which a user may gain a suitable purchase when inserting and removing the holder into a rack or another apparatus. The skilled artisan will appreciate that the location of the mechanical key 250 feature can be different than that shown in the figures provided herein. For example, the mechanical key 250 can be located at the other end of strip 110 than leading edge 190. In some embodiments, key 250 is an angled cutout that eases insertion of the holder into a rack, as well as ensures a good registration therein when abutting a complementary angled cut out in a recessed area configured to receive the holder. Other variations of a mechanical key are, of course, consistent with the description herein: for example, curved cutouts, or various combinations of notches or protrusions all would facilitate secure registration of the holder.
In some embodiments, the reagent strip can comprise an identifier affixed to the strip 100. The identifier may be a label, such as a writable label, a bar-code, a 2-dimensional bar-code, or an RFID tag. The identifier can be, e.g., for the purpose of quickly revealing what combination of reagents is present in the holder and, thus, for what type of sample preparation protocol it is intended. The identifier may also indicate the batch from which the holder was made, for quality control or record-keeping purposes. The identifier may also permit a user to match a particular holder with a particular sample.
As discussed above, reagent tubes 140, 160, such as containing the lyophilized reagents, can be sealed across their tops by a metal foil, such as an aluminum foil, with no plastic lining layer, as further described herein. Reagent tubes 160 containing reagents can be provided as singular tubes, or multiple tubes that comprise completely separated vessels, wherein the vessels are adjoined together, e.g., via a connector. For example, in some embodiments, more than one reagent tube 160 (e.g., two three, four, five, six, seven, eight, nine, ten, or more), can be provided together, wherein the reagent tubes are together snapped into place in adjacent receptacles 150. By way of example, a plurality of reagent tubes 160 containing reagents specific for a particular NAT assay (e.g., containing specific, lyophilized amplification primers and/or probes and/or control nucleic acids) can be adjoined together, and readily snapped into a strip 110 configured to receive the plurality of separate reagent tubes adjoined together. In other embodiments, the receptacles are configured such that reagent tubes 160 can be inserted individually into each receptacle 150.
Integral reagent tubes 140, and/or snap-in reagent tubes 160 containing different reagents may be of different colors, or color-coded for easy identification by the user. For example, color-coding integral reagent tubes 140 may be useful to distinguish different types of unitized reagent strips, e.g., that can be used in different sample preparations. In the case of the snap-in reagent tubes 160, color coding the tubes may be used to distinguish different reagents from each other. By way of example, in the case of unitized reagent strips used for DNA isolation and generating a PCR-ready sample, different color coded reagent tubes 160 can be used to distinguish tubes used in connection with different NATs, e.g., that contain different primer pairs, probes, and the like. For example they may be made of different color material, such as tinted plastic, or may have some kind of identifying tag on them, such as a color stripe or dot. They may also have a label printed on the side, and/or may have an identifier such as a barcode on the sealing layer on the top. In some embodiments, the process 130 and/or reagent tubes 140, 160 can be translucent.
The reagent strips 100 are shown configured with a waste chamber 200, having a waste inlet aperture 210 in the upper side of the strip 110. Waste chamber 200 is optional and, in embodiments where it is present, is configured to receive spent liquid reagents. In other embodiments, where it is not present, spent liquid reagents can be transferred to and disposed of at a location outside of the holder, such as, for example, a sample tube that contained the original sample whose contents are being analyzed. Waste chamber 200 is shown as part of an assembly comprising additionally two or more reagent tubes 140. It would be understood that such an arrangement is done for convenience, e.g., of manufacture; other locations of the waste chamber 200 are possible, as are embodiments in which the waste chamber 200 is adjacent a reagent tube 140, but not connected to it other than via the strip 110.
The holder is typically such that the strip 110, pipette sheath(s) 120, process tube 130, the two or more reagent tubes 140, and the waste chamber (if present) are made from a single piece, made from a material such as polypropylene. As discussed elsewhere above, the design of the embodiments disclosed herein advantageously facilitate manufacture of a unitized reagent strip from, e.g, an injection mold.
FIGS. 1G and 2C show the underside 320 of reagent strip 100. As shown in FIG. 2C, the underside 320 can comprise struts 300, which provide for stability and flexibility.
FIG. 1H shows a cut-away view of a pipette tip 360 contained in one of the pipette sheaths 120.
While the figures provided herein show a strip that is configured so that the one or more pipette sheaths, the one or more receptacles, and the respective apertures of the process tube, and the reagent tubes, are all arranged linearly with respect to one another (i.e., their midpoints lie on the same axis) the skilled artisan will appreciate that the holders herein are not limited to particular configurations of receptacles, waste chambers, process tubes, pipette sheaths, and reagent tubes. For example, some embodiments provide a shorter reagent strip e.g., with staggered apertures, wherein some reagent, process tube, or pipette tip apertures occupy ‘off-axis’ positions. The various receptacles, etc., also do not need to occupy the same positions with respect to one another as is shown in FIGS. 1-3, wherein the process tube is disposed approximately near the middle of the holder, liquid reagents are stored in receptacles mounted on one side of the process tube, and receptacles holding solid reagents are mounted on the other side of the process tube. Thus, in FIGS. 1-3, the process tube is on one end of the strip, and the pipette sheath(s) are at the other end, adjacent to, in an interior position, a waste chamber and two or more reagent tubes. Still other dispositions are possible, such as mounting the process tube on one end of the holder, mounting the process tube adjacent the pipette tips and pipette tip sheath (as further described herein), and mounting the waste tube adjacent the process tube. It would be understood that alternative configurations of the various parts of the reagent strip give rise only to variations of form and can be accommodated within other variations of the apparatus as described, including but not limited to alternative instruction sets for automated preparation and processing of the samples.
Process tube 130 can also be a snap-in tube, rather than being part of an integrated piece. Process tube 130 can be used for various mixing and reacting processes that occur during sample preparation. For example, cell lysis can occur in process tube 130, as can extraction of nucleic acids. Process tube 130 is then advantageously positioned in a location that minimizes, overall, pipette head moving operations involved with transferring liquids to process tube 130.
Reagent tubes 140 are typically configured to hold various liquid reagents. For example, in some embodiments, the reagent strips can comprise, three reagent tubes, wherein the individual reagent tubes are supplied with a sample wash buffer, a nucleic acid release buffer, and nucleic acid neutralization buffer, e.g., to purify nucleic acids for NAT assays.
Reagent tubes 140 that hold liquids or liquid reagents can be sealed with a laminate structure 400. The laminate structure can comprise a heat seal layer, a plastic layer such as a layer of polypropylene, and a layer of metal such as aluminum foil, wherein the heat seal layer is adjacent the one or more reagent tubes 140. The additional plastic film that is used in a laminate for receptacles that contain liquid reagents is typically to prevent liquid from contacting the aluminum.
Exemplary embodiments of a laminate structure 400, differing in their layer structures, are described, e.g., in U.S. Patent Application Publication No. 2009/0129978, herein incorporated by reference. In some embodiments, the heat seal layer of the laminate structure 400 can be made, e.g., from a lacquer or other polymer with a low melting point, and located at the top of the reagent strip 100 when so applied, as shown in FIG. 5A. The laminate 400 structure can include a plastic layer 420 on top of the heat seal layer 410 made of polypropylene, having a thickness in the range 10-50 microns. The laminate structure 400 may also include a metal layer on top of the plastic layer, comprising a layer of aluminum foil 440 bonded to the plastic layer 420 with a layer of adhesive 430. Alternatively, the metal layer may be a layer of metal that is evaporated or sputtered into place directly on to the plastic layer, as shown in FIG. 5B.
The laminates deployed herein make longer term storage easier because the holder includes the presence of sealed lyophilized reagents as well as liquids sealed in close proximity, which is normally hard to achieve.
In one embodiment, the tops of the reagent tubes have beveled edges so that when an aluminum foil is heat bonded to the top, the plastic melt does not extend beyond the rim of the tube. This is advantageous because, if the plastic melt reduces the inner diameter of the tube, it will cause interference with the pipette tip during operation. In other embodiments, a raised flat portion 260 facilitates application and removal of laminate 400. Raised surface 260, on the upper side of the connecting member, and surrounding the inlet apertures to the reagent tubes and, optionally, the waste chamber, is an optional feature of the holder.
The manner in which liquid is pipetted out is such that a pipette tip piercing through the foil rips through without creating a seal around the pipette tip. Such a seal around the tip during pipetting would be disadvantageous because a certain amount of air flow is desirable for the pipetting operation. In this instance, a seal is not created because the laminate structure 400 causes the pierced foil to stay in the position initially adopted when it is pierced. The upper five panels in FIG. 4 illustrate the pipetting of a reagent out from a reagent tube sealed with a laminate as further described herein. At A, the pipette tip is positioned approximately centrally above the reagent tube 140 that contains reagent 270. At B, the pipette tip is lowered, usually controllably lowered, into the reagent tube, and in so doing pierces the foil 280. The exploded view of this area shows the edge of the pierced laminate to be in contact with the pipette tip at the widest portion at which it penetrates the reagent tube. At C, the pipette tip is withdrawn slightly, maintaining the tip within the bulk of the reagent 270. The exploded view shows that the pierced foil has retained the configuration that it adopted when it was pierced and the pipette tip descended to its deepest position within the reagent tube. At D, the pipette tip sucks up reagent 270, possibly altering its height. At E, the pipette tip is removed entirely from the reagent tube.
The materials of the various tubes and chambers may be configured to have at least an interior surface smoothness and surface coating to reduce binding of nucleic acids and other macromolecules thereto. Binding of nucleic acids is unwanted because of the reduced sensitivity that is likely to result in subsequent detection and analysis of the nucleic acids that is not trapped on the surface of the holder. The process tube also may have a low binding surface, and allows magnetic beads to slide up and down the inside wall easily without sticking to it. Moreover, it has a hydrophobic surface coating enabling low stiction of fluid and hence low binding of nucleic acids and other molecules. The reagent strips disclosed herein can be manufactured from many different polymers, including all thermoplastics, some thermosets, and elastomers. Preferably, the material is suitable for injection molding. Non limiting examples of polymers useful in the manufacture of the strips disclosed herein include, e.g., epoxy and phenolic polymers, nylon, polyethylene, and polystyrene polymers, and the like. Preferably the reagent strips are made from a plastic such as polypropylene, and are of dimensions that are rigid, so that the reagent strips will not significantly sag or flex under its own weight and will not easily deform during routine handling and transport, and thus will not permit reagents to leak out from it.
It should also be considered consistent with the description herein that a holder additionally can be configured to accept a sample, such as in a sample tube. Thus, in embodiments described elsewhere herein, a rack accepts a number of sample tubes and a number of corresponding holders in such a manner that the sample tubes and holders can be separately and independently loaded from one another. Nevertheless, in other embodiments, a holder can be configured to also accept a sample, for example in a sample tube. And thus, a complementary rack is configured to accept a number of holders, wherein each holder has a sample as well as reagents and other items. In such an embodiment, the holder is configured so that the sample is accessible to a sample identification verifier.
Kits
The reagent strips described herein may be provided as a kit. For example, individual reagent strips can be packaged together or individually in a sealed pouch, to reduce the chance of air and moisture coming into contact with the reagents in the holder. Such a sealed pouch may contain one or more of the holders described herein, such as 2, 4, 6, 8, 10, 12, 16, 20, or 24 holders.
The holder may also be provided as part of a kit for carrying out sample preparation, wherein the kit comprises a first pouch containing one or more of the holders described herein, each of the holders configured with liquid reagents for, e.g., lysis, wash, and release, and a second pouch, having an inert atmosphere inside, and one or more reagent tubes containing lyophilized PCR reagents. Such a kit may also be configured to provide for analysis of multiple samples, and contain sufficient PCR reagents (or other amplification reagents, such as for RT-PCR, transcription mediated amplification, strand displacement amplification, NASBA, helicase dependent amplification, and other familiar to one of ordinary skill in the art, and others described herein) to process such samples, and a number of individual holders such as 2, 4, 6, 8, 10, 12, 16, 20, or 24 holders.

## Claims

1. A method of detecting the presence or absence of a pipette tip within a pipette sheath of a unitized reagent strip, comprising:
providing the unitized reagent strip, the unitized reagent strip comprising:
a strip with a top side and a bottom side, comprising
a first and a second pipette sheath, the first pipette sheath comprising opposing sides and a first longitudinal axis, said first and second pipette sheaths comprising a first and second pipette tip aperture, respectively, each of which comprises a separate opening on the top side of the strip, and wherein said first and second pipette tip apertures are configured for insertion of a first and second pipette tip into said first and second pipette sheaths, respectively, and wherein each of said first and second pipette sheaths is configured to substantially surround the length of the first and second pipette tip, respectively;
a process tube; and
a receptacle, comprising an opening through the reagent strip, wherein said receptacle is configured to receive a reagent tube,
wherein said first pipette sheath comprises an aperture pair, said aperture pair comprising a first cored hole and a second cored hole, wherein the first and second cored holes are located on the opposing sides, and are positioned along the th of the first pipette sheath at the same distance from the first pipette tip aperture, the first and second cored holes having an axis transverse to the first longitudinal axis,

providing an optical beam through the first cored hole of said aperture pair; and
detecting whether said optical beam exits unobstructed through said second cored hole of said aperture pair,
determining whether the first pipette tip is present within the first pipette sheath, wherein the unobstructed exit of said optical beam through said second cored hole of said first pipette sheath is indicative of the absence of the first pipette tip within the first pipette sheath, and wherein obstructed exit of said optical beam though said second cored hole indicates the presence of the first pipette tip within said first pipette sheath.

2. The method of claim 1, wherein the first pipette sheath comprises a second aperture pair, wherein the second aperture pair is a different distance along the length of the first pipette sheath, the method further comprising determining the length of the first pipette tip inserted within the first pipette sheath.

3. The method of claim 1, wherein the first pipette sheath comprises multiple cored holes, the method further comprising determining the length of the first pipette tip inserted within the first pipette sheath.

4. The method of claim 1, wherein the first pipette tip alters the reflection or the obstruction of light directed through the first cored hole but does not alter the reflection or the obstruction of light directed through another cored hole.

5. The method of claim 1, wherein determining whether the first pipette tip is present within the first pipette sheath further comprises using optical sensors.

6. A method of determining the length of a pipette tip within a pipette sheath of a unitized reagent strip, comprising:
providing a unitized reagent strip comprising:
a strip with a top side and a bottom side, comprising:
a process tube;
a receptacle, comprising an opening through the reagent strip, wherein said receptacle is configured to receive a reagent tube; and
a first and a second pipette sheath, comprising:
a first and second pipette tip aperture, respectively, each of which comprises a separate opening on the top side of the strip, and wherein said first and second pipette tip apertures are configured for insertion of a first and second pipette tip into said first and second pipette sheaths, respectively, and wherein each of said first and second pipette sheaths is configured to substantially surround the length of the first and second pipette tip, respectively; and
a top pipette sheath aperture pair and a bottom pipette sheath aperture pair within said first pipette sheath, said top and bottom pipette sheath aperture pairs each comprising a first and a second cored hole extending through a sidewall of the first pipette sheath, wherein the first and second cored holes of said top and bottom pipette sheath aperture pairs are located on opposite sides of the first pipette sheath, and positioned along the length of the first pipette sheath at the same distance from the first pipette tip aperture, and wherein said top pipette sheath aperture pair is located more proximal to the first pipette tip aperture than said bottom pipette sheath aperture pair;


providing an optical beam through said first cored hole of said top pipette sheath aperture pair;
providing an optical beam through said first cored hole of said bottom pipette sheath aperture pair;
detecting whether said optical beam is obstructed from passing through said second cored hole of said top pipette sheath aperture pair; and
detecting whether said optical beam is obstructed from passing through said second cored hole of said bottom pipette sheath aperture pair, wherein obstruction of said optical beam through the second cored hole of the top pipette sheath aperture pair and passage of said optical beam through said second cored hole of said bottom pipette sheath aperture pair indicates that the first pipette tip within said first pipette sheath has a length that does not extend down to the bottom pipette sheath aperture pair when inserted into the first pipette sheath.

7. The method of claim 6, wherein obstruction of said optical beam through the second cored hole of the top pipette sheath aperture pair and obstruction of said optical beam through said second cored hole of said bottom pipette sheath aperture pair indicates that the first pipette tip within said first pipette sheath has a length that extends down to the bottom pipette sheath aperture pair when inserted into the first pipette sheath.

8. The method of claim 6, wherein obstruction of said optical beam through the second cored hole of the top pipette sheath aperture pair indicates that the first pipette tip is present within said first pipette sheath.

9. A method of detecting the presence or absence of a pipette tip within a pipette sheath of a unitized reagent strip, comprising:
providing the unitized reagent strip, the unitized reagent strip comprising:
a strip with a top side and a bottom side, comprising:
a first and a second pipette sheath comprising opposing sides, said first and second pipette sheaths comprising a first and second pipette tip aperture, respectively, each of which comprises a separate opening on the top side of the strip, and wherein said first and second pipette tip apertures are configured for insertion of a first and second pipette tip into said first and second pipette sheaths, respectively, and wherein each of said first and second pipette sheaths is configured to substantially surround the length of the first and second pipette tip, respectively,
a process tube; and
a receptacle, comprising an opening through the reagent strip, wherein said receptacle is configured to receive a reagent tube,
wherein the first pipette sheath comprises a first cored hole, said first cored hole extending through a sidewall of the first pipette sheath,
determining whether the first pipette tip extends within said first pipette sheath from the first pipette tip aperture at least to the distance of the first cored hole,
wherein said determining step comprises:
providing an optical beam that enters the first pipette sheath through the first cored hole, and
determining the reflection or obstruction of the optical beam as indicative of the presence or absence of the first pipette tip that extends within said first pipette sheath to the distance from the first pipette tip aperture to the first cored hole.

10. The method of claim 9, wherein said determining step comprises visual inspection of the interior of the first pipette sheath through the first cored hole.

11. The method of claim 9, wherein the first pipette sheath comprises an alternative cored hole, wherein the alternative cored hole is a different distance along the length of the first pipette sheath than the first cored hole, the method further comprising determining the length of the first pipette tip inserted within the first pipette sheath.

12. The method of claim 9, wherein the first pipette sheath comprises multiple cored holes, the method further comprising determining the length of the first pipette tip inserted within the first pipette sheath.

13. The method of claim 9, wherein the first pipette tip alters the reflection or the obstruction of light directed through the first cored hole but does not alter the reflection or the obstruction of light directed through another cored hole.

14. The method of claim 9, wherein the first pipette sheath comprises at least two cored holes, the method further comprising determining the reflection or obstruction of the optical beam as indicative of the presence or absence of the first pipette tip that extends within said first pipette sheath to the distance from the first pipette tip aperture to the at least two cored holes.

15. A method of determining the length of a pipette tip within a pipette sheath of a unitized reagent strip, comprising:
providing a unitized reagent strip comprising:
a strip with a top side and a bottom side, comprising:
a process tube; and
a receptacle, comprising an opening through the reagent strip, wherein said receptacle is configured to receive a reagent tube; and

a first and a second pipette sheath, comprising:
a first and second pipette tip aperture, respectively, each of which comprises a separate opening on the top side of the strip, and wherein said first and second pipette tip apertures are configured for insertion of a first and second pipette tip into said first and second pipette sheaths, respectively, and wherein each of said first and second pipette sheaths is configured to substantially surround the length of the first and second pipette tip, respectively; and
a top cored hole and a bottom cored hole within said first pipette sheath, said top and bottom cored holes each extending through a sidewall of the first pipette sheath, wherein said top cored hole is located more proximal to the first pipette tip aperture than said bottom cored hole;


determining whether the first pipette tip extends within said first pipette sheath from the first pipette tip aperture to the distance of the top cored hole; and
determining whether the first pipette tip extends within said first pipette sheath from the first pipette tip aperture to the distance of the bottom cored hole.

16. The method of claim 15, wherein said determining comprises visual inspection of the interior of the first pipette sheath through said top cored hole and said bottom cored hole.

17. The method of claim 15, wherein said determining comprises:
providing an optical beam through said top cored hole;
providing an optical beam through said bottom cored hole; and
determining the reflection or obstruction of the first and second optical beam as indicative of the presence or absence of the first pipette tip that extends within said first pipette sheath to the distance from the first pipette tip aperture to the top cored hole and the bottom cored hole, respectively.

18. The method of claim 15, further comprising determining whether the first pipette tip is present within the first pipette sheath.

19. The method of claim 15, wherein determining whether the first pipette tip extends within said first pipette sheath from the first pipette tip aperture to the distance of the top cored hole comprises passing a beam of light through the top cored hole.

20. The method of claim 15, wherein determining whether the first pipette tip extends within said first pipette sheath from the first pipette tip aperture to the distance of the bottom cored hole comprises passing a beam of light through the bottom cored hole.