Patent Grant
10125389
Currently the processing of biochemistry samples has a number of key drawbacks. These include the volume size—resulting in high reagent costs; high consumable costs; and labour-intensive protocols and processes which are highly susceptible to cross-contamination. For these reasons complete control and isolation of each individual sample within the biochemistry process cannot currently be ensured.
For a number of biochemistry process applications—sequence bead preparation, pyrosequencing, nucleic acid ligation, and polymerase chain reaction—and not limited to these, the limitations of volume size, chemistry cost, labour cost, and the reaction efficiency are evident.
Sequence bead preparation is a process by which small beads are coated in an application-specific chemistry. For example in DNA replication, the beads are coated initially with DNA primers in advance of the amplification process. Even for today's state-of-the-art sequencers a relatively high local concentration of the target molecule is required to sequence accurately. Current estimates for a typical protocol estimate that only 80% of the beads processed are sufficiently coated to ensure accurate sequencing. Therefore to ensure a relatively high concentration of the target sample a large number of beads must be used for statistical accuracy. Furthermore, the transferral of even coated beads from one well to another inevitably leads to losses of both the beads and the suspended fluid. This is a result of dead volumes and inefficiencies inherent in today's pipetting and liquid handling systems. This biochemistry process is generally performed in 96 or 384 static well plates with typical volumes ranging from 10 microliters to 200 microliters.
Another biochemistry process, pyrosequencing, mixes a relatively high concentration of nucleic acid with primer-coated beads. The nucleic acids attach and form a clonal colony on the beads. This is then amplified using emulsion-based PCR. The sequencing machine contains a large number of picoliter-volume wells that are large enough for a single bead along with the relevant enzymes required for sequencing. Pyrosequencing uses the luciferase enzyme to generate light as read-out, and the sequencing machine takes a picture of the wells for every added nucleotide. One of the key difficulties in this process is the efficient coating of the beads with primers. A percentage of beads using current technologies are not properly coated with primer chemistry, resulting in poorer reaction efficiencies. Using today's technologies to improve the coating efficiencies of the beads would require an unsustainable increase in reagent cost.
Within nucleic acid ligation similar biochemistry processing issues arise. Nucleic acid ligation has become an important tool in modem molecular biology research for generating recombinant nucleic acid sequences. For example, nucleic acid ligases are used with restriction enzymes to insert nucleic acid fragments, often genes, into plasmids for use in genetic engineering. Nucleic acid ligation is a relatively common technique in molecular biology wherein short strands of DNA may be joined together by the action of an enzyme called ligase at a specific temperature, commonly 16-25° C. depending on the protocol used. To join more than two sequences of short DNA strands together, for example in the construction of a synthetic genetic sequence, it is impossible to combine all the DNA strands and then perform the ligation. This would result in random sequences in which the end of one strand would be joined to the start of an incorrect strand. This incorrect sequence, or orientation, would not be desirable in a synthetically-constructed gene where the order of the genetic code is crucial. To perform the technique correctly pairwise combinations of neighbouring sequences must first be ligatated to yield the correct orientation. These paired synthetic constructs may then be ligated in the correct orientation to yield even longer synthetic constructs. The process involves a large and intricate amount of chemistry processing and manipulation. This can be quite a labour intensive process or if performed using today's liquid handling and results in large consumable costs and suffers from the known dead volume losses of the static well plates and pipette aspirations. Also using today's liquid handling technologies the mixing and control of small volumes is limited by the ability to aspirate and manipulate relatively small volumes. Typical volumes used in nucleic acid ligation are 10-200 microliters with nucleic acid strand lengths between 50-200 base pairs.
Polymerase Chain Reaction (PCR) has been used extensively to amplify targeted DNA and cDNA for many applications in molecular biology. The PCR technique amplifies a single or a few copies of a piece of DNA, generating thousands to billions of copies of a particular DNA sequence. Modem PCR instruments carry out the PCR process in reaction volumes ranging from 10-200 micro-liters. One of the largest obstacles to carrying out PCR in small volumes is the difficulty in manipulating small volumes of the constituent reagents with manual pipettes. The large volume size is a direct result of the poor capability of existing technologies to dispense and mix sub-nanoliter volumes. Furthermore, for the next generation microfluidic technologies based on flowing systems, these are still limited by the starting volume dispensed versus the actual amount of sample required for the biochemistry process. These microfluidic systems are also limited during the biochemistry process to a defined protocol control of the samples. These systems typically rely on micro-scale fluid channel networks to transport and mix sub-microliter volumes. Some of the major drawbacks of these technologies are: the single use of the microfluidic cards—to prevent contamination—the lack of dynamic control of the each individual sample—transporting and mixing any individual sample at any point in the biochemistry process—and the closed architecture of the system.
In particular, current methods of Digital Polymerase Chain Reaction (dPCR) are performed through the division of an initial sample into multiple smaller volumes samples until one DNA template remains in each subvolume. Counting the number of positive subvolumes which contain DNA, the starting copy number in the original volume can be calculated. Typically, this involves multiple serial dilution steps to generate a sample volume with statistically one DNA target per reaction volume. Statistically a subset of the total volume may be tested to determine the initial copy number, allowing for a reduction in the total number of PCR reactions. However for rare target detection a larger subset of volumes need to be tested to improve the statistical accuracy. This results in a larger number of blank volumes and a larger test volume—resulting in the use of more chemistry, time, instrumentation, sample handling, and processing steps.
Another method of dPCR is whereby an emulsion of the test volume is generated in an oil-based carrier. This method is an effort to reduce the number of instruments required and time required for a result. First, the target sample is diluted and emulsified into small enough volumes with a statistical distribution of less than one copy per droplet, within the carrier oil. This larger volume can then be treated as a single sample volume and processed using PCR protocols. However this method is generally limited to end point detection. Further instrumentation is required in the form of a flow cytometer, thereby being able to detect the target presence per droplet flowing past a sensor. Flow cytometers are low speed; expensive; can require specific fluid mediums and only allow for endpoint detection. The limitations of endpoint detection include the requirement of a post processing step; lower sensitivity;
longer time to result; specificity and more instrumentation. A further challenge for emulsion based PCR methods is the stability required and control of each droplet. Droplet merging or splitting introduces further statistical errors into the processing.
Today's pipetting and liquid handling systems are unable to process 100% of the given starting volume. For pipettes both the liquid storage system—static well plates—and the mechanical actuation within the system prevent complete aspiration of the sample. This loss or dead volume in static plates can be accounted for by the surface wetting characteristics and the geometry, neither of which current technologies can account for.
In flowing systems the collection of individual biological samples during or at the end of the biochemistry process is proving to be very challenging for existing technologies. The typical continuous flowing systems comprise of pumps and reservoirs which generally make the easy retrieval of critical fluids, particularly at the microscale, technically difficult. Also, within flowing systems initial priming of the system is time consuming, costly and if done incorrectly leads to a catastrophic failure of the test requiring a retest of the biological sample.
Another drawback to existing biochemistry processing is the inability to automate the biochemistry process for nano-liter and sub-nano-liter volumes. The transport, mixing or retrieval of each individual sample cannot be performed by existing automated technologies.
In more general chemistry processing, such as generic microchemistry, where the manipulation of small amounts of fluid is necessary, one can clearly see the limitations of current technology in the volume waste fluid remaining in the static well plates or within the system. This is a result of current technology's lack of capability to dispense and control smaller volumes demanded by evermore sophisticated molecular biology techniques, and the call for improved efficiencies.
The invention is therefore directed towards providing improved sample handling to overcome at least some of the above problems.
Devices, systems and methods for making and handling composite liquid cells are disclosed.
The invention provides in some embodiments systems and methods for the generation of a biological sample within an immiscible fluid cell and positioned on a free surface of a mutually immiscible carrier fluid. This involves generation, and/or location control, and/or movement control, and/or mixing, and/or processing of biological samples within such composite liquid cells (synonymous with “composite fluid cell”) and positioned on an immiscible carrier fluid.
The biological sample typically has a density between that of the carrier fluid and the outer fluid of the composite liquid cell. The carrier fluid typically has a density higher than that of the outer fluid of the composite liquid cell.
Typical values of densities for the fluids involved range within the values 1,300 to 2,000 kg/m3 for the carrier fluid, 700 to 990 kg/m3 for the immiscible fluid cell and 900 to 1200 kg/m3 for the biological sample. An example of one such set of operating fluids and densities is outlined herein but is not limited to these; carrier fluid is Fluorinert FC-40 (fluorocarbonated oil) density of approximately 1,900 kg/m3; outer fluid of the composite liquid cell is phenylmethylpolysiloxane (silicone oil) density of approximately 920 kg/m3; and the biological sample is an aqueous based solution of PCR reagents with a density of approximately 1000 kg/m3.
In another embodiment the carrier fluid is a perfluorinated amine oil.
In another embodiment, the encapsulating fluid is a solution of a Phenylmethylpolysiloxane—based oil and a polysorbate additive. The additives have a hydrophilic-lipophilic balance number in the range of 2 to 8. The combined total hydrophilic-lipophilic balance number of the additives is in the range of 2 to 8. Examples of polysorbate additives are SPAN 80, SPAN 65 and Tween 20 but are not limited to these. These additives within the buffer encapsulating fluid range between 0.001% and 10%.
In another embodiment, the target sample is a solid particle suspension in aqueous media and the encapsulating fluid is a Phenylmethylpolysiloxane-based oil, on a carrier fluid which is a fluorocarbon-based oil.
In another embodiment the target sample is an aqueous media-in-Phenylmethylpolysiloxane-based oil and the encapsulating fluid is a Phenylmethylpolysiloxane-based oil, on a carrier fluid which is a fluorocarbon-based oil.
In some embodiments the control surfaces are a hydrophobic material.
A system used for making and manipulating composite liquid cells will typically include a liquid handling system under the control of a controller (such as a programmable computer). The controller is typically programmed to cause the liquid handling system to carry out various steps, with the program steps stored in a nontransitory computer-readable medium.
Generating Composite Liquid Cells
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Transporting Composite Liquid Cells
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In another embodiment, a composite liquid cell can be moved using a combination of electrostatic forces and the hydrophobic effect. Referring to
In another embodiment the hydrophobic spars are partially submerged in the carrier fluid.
In another embodiment there are multiple controlling surfaces, allowing for independent motion of discrete composite liquid cells.
In another embodiment, the transport motion is a combination of dynamic control using the hydrophobic effect. A composite liquid cell is positioned on an immiscible carrier fluid and located in contact with a hydrophobic track. A dynamic controlling surface using the hydrophobic effect moves the composite liquid cell along the defined hydrophobic track. The controlling surface can also be used to separate the composite liquid cell from the hydrophobic spar and move the composite liquid cell independently or to another hydrophobic location. Using this transport motion one or more composite liquid cells can be merged or additional biological samples can be added to a composite liquid cell.
In another embodiment, the carrier fluid is a continuously flowing fluid and with it's resulting momentum transporting the composite liquid cells along its streamlines. In another embodiment the carrier fluid momentum is assisted by static hydrophobic surfaces along which the composite liquid cells can progress. In another embodiment the carrier fluid momentum is assisted by dynamic hydrophobic surfaces by which the composite liquid cells can be transported.
Unless otherwise stated, any of the disclosure herein related to composite liquid cells generally, also applies to multi-sample composite liquid cells in particular.
Generating Composite Liquid Cells with Multiple Samples
In one embodiment, referring to
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In another embodiment, a composite liquid cell with multiple samples of multiple distinct sample targets is generated. Referring to
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Transporting the Composite Liquid Cells with Multiple Samples
All general methods of transporting composite liquid cells, for example those discussed above, are also applicable to multi-sample composite liquid cells.
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In another embodiment the control surface is partially submerged in the carrier fluid. Referring to
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Internal control of multiple sample volumes with a composite liquid cell
In one embodiment the internal sample volumes with a multi-sample composite liquid cell can be arrayed for 2D analysis. Referring to
In one embodiment the internal samples of a multi-sample composite liquid cell are recombined using a sorbate additive. Examples of polysorbate additives are SPAN 80 and Tween 20 but are not limited to these. These additives within the buffer encapsulating fluid range between 0.001% and 10%.
Mechanical Features for Stabilisation
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Generating Composite Liquid Cell with Mechanical Features
Composite liquid cells may be generated as described earlier, for example,
In another embodiment two or more hydrophobic surfaces with stabilisation features are used to control the composite liquid cell location. The use of stabilisation features on a hydrophobic spar allow for the generation of composite liquid cells at controlled and discrete locations, therefore improving sample tracking and/or automation and/or process control.
Transporting Composite Liquid Cells with Mechanical Features
In some embodiments, referring to
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Composite Liquid Cell Network
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In another embodiment, two or more composite liquid cells can be transported simultaneously using a controlled injection and withdrawal of encapsulating buffer fluid.
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Examples of composite liquid cell networks are outlined herein but are not limited to these; Referring to
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Processing the Composite Liquid Cells
In certain embodiments, the system may involve one or more of the following steps in any order which achieves the target sample combination at the end of the method: extracting samples for target; processing the samples for loading into the dispensing system; dispensing the target sample; dispensing the immiscible encapsulating fluid cell; dispensing the carrier fluid; combining the biological sample and immiscible encapsulating fluid cell; combining the biological sample and composite liquid cell; combining the biological sample and multi-sample composite liquid cell; controlling the motion of the immiscible encapsulating fluid cell; controlling the motion of the carrier fluid; transporting one or more immiscible fluid cells; transporting one or more immiscible fluid cells to combine with one or more biological samples; transporting one or more composite liquid cells to combine with one or more biological samples; transporting one or more multi-sample composite liquid cells to combine with one or more biological samples; transporting one or more composite liquid cells to combine with one or more composite liquid cells; transporting one or more multi-sample composite liquid cells to combine with one or more composite liquid cells; transporting one or more multi-sample composite liquid cells to combine with one or more multi-sample composite liquid cells; detecting an effect of the biological sample within the composite liquid cell; detecting an effect of the biological sample within the multi-sample composite liquid cell; detecting effects of biological samples within the multi-sample composite liquid cell; providing output information to a user of the detection; analysing the output data of the detection. Examples of the biological protocols are given in the ensuing sections.
PCR
Polymerase Chain Reaction (PCR) has been used extensively to amplify targeted DNA and cDNA for many applications in molecular biology. The PCR technique amplifies a single or a few copies of a piece of DNA, generating thousands to billions of copies of a particular DNA sequence. Modem PCR instruments carry out the PCR process in reaction volumes ranging from 10-200 micro-liters. One of the largest obstacles to carrying out PCR in small volumes is the difficulty in manipulating small volumes of the constituent reagents with manual pipettes. Another obstacle for PCR is the difficulties in multiplexing reactions allowing for increased thought put.
The methods of the invention generally involve combining the necessary fluids to form the resulting multi-sample composite liquid cell. In one embodiment the target sample is an aqueous biological sample, comprising reagents required for nucleic acid amplification, and the outer fluid cell is a silicone oil (Phenylmethylpolysiloxane, PD 5) with a polysorbate additive (SPAN 80), on a carrier fluid which is a fluorocarbon-based oil (Fluorinert FC-40). The individual reagents are arrayed such that all the necessary components for PCR are placed as individual composite liquid cells. This prevents cross-contamination of biological reagents. The individual composite liquid cell components are combined together in the correct sequence. The individual composite liquid cells are then combined together forming a multi-sample composite liquid cell. The multi-sample composite liquid cell is then transported into different thermal zones or optical interrogation zones where quantitative measurement of the products are performed via fluorescent measurement. The placement of PCR target volumes within composite liquid cells prevents evaporation during thermal cycling. Typical thermal cycling temperatures range between 55-95° C.
In a further embodiment the composite liquid cells may have an associated detection mark added as a discrete sample.
In a further embodiment, the combination of post-PCR reactions may be required for further processing that may include genetic sequencing. The use of multi-sample composite liquid cells greatly simplifies the collection and sequencing procedure for these relatively small target volumes. The multi-sample composite liquid cells following individual processing can be combined selectively, removing any unspecific amplification reactions or inefficient reaction from the final collected volume. The amalgamated final target volume, consisting of many differing target molecules, is transferred into a sequencing instrument for detailed analysis. The composite liquid cell facilitates 100% volume retrieval as the biological sample is processing and does not need to touch any solid surface and also has the additional benefit of an anti-wetting characteristic. Additionally, the fluid volume requiring thermal cycling has been greatly reduced—removed the entire mass and thermal resistance of the static well plates—targeted heating strategies can facilitated lower power instruments and faster reaction processing times.
Referring to Table 1 the composite liquid cell has successfully performed Single Nucleotide Polymorphism detection. Two positive samples were used, each containing a different allele of the gene, named allele 1 and allele 2. Each allele was labelled with a different dye and reading at the correct intensity allowed detection of each allele. A no template control was added in a composite liquid cell and amplified. This was repeated in the following order for a positive allele 1, a no template control, a positive allele 2 and finally another no template control. Referring to Table 1 the results show that amplification was successfully performed in composite liquid cells with no cross contamination between samples. This is indicated by no rise in fluorescence intensity between the initial no template control and the no template control samples that followed each positive samples.
Referring to
Digital PCR
The Polymerase Chain Reaction (PCR) is a widely used molecular amplification technique. The technique has widespread applications in clinical diagnostics, agricultural biotechnology and bioresearch. It is routinely used for the detection of SNP's, diagnosis of hereditary diseases, genetic fingerprinting, forensic analysis, gene expression and other types of nucleic acid analysis. The development of Digital PCR has increased the use of conventional PCR. Digital PCR is a technique that amplifies a single DNA template. For a review of the PCR methodology see Digital PCR (Proc Natl Acad Sci USA 96(16):9236-41 (1999)) by Vogelstein and Kinzler; Principle and application of digital PCR (Expert Review Molecular Diagnostics 4(1):41-47 (2004)) by Pohl and Shih.
The methods of the invention generally involve combining and distributing the necessary fluids to form the resulting multi-sample composite liquid cell. In one embodiment the target sample is an aqueous biological sample, comprising reagents required for nucleic acid amplification, and the outer fluid cell is a silicone oil (Phenylmethylpolysiloxane, PD 5) with a polysorbate additive (SPAN 80), on a carrier fluid which is a fluorocarbon-based oil (Fluorinert FC-40). The individual reagents are arrayed such that all the necessary components for digital PCR are placed as individual composite liquid cells. This prevents cross-contamination of biological reagents. The individual composite liquid cell components are combined together in the correct sequence. The individual composite liquid cells are then ultrasonicated to form a multi-sample composite liquid cell. The multi-sample composite liquid cell is then transported into different thermal zones or optical interrogation zones where quantitative measurement of the products are performed via fluorescent measurement. The placement of digital PCR target volumes within composite liquid cells prevents evaporation during thermal cycling. Typical thermal cycling temperatures range between 55-95° C. The multi-sample composite liquid cell facilitates the use of simpler detection methods as the multi-sample composite liquid cell does not require optics for three dimensional integration for quantification determination.
In another embodiment the individual composite liquid cells are mechanically agitated to form a multi-sample composite liquid cell.
Nucleic Acid/DNA Ligation
Nucleic acid ligation involves the use of nucleic acid ligases, which are enzymes that are used to join fragments of nucleic acid together. In constructing long DNA strands multiple shorter DNA fragments are combined together, it is therefore necessary to perform multiple ligation steps to achieve these results. The product of one ligation reaction becomes the fragment of another. The ligation must be performed in a pairwise fashion to avoid efficiency and orientation problems affecting the reaction.
In one embodiment, the reaction reagents—the DNA fragments to be joined; the ligase enzyme; and the buffer reagents—are pipetted individually into separate wells of a microtitre plate. The outer composite fluid, a silicone oil (Phenylmethylpolysiloxane, PD 5), is pipetted on top of the aqueous reagents within each well, creating an oil-aqueous interface.
A hydrophobic sampling capillary manipulated by an automated robotic platform, aspirates a volume of oil, in the range of 500-2000 nanoliters of silicone oil (Phenylmethylpolysiloxane, PD 5) from the first sampling well, followed by aspirating 100-700 nl of the target volume (aqueous reagents), followed by a similar volume of silicone oil (Phenylmethylpolysiloxane, PD 5) in the range of 500-2000 nanoliters. The sampling capillary then translates through the air, still aspirating, into the next sampling well. The procedure is repeated for the next sampling well, aspirating the covering oil, followed by the aqueous reagents, followed by the covering oil. The hydrophobic sampling capillary tube then translates until a predetermined number of samples have been aspirated. The hydrophobic sampling capillary now has a series of discrete liquids segmented by air, aspirated during translation.
The hydrophobic sampling capillary tube is translated over the processing platform. The direction of flow in the hydrophobic sampling capillary tube is reversed to dispense each fluid sequence as an individual composite liquid cell on to the surface of a carrier oil, a fluorocarbon-based oil (Fluorinert FC-40). The hydrophobic sampling capillary tube is translated between discreet liquid dispensing to a new composite liquid cell initial location. The composite liquid cells are dispensed such that they interface with a hydrophobic spar which secures the composite liquid cells location. The sequence of composite liquid cells combining to give the final DNA synthetic construction is placed on a single hydrophobic spar. The dispensing process generates a series of composite liquid cells separated by a distance in the range of 0.5mm-10mm, positioned on hydrophobic spars.
In the case of single-sample composite liquid cells, a control surface manipulated by an automated robotic platform creates a pairwise combinations of composite liquid cells such that the reagents within composite liquid cells combine and mix via the action of capillary tension with the control surface. Or, if a fluid cell network is being used, then the injection/withdraw immiscible encapsulating buffer fluid controls of the composite fluid network make pairwise combinations of composite liquid cells such that the reagents within composite liquid cells combine and mix.
These reagents contain the neighbouring DNA fragments and other reagents necessary for ligation to occur. The composite liquid cells are controlled at specific temperature conditions for a specific time for ligation to occur. Typical conditions are 16° C. for 1 hour to ensure ligation of cohesive-ended fragments. After this ligation step, further pairwise combinations of neighbouring composite liquid cells are formed and processed at the correct temperature generating longer fragments. This process is repeated until the desired final fragment length is reached. The newly constructed synthetic DNA strand is then aspirated and stored for future use.
The creation of composite liquid cells greatly simplifies the method of DNA ligation. The smaller reaction volume, not normally used in this process ensures higher reaction efficiency and faster reaction times. The combination of target DNA strand fragments for each ensuing pairwise ligation is greatly simplified and the number of overall liquid manipulations is greatly reduced, as the entire sequence of target DNA composite liquid cells are co-located on the hydrophobic spar network. Coalescence by this method is easy to achieve by manipulating the position of the composite liquid cells. This method of ligation is particularly useful where the products of one ligation step are necessary for another step.
The use of composite liquid cells greatly simplifies the collection procedure for these relatively small target volumes. The composite liquid cells following individual processing can be combined selectively, removing any non-reactive sample or inefficient reactions from the ligation process. The composite liquid cell facilitates 100% volume retrieval as the biological sample in processing does not need to touch any solid surface and also has the additional benefit of an anti-wetting characteristic.
More particularly, multi-sample composite liquid cells may be used. The multi-sample composite liquid cells are controlled at specific temperature conditions for a specific time for ligation to occur. Typical conditions are 16° C. for 1 hour to ensure ligation of cohesive-ended fragments. Following ligation nucleic acid amplification is performed to selectively amplify the correct region of interest and next ligation step. After this step, internal samples are combined in a pairwise sequence, additional reagents are added if required and processed at the correct temperature generating longer fragments. This process is repeated until the desired final fragment length is reached. The newly constructed synthetic DNA strand is then aspirated and stored for future use.
The creation of multi-sample composite liquid cells greatly simplifies the method of DNA ligation. The smaller reaction volume, not normally used in this process ensures higher reaction efficiency and faster reaction times. The combination of target DNA strand fragments for each ensuing pairwise ligation is greatly simplified and the number of overall liquid manipulations is greatly reduced, as the entire sequence of target DNA samples are co-located within the one multi-sample composite liquid cell. Internal sample coalescence by this method is easy to achieve by manipulating the outer oil surface positions within the location features of the hydrophobic surface. This method of ligation is particularly useful where the products of one ligation step are necessary for another step.
Genetic Sequencing Bead Coating
Genetic sequencing bead preparation is a process by which small beads are coated in an application-specific chemistry. In one embodiment the coating of beads in advance of genetic screening is achieved by generating composite liquid cells with an aqueous solution of beads as the target volumes. The specific primer chemistry, used to coat the beads, is introduced into the fluid cell via a capillary depositing an aqueous droplet directly into the fluid cell, such that the target volumes combine, resulting in mixing and coalescence of the primer chemistry with the aqueous bead solution.
In another embodiment, there is creation of a composite liquid cell for the primer chemistry and then manipulation to coalesce with the composite liquid cell containing the aqueous bead solution, such that the target volumes combine and mix.
These methods provide for a convenient way of manipulating and combining sub-microliter volumes of fluid that is currently not possible to achieve using conventional techniques, thereby reducing the initial sample volumes and improving the bead coating efficiency by reducing the reaction volume. Further processing using PCR and thermal cycling and genetic sequencing is application-specific.
The use of composite liquid cells greatly simplifies the collection procedure for these relatively small target volumes. The composite liquid cells following individual processing can be combined selectively, removing any non-reactivated beads. The composite liquid cell facilitates 100% volume retrieval as the biological sample in processing does not need to touch any solid surface and also has the additional benefit of an anti-wetting characteristic. These features make automation of the biochemistry process easier to facilitate.
The invention is not limited to the embodiments described but may be varied in construction and detail. For example the encapsulating buffer fluid may be any suitable liquid or gas, most commonly a liquid. The carrier fluid may be any suitable liquid or gas, but most commonly a liquid. The choice of encapsulating and carrier fluid may be chosen such that the functional groups of the fluids result in mutual immiscibility that limits diffusion of carrier fluid molecules into the encapsulating fluid and vice versa. This immiscibility constraint must also apply between the encapsulating fluid and the target sample such that molecular diffusion is limited by the differing functional groups of the constituent fluids. For example the phenylmethyl functional groups present in phenylmethylpolysiloxanes (silicone oils) chosen for encapsulating fluids are immiscible with the perfluoro functional groups present in fluorocarbon based carrier oils that are commonly chosen as carrier fluids. These two oils are furthermore immiscible with aqueous based samples that are common in molecular biochemistry. It is also advantageous to choose fluids of differing densities such that the carrier fluid has the highest density and forms the lowest layer of fluid, the encapsulating fluid has the lowest density and the target sample has an intermediate density between that of the carrier fluid and the encapsulating fluid.
Embodiments
Some embodiments of the invention encompasses a sample handling system comprising a sample-liquid input, an encapsulating-liquid input, a carrier-liquid conduit comprising a stabilisation feature, a liquid-handling system, and a controller operably connected to the liquid-handling system. In some embodiments the controller may be programmed to: (1) draw an encapsulating liquid from the encapsulating-liquid input; (2) discharge the drawn encapsulating liquid (a) onto a free surface of a carrier liquid in the carrier-liquid conduit and (b) proximate to the stabilisation feature, the encapsulating liquid being immiscible with the carrier liquid, so that the discharged encapsulating liquid does not mix with the carrier liquid, floats on top of the carrier liquid, and is immobilised by the stabilisation feature; (3) draw a sample liquid from the sample-liquid input; and (4) discharge the drawn sample liquid, the sample liquid being immiscible with the encapsulating liquid and with the carrier liquid, so that the sample liquid does not mix with the encapsulating liquid or with the carrier liquid. Exemplary flowcharts are shown in
In some embodiments the liquid handling system comprises a control tube and a driver. In some embodiments the controller may be programmed to actuate the driver to cause the control tube to carry out steps (1) and (3) before carrying out steps (2) and (4) (
In some embodiments the controller is further programmed to actuate the driver to cause the control tube, after step (5) and before step (6), to (8) draw a second sample liquid from a second sample-liquid input, the second sample liquid being immiscible with the carrier liquid and the encapsulating liquid, then (9) draw additional encapsulating liquid, then (10) discharge the additional encapsulating liquid of step (9) and the second sample liquid into the unit, so that the composite liquid cell thereby formed comprises a droplet of the sample liquid and a droplet of the second sample liquid (
In some embodiments the liquid-handling system comprises a control tube and a driver, and the controller is programmed to actuate the driver to cause the control tube to carry out steps (1) through (4) in the order recited (
In some embodiments, (a) the carrier-liquid conduit comprises a bath sized to receive a disc rotatable therewithin upon a bath of carrier liquid; (b) the stabilisation feature is formed in the disc; (c) the system further comprises (1) a rotation driver operably coupled to the disc to cause it to rotate in the bath, and (2) a motion system that translates at least a discharging portion of the liquid-handling system vertically relative to the carrier-liquid conduit; and (d) the controller is operably connected to the rotation driver and to the motion system and is programmed to cause the rotation system to rotate the disc and to cause the motion system to translate the discharging portion of the liquid-handling system vertically relative to the disc.
In some embodiments the controller may be programmed to cause the liquid-handling system to discharge sufficient encapsulating liquid between two composite liquid cells, formed on the free surface of the carrier liquid and separated by a gap, liquid to bridge the gap, thereby causing the two composite liquid cells to merge with one another. In some embodiments the controller may be programmed to cause the liquid-handling system to discharge the sample liquid of step (4) proximate to the discharged encapsulating liquid.
In some embodiments the invention encompasses a sample handling method comprising drawing an encapsulating liquid from an encapsulating-liquid input; discharging the drawn encapsulating liquid (a) onto a free surface of a carrier liquid in a carrier-liquid conduit comprising a stabilisation feature and (b) proximate to the stabilisation feature, the encapsulating liquid being immiscible with the carrier liquid, so that the discharged encapsulating liquid does not mix with the carrier liquid, floats on top of the carrier liquid, and is immobilised by the stabilisation feature; drawing a sample liquid from a sample-liquid input; and discharging the drawn sample liquid, the sample liquid being immiscible with the encapsulating liquid and with the carrier liquid, so that the sample liquid does not mix with the encapsulating liquid or with the carrier liquid.
In some embodiments the invention encompasses a method for processing biological samples, the method comprising encapsulating a sample in an immiscible buffer fluid and moving them as a combined unit for sample handling.
In some embodiments, the sample, while encapsulated, is placed on or in a carrier fluid.
In some embodiments, the carrier fluid is a liquid and the sample is placed on the surface of the liquid, the carrier fluid being immiscible with the encapsulating buffer fluid.
In some embodiments, the carrier fluid has a higher density than the encapsulating buffer fluid.
In some embodiments, the encapsulating fluid is non-reactive with the target sample.
In another embodiment, there is a control surface which controls the motion of the encapsulating buffer fluid through electrostatic forces such as for introducing samples into the buffer fluid.
In some embodiments, there is a control surface which controls the motion of the encapsulating buffer fluid through surface tension forces such as for introducing samples into the buffer fluid.
In some embodiments, there are a plurality of controlling surfaces.
In some embodiments, the controlling surfaces include a dynamic surface.
In some embodiments, the controlling surfaces include a static surface.
In some embodiments, the controlling surfaces include a combination of dynamic and static surfaces.
In some embodiments, the controlling surfaces are submerged within the carrier fluid at some times.
In some embodiments, the controlling surfaces are on the carrier fluid interface.
In some embodiments, the controlling surfaces are above the carrier fluid.
In some embodiments, the carrier fluid flows.
In some embodiments, at least one analysis system performs analysis of the biological sample within the encapsulating buffer fluid on the carrier fluid.
In some embodiments, there is a plurality of analysis stages.
In some embodiments, the analysis includes thermal cycling the encapsulating buffer fluid.
In some embodiments, the buffer encapsulating fluid is a silicone-based oil or a fluorocarbon-based oil.
In some embodiments, the carrier fluid is a silicone-based oil or a fluorocarbon-based oil.
In some embodiments, the sample is a biological sample.
In some embodiments, the sample is an aqueous-based biological sample.
In some embodiments, the sample is a solid particle.
In some embodiments, the sample is an aqueous-in-oil emulsion.
In some embodiments, sample amplification is performed, and in some cases quantification of the amplification is performed.
In some embodiments, real time quantification of the amplification is performed.
In some embodiments, the method comprises forming a target sample encapsulated in an immiscible fluid volume and depositing it on a carrier fluid which is immiscible with the encapsulating buffer fluid; and controlling the encapsulated buffer fluid with electrostatic forces.
In some embodiments, the target sample is encapsulated in an immiscible fluid volume dispensed into a flowing carrier fluid.
In some embodiments, the encapsulated sample is dispensed into a static location.
In some embodiments, biological processing of the encapsulated sample is performed, and the encapsulated sample is combined with one or more encapsulated samples.
In some embodiments, genomic amplification is performed.
In some embodiments, the method comprises the step of controlling the encapsulating buffer fluid with surface tension forces.
In some embodiments, nucleic acid ligation is performed.
In another aspect, the invention provides a sample handling system comprising means for performing the steps of any method as defined herein.
In some embodiments, the system comprises: a conduit for continuous flow of the carrier fluid such as oil which carries the encapsulating fluid with the target sample; an analysis stage; and a controller to control the system.
In some embodiments, the system comprises a thermal cycling stage.
In some embodiments, the system is adapted to deposit the encapsulated into or onto a static position on a carrier fluid.
In some embodiments, herein there are a plurality of positions.
In some embodiments, there are a plurality of conduits.
In some embodiments, the system further comprises means for controlling movement of an encapsulated sample by electrostatic forces.
In some embodiments, the system is adapted to move an encapsulated sample onto or on a static carrier fluid.
In some embodiments, the sample is moved to any of a plurality of locations and there may be a plurality of samples on the static carrier fluid.
In some embodiments, a conduit is closed.
In some embodiments, the invention encompasses a method for processing samples, in some cases biological samples, the method comprising encapsulating two or more samples in an buffer fluid immiscibly with the samples and moving them as a combined unit.
In some embodiments the buffer fluid may be a liquid.
In some embodiments, two or more samples, while encapsulated, are placed on or in a carrier fluid.
In some embodiments, the sample is a multiplex reaction.
In some embodiments, two or more samples are encapsulated within the one encapsulant fluid surface.
In some embodiments, the carrier fluid is a liquid and the sample or samples, while encapsulated are placed on the surface of the liquid, the carrier fluid being immiscible with the encapsulating buffer fluid.
In some embodiments, the sample, while encapsulated, is combined with another sample, while encapsulated, resulting in two discrete samples, while encapsulated within one encapsulating surface.
In some embodiments, the sample, while encapsulated, will be processed for one or more targets.
In some embodiments, at least one analysis system performs analysis of one or more biological samples within the encapsulating buffer fluid, in some cases on the carrier fluid.
In some embodiments, the buffer encapsulating fluid has a additive added for sample stability.
In some embodiments, the buffer encapsulating fluid is a silicone-based oil with a polysorbate additive.
In some embodiments, the polysorbate additive is added in the range of 0.001% to 10%.
In some embodiments the buffer fluid includes an additive including a surfactant.
In some embodiments, the total hydrophilic-lipophilic balance number of the added surfactants are in a range of 2 to 8.
In some embodiments, the method comprises forming two or more target samples encapsulated in an immiscible fluid volume and depositing it on a carrier fluid which is immiscible with the encapsulating buffer fluid; and controlling the encapsulated buffer fluid with electrostatic forces.
In some embodiments, two or more target samples are encapsulated in an immiscible fluid volume dispensed into a flowing carrier fluid.
In some embodiments, at least one encapsulated sample is dispensed into a static location.
In some embodiments, biological processing of at least one encapsulated sample is performed, and at least encapsulated sample is combined with one or more other encapsulated samples.
In some embodiments a further sample may be added to the cell thereby arraying samples.
In some embodiments the samples are arrayed for optical detection.
In some embodiments the cell is transported by impingement of a gas from a direction al outlet such as a tube.
In some embodiments, the invention provides a sample handling system comprising means for performing the steps of any method as defined above.
In some embodiments, the system comprises: a conduit for continuous flow of the carrier fluid such as oil which carries the encapsulating fluid with two or more target samples; an analysis stage; and a controller to control the system.
In some embodiments the system comprises: a conduit for flow of a buffer fluid such as oil with two or more target samples which is interfaced with a carrier fluid; an analysis stage; and a controller to control the system.
In some embodiments the system comprises: a moving hydrophobic spar on which a carrier fluid such as oil carries buffer fluid with two or more target samples; an analysis stage; and a controller to control the system.
In some embodiments, the carrier oil has a surfactant additive.
In some embodiments the invention is used for processing a sample, the sample being encapsulated in an immiscible buffer fluid and positioned at a hydrophobic control surface for sample handling.
In some embodiments, the hydrophobic control surface is stationary.
In some embodiments, the hydrophobic control surface is dynamic.
In some embodiments, the hydrophobic control surface is a fluoropolymer.
In some embodiments, there are a plurality of hydrophobic controlling surfaces.
In some embodiments, the controlling surface is electrostatically energised.
In some embodiments, the hydrophobic controlling surfaces include a combination of dynamic and static surfaces.
In some embodiments, the composite liquid cell is controlled by one or more hydrophobic controlling surfaces.
In some embodiments, the hydrophobic control surface is temperature controlled.
In some embodiments, the hydrophobic control surface is part of an optical detection system.
In some embodiments, the hydrophobic control surface has a marker for optical detection.
In some embodiments, the hydrophobic control surface has a radio frequency identification circuit.
In some embodiments, the hydrophobic control surface controls a plurality of composite liquid cells.
In some embodiments, the hydrophobic control surface has stabilisation features.
In some embodiments, there are a plurality of stabilisation features.
In some embodiments, the stabilisation features are pockets into the hydrophobic control surface.
In some embodiments, the stabilisation features are v shaped.
In some embodiments, the stabilisation features are circular shaped.
In some embodiments, the stabilisation features are tapered.
In some embodiments, the stabilisation features are used to locate the sample encapsulated in an immiscible buffer fluid on a mutually immiscible carrier fluid.
In some embodiments, the stabilisation features are arrayed to form a network.
In some embodiments, the network is used for mixing composite liquid cells.
In some embodiments, the network is used for transporting a composite liquid cell.
In some embodiments, the network comprises a static hydrophobic control surface.
In some embodiments, the network comprises a dynamic hydrophobic control surface.
In some embodiments, the network comprises a combination of static and dynamic control surfaces.
In some embodiments, real time quantification of proteins is performed.
In some embodiments, the encapsulated sample is dispensed, for example, into a static location.
In some embodiments, biological processing of the encapsulated sample is performed, and/or the encapsulated sample is combined with one or more encapsulated samples.
In some embodiments, the system comprises: a conduit for deposition of encapsulating fluid adjacent to a hydrophobic control surface with periodic target sample depositions; such that the hydrophobic control surface carries the encapsulating fluid with the target sample; an analysis stage; and a controller to control the system. The deposition may be continuous.
In some embodiments the invention provides methods and systems for generating, and/or transporting, and/or mixing, and/or processing biological samples. It achieves this by the formation of an immiscible fluid cell within which the biological sample (solid, liquid, emulsion of aqueous-in-oil or suspension of solid in immiscible liquid) may be manipulated. The method and system can generate, and/or transport, and/or mix, and/or process a range of volumes from micro-liter to sub-nanoliter volumes.
In some embodiments, the invention provides a method and/or a system for processing biological samples, comprising encapsulating two or more samples in a buffer fluid which is immiscible with the samples, to provide a multi-sample cell, and moving the cell as a combined unit for sample handling.
In some embodiments the method and system may generate non-contaminating microliter or nanoliter or sub-nanoliter volumes which can be controlled by a number of methods.
In some embodiments it generates one or more biological samples within an immiscible fluid cell and this composite liquid cell is then placed on a free surface of a mutually immiscible fluid, referred to as a carrier fluid.
The carrier fluid may provide a manipulation platform for the composite liquid cell. The composite liquid cell may be generated by collecting within a tube the composite components in the following sequence: immiscible fluid, biological sample (fluid, emulsion, solid or suspended particles), immiscible fluid, and in some cases air. This can be repeated for multiple composite liquid cells with the tube, or in some cases for one or more multi-sample composite liquid cells.
The contents of the tube may then be dispensed on the carrier fluid generating the composite liquid cells.
The method and system may generate non-contaminating nanoliter or sub-nanoliter volumes which can be controlled by a number of methods. The invention method provides for the composite liquid cell to be controlled by electrostatic forces.
In some embodiments the invention may have at least one electrically charged control surface which can control the composite liquid cell. The invention may provide an independent method of control through use of the hydrophobic effect.
In some embodiments the invention may have at least one control surface which has a hydrophobicity property which allows adhesion between it and the outer fluid of an immiscible fluid cell while repelling the internal fluid volume, preventing contamination. Using solid structures embedded or partly embedded in the carrier oil, the composite liquid cell can be guided in a controlled manner or anchored, increasing the dynamic control of the composite liquid cell.
In some embodiments the invention may provide transport of composite liquid cells in any of the methods outlined above. Mixing of the composite liquid cells in some embodiments involves transporting the composite liquid cells to contact, promoting fluid coalescence of the encapsulating oil and biological samples. This mixing process facilitates the combination of sub-microliter target volumes with great efficiency, prevents contamination from other sources and ensures no dead volume per chemistry manipulation. In some embodiments, the samples are not mixed, resulting in a multi-sample composite liquid cells.
In some embodiments the transport of composite liquid cells through a biological process is not susceptible to air, which leads to the evaporation of target volumes at elevated temperatures. The independent transport of each composite liquid cell within the system through the carrier oil reduces power consumption of the overall system that would otherwise be required for heating, cooling, or pumping of the carrier fluid, and instead the thermal protocol can be targeted at the composite liquid cell.
In some embodiments the invention allows for easy automation of the biochemistry processes. It allows for the dynamic control of individual samples, thereby allowing for full volume retrieval of samples. It allows for use in both an open or closed architecture manipulation platform. It allows for the analysis and manipulation of biological samples. The samples can be analysed easily by optical, acoustic, or electromagnetic methods.
Individual features of various embodiments disclosed herein may be combined as desired mutatis mutandis, to the extent they are not mutually exclusive to one another.
This application is a continuation application of U.S. application Ser. No. 14/685,230 filed Apr. 13, 2015, which is a continuation application of U.S. application Ser. No. 13/895,930 filed on May 16, 2013, now U.S. Pat. No. 9,080,208, which is a continuation application of U.S. application Ser. No. 13/147,679 filed on Aug. 3, 2011, now U.S. Pat. No. 8,465,707, which claims the benefit of the national stage of International application Ser. No. PCT/IE2011/000040, filed Jul. 22, 2011, which claims the benefit of U.S. provisional application Ser. Nos. 61/344,434, filed Jul. 22, 2010, 61/470,515, filed Apr. 1, 2011, and 61/470,520, filed Apr. 1, 2011, each of which is hereby incorporated herein by reference.
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