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Definitions

• Biological systems are incredibly complex, and are governed largely by fluctuations in the expression levels of a multitude of genes. Such differential expression reflects the way those cells interact with others and react to our world.
• the expression levels of all genes at a particular time point, or in a particular environmental situation can represent one particular "state”. Gene expression levels can change very rapidly, and so therefore can the "state" of a particular biological system, for example a cell or tissue or organ. Determining the "state”, i.e. the relative expression of a number of genes at a particular point has clear utility in diagnostics, prognostics and in for example industrial biotechnology, since it is important to know whether a particular biological system is behaving as expected/desired.
• Genes do not act in isolation, but as part of complex networks. Because there are so many interacting genes and separate gene networks, fully determining the state of a biological system, such as a cell, is itself highly complex. Although it is now possible to relatively routinely analyse the expression level of all genes within a biological system, for example via RNA-seq, this is not cost nor time effective, both in terms of the sequencing and the subsequent bioinformatics, particularly since only a subset of genes are likely relevant to predict or classify whether a biological system is in a particular state or is in a different particular state, or is exhibiting a particular activity, for example a high protein production state. Determining such complex relationships require pattern recognition, rather than simple algebraic thresholds.
• transcriptome data has been obtained from two or more different types of sample and has been analysed, using bioinformatics including machine learning, to identify particular subsets of genes/mRNAs that are under or overexpressed, and to different levels, between the two sample types.
• diagnostic or predictive expression patterns has been used in for example cancer diagnostics, cancer prognostics, diagnosis of tuberculosis and sepsis, as well as veterinary uses such as diagnosing bovine tuberculosis and mastitis, and prediction of response to therapy.
• the same types of diagnostic and predictive relationships, decision surface or differential gene regulation signatures based on the relative gene expression of a given set of genes can be used in cell and tissue engineering.
• the goal of "regenerative medicine” is to guide stem cells to differentiate into a specific terminal cell type, or to shift the activity of differentiated cells towards one task or another.
• gene expression profiling and specifically the idea of "molecular time”, it is possible to determine "How differentiated are the cells? How polarized are the cells?".
• the field of synthetic biology presents a unique challenge. In a population of cells with highly engineered gene pathways, or several such populations cooperating towards a given task, the bioprocess engineer requires a means of determining whether the system is behaving the way it was designed to.
• such a predictive relationship, decision surface or differential gene regulation signature can involve the assessment of the presence or absence of expression from a single gene. For example, the presence of mRNA from gene A in a sample predicts that the sample is in a state A (for example "has disease A") and the absence of mRNA from gene A predicts that the sample is in a state B (for example "does not have disease A" i.e. has a different disease or has no disease).
• the present invention solves at least the above-mentioned problems with the prior art methods of using predictive relationships or differential gene regulation signatures generated from biological data.
• the inventors of the present invention have developed methods and components that can be used to significantly reduce the complexity of converting the pre-determined predictive relationship, decision surface or differential target oligonucleotide pattern (such as a gene regulation signature between gene expression pattern and a particular state) into a useful diagnostic or predictive result.
• the methods described herein use the molecules of the assay themselves to reflect the complex math and artificial intelligence currently used to analyse the standard target oligonucleotide pattern (for example expression data) that is routinely obtained in, for example, medical diagnostics.
• the methods disclosed are easy to use, with no requirement for particularly specialist instrumentation, and sample preparation is standard. Once the necessary components have been optimised through routine procedures, actually putting the methods into practice for example in diagnostics/prognostics is very simple and requires in some embodiments a simple multiplex PCR amplification reaction and the reading of two fluorophores. This is in contrast to the present methods that require for example amplification of a number of RNA species using multiple fluorophores, determining the amount of each fluorophore, and subsequently feeding those data into a complicated bioinformatics system that compares the relative levels of each RNA species to determine the "state".
• a key advantage of the present invention is that it reduces the number of readings down, in some cases to a single reading of two different fluorophores (or of all fluorophores used), in a single tube.
• results produced by the methods of the invention are easy to obtain, are clear and can be interpreted by the laboratory researcher, the fermentation specialist and the bedside clinician.
• the methods are typically centred around nucleic acid amplification, which the skilled person will understand is highly routine and can be performed with minimal equipment.
• an Al system may determine that if the expression of gene A is above an arbitrary expression threshold of 10 and the expression of gene B is below a threshold of 5, and the expression of gene C is above a threshold of 7, then the sample is in a particular state, e.g. State A; whereas if the expression of gene A is above a threshold of 10 and the expression of gene B is above a threshold of 10 and the expression of C is below a threshold of 7 then the sample is in a different particular state, State B.
• the methods of the present invention are able to capture this complex interdependent relationship and condense it down to a single output which tells the user whether the sample is in, or is likely to be, State A or State B; or is in State A and not in State B or State C, for example.
• the methods of the present invention can be termed Competitive Amplification Networks (CANs).
• CANs Competitive Amplification Networks
• the methods adapt RNA/DNA amplification technologies such as PCR to the recognition of complex gene expression patterns.
• the reaction is engineered with competitive interactions that translate the information provided by a given gene transcript or a set of transcripts into the relative probability of state A versus state B.
• these probabilities combine to provide an overall diagnosis represented by two colours: interpretation is as simple as checking which colour is brighter.
• the networks are scalable to encompass a large number of genes without a significant increase in cost or operational complexity.
• these networks can be engineered to perform complex, nonlinear operations on multiple targets simultaneously. This technology provides a platform for engineering application-specific kits for disease diagnosis, therapeutics monitoring, regenerative medicine research, and quality control of bioprocess manufacturing.
• the invention provides a method of translating the relative abundance of (or presence or absence of) at least two oligonucleotides, for example the relative expression of at least two genes, or presence or absence of at least two mutations, into the relative probability of a particular state, for example the relative probability of State A versus State B.
• the invention also provides a method of combining the relative abundance of at least two oligonucleotides, for example the relative expression of at least two genes, or presence or absence of at least two mutations, into a single value.
• the invention also provides: a method of translating the relative abundance of at least two oligonucleotides, for example the relative expression of at least two genes, or presence or absence of at least two mutations, in a sample into the relative probability of a particular state. a method of detecting the relative abundance of at least three oligonucleotides, for example the relative expression of at least three genes, or presence or absence of at least three mutations, in a sample using only two fluorophore labelled probes. a method of combining the relative abundance of at least two oligonucleotides, for example the relative expression of at least two genes, or presence or absence of at least two mutations, in a sample into a single value.
• each input dimension represents the concentration of a particular target sequence and each output dimension represents a different class.
• the input domain could consist of two genes and the output domain two classes, healthy and sick.
• the "decision surface” is then a two-dimensional surface where a given point represents the concentration of the two gene transcripts and the height of the surface at that point corresponds to the probability of being sick if a patient's two genes are expressed at those respective levels.
• the input domain could consist of 10 distinct mutations observed in circulating tumour DNA (ctDNA) of a post-surgical prostate cancer patient and the output domain could consist of three categories: no recurrence, mild recurrence, and aggressive recurrence, each of which recommends to the physician a different course of action.
• the decision surface in this case is (more or less) a 10-dimensional cube, where each point translates a particular combination of mutation concentrations to a relative probability of the three categories, perhaps visualized with color as the relative intensities of the red, green, and blue components of an image.
• the expert would begin with a dataset containing the measured concentrations of many potential targets, such as expression of various genes or mutational profile of post-surgical ctDNA, from many individuals, where each individual is known to belong to a different category (e.g., healthy/sick or no/mild/aggressive recurrence).
• the expert would then apply any of several classification algorithms to arrive at the decision surface, including but not limited to logistic regression, Gaussian process classification, artificial neural network classification, decision trees, random forests, naive bayes, support vector machines, or nearest neighbours.
• the decision surface may be constructed in a more manual, principled manner.
• the bioproduction engineer may know the optimal expression level and respective tolerance for each of several genes expressed by their engineered organism or population of organisms.
• the engineer may wish to know if any of those genes is outside that tolerance window.
• the decision surface could be represented as a multidimensional Gaussian distribution that extends from -1 to +1 in the output domain.
• Each dimension, as specified above, would represent the concentration of the particular gene transcript, and the marginal Gaussian distribution along that dimension would have its mean (peak) at that gene's ideal concentration and its standard deviation (width) correspond to the respective tolerance window.
• the competitive amplification network implementation of such a decision surface would exhibit one fluorescent color if all transcripts are at or near their ideal, and another if any transcript is too far beyond its tolerance window.
• Another such principled decision surface could arise from personalized surveillance of circulating tumour DNA for the purposes of monitoring a post-surgical prostate cancer patient for early signs of relapse (Coombes et al Clinical Cancer Research 2019 25: DOI: 10.1158/1078-0432.CCR-18-3663).
• the target mutations of interest would be identified at the time of surgery by comparing the genome of the tumour to that of the patient's healthy tissue.
• the expert would then select a threshold concentration so that if any of the mutations are observed in the ctDNA above this threshold, the expert would conclude that the cancer has relapsed.
• the marginal decision surface for a given mutation in this case would consist of a transition from 0 in the absence of the mutation to +1 at that threshold concentration.
• a given signal fluorophore color, such as FAM, or band intensity on a lateral flow strip
• FAM fluorophore color
• HEX band intensity on a lateral flow strip
• the difference between the intensities of these two colors thus corresponds to the "height" of the decision surface.
• an appropriate number of signals can be chosen so that certain pairwise differences between them correspond to the probability of different output categories.
• the expert would choose the architecture of the network.
• This architecture consists of determining how many synthetic competitors to include, how many primers to include, which oligonucleotide strands share which primers, and which strands are targeted by which probes. For each architecture, then, there are numerous combinations of amplification parameters for each oligo in the system. Choosing among architectures and parameter values would be done by simulating the surface produced by a numerous different architectures each at numerous different parameter values (see section "Simulating competitive amplification") to identify the architecture and combination of parameter values that resemble the pre-determined decision surface.
• Each of these methods involves the amplification of one or more target polynucleotides in such a way so that the amount of each product that indicates a first state can be cumulatively quantified, and each product that indicates a second state can be cumulatively quantified. Combining these two readings produces a single overall reading that indicates whether the sample is more likely to be in a first state or a second state, i.e. regardless of the number of genes under investigation, the difference between the total green intensity and the total orange intensity (for example), integrates the information from the whole system. For example, in one embodiment all products that are associated with a first state are labelled with a first fluorophore and all products that are labelled with a second state are labelled with a second fluorophore.
• the competitive polynucleotides of the invention and that are used in the methods described herein are engineered, designed or tuned to reflect this predictive relationship or differential gene regulation signature.
• the invention provides: a method of translating the relative abundance of at least two oligonucleotides, for example the relative expression of at least two genes, or presence or absence of at least two mutations, in a sample into the relative probability of a particular state; a method of detecting the relative abundance of at least three oligonucleotides, for example the relative expression of at least three genes, or presence or absence of at least three mutations, in a sample using only two fluorophore labelled probes; a method of combining the relative abundance of at least two oligonucleotides, for example the relative expression of at least two genes, or presence or absence of at least two mutations, in a sample into a single value; a method of converting the predictive relationship, decision surface or differential target oligonucleotide pattern such as a differential gene regulation signature provided by the relative abundance of at least two oligonucleotides or the presence or absence of at least two mutations, in a sample into a single value; a method of mimic
• the method of amplifying one or more target polynucleotides in a sample as described herein is itself provided by the invention.
• every target molecule in solution should be replicated every cycle until these primers are used up, but, crucially to CAN design principles, i.e. the methods disclosed herein, perfect doubling is actually difficult to achieve. It is the tuned competitor polynucleotides that comprise the appropriate features that allows a single output to reflect a complex network of expression levels.
• Target sequence characteristics such as GC content influence the proportion of molecules that are replicated each cycle and these features are deliberately built into the competitor polynucleotides used herein so that the target polynucleotide(s) is amplified with the appropriate efficiency where the efficiency is tailored to mimic the contribution of that particular target in the overall predictive relationship or differential gene regulation signature.
• a particular gene ( G1) is associated with "disease” if expressed at an arbitrary level of greater than 12, and is associated with "non-disease” at an expression level of less than 12, and G1 is weakly predictive; and a second gene (G2) is associated with disease if the expression level is greater than 6, and is associated with non-disease when the expression level is less than 6, and G2 is strongly predictive.
• G1 is amplified along with a corresponding competitor polynucleotide that strongly competes with the natural G1 target i.e. the competitor has a higher amplification efficiency that the natural target G1.
• the high expression of G1 in the first sample (which has an equivalent of 10 target molecules) is converted into a lower actual G1 target product (e.g. 3), which reflects the lower predictive power of G1.
• the G1 target product may then be probed with a green labelled probe, and the G1 competitor product may be probed with an orange labelled probe.
• the amount of green label may be less than the orange label (for example green reading of 3 and an orange reading of 7).
• G2 on the other hand, due to the high predictive power, may be amplified in the presence of a corresponding competitor polynucleotide that is very difficult to amplify, so that more of the G2 natural target is amplified than the G2 competitor polynucleotide.
• the amount of G2 target produced may be 6 and the amount of G2 competitor produced may be 1.
• the G2 target may be probed with a green labelled probe (i.e. 6 green) and the G2 competitor may be probed with an orange labelled probe (i.e. 1 orange). Adding the results from G1 and G2 together this example would provide a green reading (i.e. disease) of 9 and an orange reading of 8.
• G1 may produce a green reading of 0.5 and an orange reading of 1; and G2 may produce a green reading of 9 and an orange reading of 2, with a cumulative reading of 9.5 green versus 3 orange.
• an increased expression of one gene and a repressed expression of a different gene may be indicative of a particular state, for example a diseased state.
• the predictive relationship or differential gene regulation signature derived from the original data set(s) (e.g. microarray data, RNAseq data) will provide a threshold of how "green” the overall cumulative fluorescence needs to be to result in a diagnosis of "state A” (i.e. "disease”).
• sample 1 would have an overall green reading of 17 and sample 2 would have a reading of 11 which does not accurately reflect how likely the samples are to be in that particular state, e.g. a diseased state.
• Amplification progression can be monitored in real-time by inclusion of a fluorescently labelled probe oligonucleotide specific to a region of the target product or competitor product between the primer-binding sites (see Figure IB for an example).
• probe oligonucleotide specific to a region of the target product or competitor product between the primer-binding sites
• Figure IB for an example.
• the polymerase degrades the probe into (more or less) individual nucleotides, liberating the fluorophore from the quencher and producing a fluorescent signal.
• the resulting curve can be modelled as a densitylimited exponential growth process:
• Equation (1) where F is the fluorescence intensity, r is the exponential growth rate (base e), K is the signal plateau, and m is the drift of this plateau.
• the key component here is the r, which, when expressed in base 2, represents the fraction of (probe-bound) target strands which replicate each cycle. The r can be changed by altering the sequence of the target between the primer regions, as demonstrated in Figure 2.
• the amplification is a "competitive" amplification that involves the use of a competitor polynucleotide that has been "tuned” to have particular features that are described herein.
• the skilled person will appreciate that prior art methods of competitive PCR are typically used for target nucleic acid quantification and the competitive polynucleotide used is designed to be as close in sequence to the target as possible, to avoid any discrepancies in amplification efficiency.
• the amount of target product is compared to the amount of competitor product, typically using gel electrophoresis, and from this the amount of starting target material can be quantified.
• the present invention specifically requires that the competitor polynucleotide be designed to have a sequence that intentionally results in a particular difference in amplification efficiency between amplification of the target and amplification of the competitor.
• the invention provides a method of amplifying one or more target polynucleotides in a sample, wherein the method comprises: providing: a) a sample comprising polynucleotides b) a first tuned competitor polynucleotide c) at least a first primer wherein at least the first primer is capable of hybridising to: a first target polynucleotide; and the first tuned competitor polynucleotide; and initiating a primer extension reaction such that the target polynucleotide (if present in the sample) and the first tuned competitor polynucleotide are amplified, wherein amplification results in a first target product and a first tuned competitor product.
• the methods of the present invention are different to “toehold” methods in which a "toe hold” primer is initially bound to a shorter “protector” strand, so this protector and the target compete for binding to the target.
• the "protector” isn't amplified (it's shorter than the primer.
• the first tuned competitor polynucleotide is a polynucleotide that has been specifically designed, or "tuned” to have particular properties and has been intentionally introduced into the amplification reaction.
• a competitor polynucleotide as described herein is considered to be distinct from, for example, other polynucleotides that just happen to also be present in the sample.
• a competitor polynucleotide according to the invention is not simply another piece of genomic DNA that may compete for hybridisation to the primers, resulting in unwanted background amplification.
• the competitor polynucleotides described herein at intentionally amplified.
• the competitor polynucleotides described herein are not naturally present in the sample.
• the present method is distinct from prior art methods of competitive amplification whereby the competitor oligonucleotide is designed to intentionally have similar amplification kinetic properties to the target polynucleotide.
• Such methods are using the art to estimate the concentration of the target polynucleotide, for example where a known amount of competitor polynucleotide is included in the amplification reaction. It is imperative in such methods that the rate of amplification of the competitor mirrors that of the target. It will be clear to the skilled person that this is not the case for the present invention.
• the present invention requires the tuned competitor oligonucleotide to have different amplification kinetics to the respective target polynucleotide so that the rate of relative amplification of the target and competitor result in products that match the predictive relationship, decision surface or differential target oligonucleotide pattern such as a differential gene regulation signature that is indicative of one of at least two states.
• the competitor polynucleotide does not have the same or does not have substantially similar amplification kinetics to the respective target polynucleotide.
• the present methods are also distinct to methods such as 16s nested PCR which first amplifies a genetic sequence common to most bacteria (a ribosomal subunit) before amplifying or sequencing species-specific sub-regions (Yu et al PLoS One 2015 10: 60132253).
• a similar approach is used to probe VDJ recombination in human B cells (Koning et al British Journal of Haematology 2016 178: 983-968. In both cases competition occurs, though only among natural sequences.
• the method is not a 16s nested PCR method, and/or is not a method used to probe VDJ recombination in human B cells.
• Two primers may be used to amplify the target sequence, and/or may be used to amplify a portion of or all of the tuned competitor polynucleotide.
• the skilled person will understand what is required for an appropriate primer, for example length, sequence identify to a portion of the target/competitor sequence. Accordingly, in some embodiments the method comprises providing a second primer.
• the second primer is capable of hybridising to the first target polynucleotide, wherein the first and second primer hybridise on opposite strands of the target so as to result in the production of the first target product, optionally a first target polymerase chain reaction (PCR) product.
• PCR polymerase chain reaction
• first primer to be capable of hybridising to a first target polynucleotide and to a first tuned competitor polynucleotide
• a portion of the first target polynucleotide and a portion of the first tuned competitor will have the same, or substantially the same sequence, so as to allow a single primer to hybridise to the two different polynucleotides.
• the remaining sequence of the target and competitor can be entirely different.
• the method comprises the use of a second primer that is capable of hybridising to the first target polynucleotide
• the same second primer is also capable of hybridising to the first tuned competitor polynucleotide, wherein the first and second primer hybridise on opposite strands of the first tuned competitor polynucleotide so as to result in the production of the first tuned competitor product, optionally first tuned competitor PCR product.
• the first target polynucleotide and the first tuned competitor polynucleotide will share two regions that are identical, or that are substantially identical, so as to allow the hybridisation of the first and second primer to each polynucleotide. The skilled person will understand how similar two sequences need to be so as to allow hybridisation of the same primer.
• FIG. 3 This arrangement, whereby the first target and the first competitor polynucleotides are amplified using the same first and second primers is depicted in Figure 3, and can be termed a "direct" method, or a direct CAN.
• the first also shows one particular embodiment which uses two labelled probes. However, as described herein, different probe systems, and different detection methods can be used. Typically, the method will require a labelled probe that can hybridise to the target polynucleotide product, and a probe labelled with a different label that can bind to the first competitor polynucleotide product.
• the target and the competitor are amplified in the same amplification reaction, they compete for the primers. Since primers are consumed by each replication of a target strand, the amplification of both sequences stops as soon as the primer pool is exhausted.
• the quantity of each amplification product at the end of the reaction depends on the relative starting quantity of the two targets. This is reflected in the resulting fluorescent signal (see for example Figure 4).
• the fluorescent signal derived from each will be the same at the end of the reaction. If there is more "target" than competitor at the start of the reaction, the fluorescence associated with the target product will be more intense at the end, and vice versa.
• the sharpness or gradient of the transition from pure target signal to pure competitor signal can be tuned by adjusting the amplification rate of the competitor.
• each competitor can be amplified in a reaction containing the appropriate primers, the relevant fluorophore- la belled probe, and standard qPCR master mix (TaqMan Fast Advanced Master Mix from ThermoFisher Scientific).
• the resulting fluorescent data should be fitted with one of a number of algorithms which the skilled person will able to select, for example (herein referred to as the mechanistic model as used in the Examples) using standard non-linear least squares estimation, where / is defined as where r is the amplification rate, F o is the initial fluorescence at the beginning of the reaction, m indicates the degree of drift of the steady-state fluorescence, and K gives the steady-state fluorescence in the absence of drift.
• the input parameters to the model are the length of region of the sequence between the primers, in base pairs (BP), the GC content of that region in percent (GC), and the concentration of the sequence in copies (Q).
• the input and output (p, K, and m) parameters are first put into "standardized" form (indicated by a ⁇ ) as follows:
• the regression model is then given by: where a denotes the "typical" value of the given parameter across all sequences and concentrations, ⁇ indicates the dependence on the length or GC content of a given sequence, respectively, ⁇ represents the "typical” dependence on concentration across all sequences, and ⁇ defines how the dependence on concentration varies with length and GC content.
• ⁇ represents the deviation of a given sequence's behavior from the global trend indicated by the remaining parameters; the prediction model, which supplies parameter values for new, untested sequences, is the same as the regression model but without the e components.
• 16 different competitors ranging in length from 30 to 240 base pairs and GC content from 15% to 85% are amplified.
• Each competitor at seven different concentrations (i.e., the reaction contained 10 2 , 10 3 , 10 4 , 10 s , 10 6 , 10 7 , or 10 8 copies of the competitor) in duplicate.
• the skilled person will be able to select an appropriate number of competitors, appropriate length, appropriate GC content and concentration, depending on the particular circumstances.
• the parameter values for the model above can be estimated using a Bayesian approach; however, other linear regression techniques could be used, including but not limited to maximum-likelihood estimation, least-squares estimation, ridge regression, and lasso regression.
• regression techniques could be used, including but not limited to non-linear regression and non-parametric regression such as polynomial regression, Gaussian Processes, Artificial Neural Networks, Support Vector Machines, Nearest Neighbours, Decision Trees, Random Forests, and Naive Bayes.
• non-linear regression and non-parametric regression such as polynomial regression, Gaussian Processes, Artificial Neural Networks, Support Vector Machines, Nearest Neighbours, Decision Trees, Random Forests, and Naive Bayes.
• the model consists of the following system of ordinary differential equations: where A+ and A- are the concentrations of the positive and negative strands of a sequence A, p1 and p2 are the concentration of two primers, and r is the amplification rate for the sequence (note that the ⁇ here is unrelated to the ⁇ in the previous equations.
• the model for direct competitive PCR (two targets WT and REF, two primers) is as follows:
• the FAM signal is thus given by the concentration of the WT+ strand, and the HEX signal is given by the concentration of the REF+ strand. If an additional FAM-labeled probe was designed to bind to the REF+ strand, the FAM signal would be given by the sum of the WT+ and REF- strand concentrations.
• one target polynucleotide and one corresponding competitor polynucleotide represents one of the simplest applications of the invention.
• assessing the expression level of one gene does not really represent a gene network.
• the expression level of multiple genes in a gene network can be assessed using a combination of amplifying more than one target polynucleotide and/or providing more than one competitor polynucleotide.
• the invention provides different combinations, some of which will be described in more detail, but the skilled person will understand that a large number of combinations of different target polypeptides, different competitors and different arrangements of primers, e.g. primers shared between target and competitor, shared between competitor and competitor, and/or shared between target and target.
• indirect CAN methods described herein are considered to be less expensive when larger gene signatures are to be analysed, since in the "direct” methods at least one if not two probes need to be designed for each transcript targeted.
• gene signatures e.g. gene expression levels, presence or absence of particular mutations, abundance of non-coding RNA
• indirect CANs provide similar functionality at a more or less fixed cost regardless of the number of genes under investigation. Indirect competition also opens the possibility of higher-order networks capable of complex, non-linear analysis of multiple targets simultaneously. Finally, redundant targeting allows additional flexibility for all CAN architectures.
• the direct competition methods described herein use competition between a probed target polynucleotide product and a probed competitor polynucleotide product.
• the indirect method uses an un-probed target polynucleotide to simply mediate the competition between competitor polynucleotide. Because both primers are necessary for exponential amplification of a given target, replication can be arrested by depletion of only one primer.
• a competitor polynucleotide shown as REFH in Figure 5 is designed that shares one primer with a target polynucleotide, WT, and its second primer with a second competitor polynucleotide, REFF ( Figure 5).
• This response curve can be tuned by adjusting the amplification rate of any of the targets, the starting concentration of the competitor polynucleotides, the concentration of any of the primers, or the topology of the network itself (Figure 5B,C).
• the key advantage of this system is that, because the sequence of the competitor polynucleotide is not restricted (only the regions that hybridise to the primers have any sequence constraints), the same two probe sequences can be reused to probe multiple competitor polynucleotide products, minimizing development costs regardless of how many natural targets are utilized or how complex the network is.
• the method comprises providing a second tuned competitor polynucleotide.
• the second primer is: a) capable of hybridising to the first tuned competitor polynucleotide, wherein the first and second primer hybridise on opposite strands of the first tuned competitor polynucleotide so as to result in the production of the first tuned competitor product, optionally first tuned competitor PCR product; and b) is capable of hybridising to the second tuned competitor polynucleotide and initiating a primer extension reaction such that the second tuned competitor polynucleotide is amplified so as to result in the production of the second tuned competitor product, optionally in combination with a further primer wherein the second and further primer hybridise on opposite strands of the second tuned competitor polynucleotide so as to result in the production of the second tuned competitor product, optionally a first target polymerase chain reaction (PCR) product, optionally wherein the second primer is not capable of hybridising to the first target polynucleotide.
• PCR target polymerase chain reaction
• the second primer is: a) capable of hybridising to the first target polynucleotide, wherein the first and second primer hybridise on opposite strands of the target so as to result in the production of the first target product, optionally a first target polymerase chain reaction (PCR) product; and b) capable of hybridising to the second tuned competitor polynucleotide, and is optionally not capable of hybridising to the first competitor polynucleotide.
• PCR polymerase chain reaction
• the second primer is capable of hybridising to a second target polynucleotide, and is optionally not capable of hybridising to the first target polynucleotide.
• the method can be used in the context of more than one target polynucleotide.
• the method is used to determine the expression of more than one gene, the presence or absence of more than one particular mutation, and/or the abundance of more than one non-coding RNA.
• the relevant primers may be designed so that the more than one target polynucleotide are part of the same actual RNA molecule. For example several primer pairs can be designed to amplify several different regions from a single mRNA. In conjunction with the appropriate competitor polynucleotides this embodiment of the methods of the invention is termed a "redundant" method.
• the second target polynucleotide is part of the same polynucleotide molecule as the first target polynucleotide.
• the second target polynucleotide is on a different polynucleotide molecule to the first target polynucleotide.
• the methods of the invention may comprise more than two primers, for example at least 3, 4, 5, 6 or more primers.
• the second primer is: a) capable of hybridising to the first target polynucleotide, wherein the first and second primer hybridise on opposite strands of the target so as to result in the production of the first target product, optionally a first target polymerase chain reaction (PCR) product; and b) is not capable of hybridising to the first or second tuned competitor polynucleotide and wherein the method comprises a third primer capable of hybridising to the first and to the second tuned competitor polynucleotide.
• PCR polymerase chain reaction
• the method comprises providing a fourth primer, wherein the fourth primer is capable of hybridising to the first target polynucleotide, wherein the first and fourth primer hybridise on opposite strands of the target so as to permit formation of the first target product, optionally a first target PCR product.
• any suitable arrangement of primers is provided by the methods of the invention, so that each relevant target or competitor is amplified, and so that each target and competitor compete appropriately for the relevant primers.
• the method comprises providing: a) a second primer capable of i) hybridising to the first target polynucleotide, wherein the first and second primer hybridise on opposite strands of the target so as to result in the production of the first target product, optionally a first target polymerase chain reaction (PCR) product; and ii) capable of hybridising to the first tuned competitor polynucleotide; and b) a third primer capable of i) hybridising to the first tuned competitor polynucleotide wherein the third and second primer hybridise on opposite strands of the first tuned competitor polynucleotide so as to result in the production of the first tuned competitor polynucleotide product, optionally a first tuned competitor polynucleotide polymerase chain reaction (PCR) product; and ii) capable of hybridising to the second tuned competitor polynucleotide; and c) a fourth primer capable of i) hybridising to the first target polynucleotide, wherein the first and second
• the fourth and fifth primers may bind to other target polynucleotides and/or to other competitor polynucleotides, expanding the complexity of the network that is assessed.
• a key feature of the present invention is the use of one or more tuned competitor polynucleotides, that has an amplification rate that has been specifically tuned relative to the corresponding target polynucleotide or relative to the amplification rate of other target or competitor polynucleotides within the network.
• This tuning provides the discrimination in amplification that translates the predictive relationship, decision surface, or differential target oligonucleotide pattern (such as a differential gene regulation signature or presence or absence of particular mutations) into a relative abundance of each amplification product that can be simply interrogated, for example by using labelled nucleic acid probes.
• the amplification rate of the first target polynucleotide is different to the amplification rate of the first tuned competitor polynucleotide. In other embodiments the amplification rate of a target polynucleotide is different to the amplification rate of its corresponding tuned competitor polynucleotide.
• the amplification rates are optimised, so that amplification is as efficient as possible.
• the skilled person is aware of techniques to increase the efficiency of amplification, for example altering the length of the product, altering the G/C content and changing the concentration of the primers. Since the skilled person knows how to improve amplification, so the skilled person knows how to make amplification less efficient, i.e. decrease the rate of amplification.
• the skilled person will understand that it is the relative amplification rate between the target and the competitor (or in some cases between the target and competitors, or between the targets and competitor, or between the targets and competitors) that is important, not necessarily the absolute amplification rate. Accordingly, it is important that the most appropriate region of the target is chosen for amplification, for example the most appropriate 200bp region of a particular target mRNA, so that the relative amplification rate between target and competitor is appropriate.
• the amplification rate of any of the target polynucleotides or competitor polynucleotides can be altered by one or more of: a) Selecting the target nucleic acid sequence based on length and/or percentage GC content; b) Designing the competitor nucleic acid sequence to alter length and/or percentage GC content; c) Increasing or decreasing the starting concentration of the competitor nucleic acid sequence; and/or d) Increasing or decreasing the starting concentration of any of the nucleic acid primers.
• the amplification rate of the competitor polynucleotide can be altered by increasing or decreasing the number of base pairs of the competitor polynucleotide product.
• the amplification rate of the competitor polynucleotide is: increased by decreasing the number of base pairs; reduced by increasing the number of base pairs; altered by increasing or decreasing the percentage GC content of the competitor polynucleotide; is decreased by increasing percentage GC content; and/or is reduced by increasing percentage GC content.
• sequences of pairs of target product and corresponding competitor product tuned to provide various relative rates of amplification and exemplified in the Examples, are provided below.
• the amplification rate can be defined as the "r" estimated from fitting the following equation to a fluorescent trace of standard quantitative PCR run on the polynucleotide with only the primers capable of hybridizing to it, in the absence of any other polynucleotides:
• t is the cycle at which each fluorescence value was measured.
• a typical reaction would include commercially available qPCR master mix, 125 nM of each of the two primers, 250 nM of the respective probe, run for 60 cycles at 60°C.
• the curve fitting would typically be performed through a non-linear least-squares (NILS) algorithm. Variations in this procedure, including substituting the probe with a fluorescent dye (e.g., Sybr Green, EvaGreen), altering the duration, temperature, or concentrations involved, or alternative statistical approaches such as Bayesian estimation are permissible as long as the same approach is used for all polynucleotides being evaluated.
• a fluorescent dye e.g., Sybr Green, EvaGreen
• f is defined as F from any of the above equations Since the competitor polynucleotide is tuned to have a different amplification rate to the target polynucleotide, in a situation wherein the amplification reaction comprises the same or substantially the same number of initial target and competitor template molecules, the number of target product polynucleotides generated is different to the number of tuned competitor product polynucleotides generated.
• the number of target product polynucleotides generated is different to the number of tuned competitor product polynucleotides generated, when the initial number of target polynucleotides and the number of tuned competitor polynucleotides prior to primer extension is the same or is substantially the same.
• the sequence of the first target polynucleotide to be amplified, and the sequence of the at least first tuned competitor polynucleotide is selected so as to result in a final detectable signal that varies with the initial concentration of the first target polynucleotide in such a way that approximates, reproduces or matches the predictive relationship or differential gene regulation signature of the target to one or more states.
• the final detectable level of the target product may be high (the corresponding competitor polynucleotide is designed to have a sequence that is a poor competitor); whereas a gene that has a high level of expression but is poorly predictive of a disease may have a lower final detectable level of target product (i.e. the corresponding competitor polynucleotide is designed to have a sequence that is highly competitive, converting the high gene expression to a lower amount of target product), since the competitor sequences are chosen to apply the correct weighting to the amplification of each target.
• each target polynucleotide is amplified by two primers, which also amplify a corresponding tuned competitor polynucleotide (keeping in mind that in each reaction is it possible to have a number of different targets and different corresponding competitor polynucleotides being amplified, as described below); and also applies to indirect methods whereby for example the target is amplified by two primers, one of which is also used to amplify a first competitor along with a second competitor primer, which itself is used to amplify a second competitor polynucleotide, e.g.- target - competitor! - competitor -, wherein each is a primer.
• the skilled person is able to generate such amplification networks that effectively encode the predictive relationship or differential gene regulation signature, such that the output, i.e. the amount of product of target and competitor, is diagnostic, prognostic, or otherwise predicts the probability of state A versus state B.
• the rate of amplification of a first target polynucleotide and the rate of amplification of a second target polynucleotide approximates, reproduces or matches a pre-defined weighting.
• the skilled person will understand that the weighting is derived from whatever is necessary for the assay signal to approximate, reproduce or match the predictive signal, which will typically be identified via simulation.
• the competitor polynucleotides of the present invention are intentionally designed to have a different amplification rate to the target. This can be achieved by having a different sequence to the target.
• the sequence of the first tuned competitor polynucleotide to be amplified shares less than 95%, 90%, 88%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30% sequence identity with the sequence of the first target polynucleotide to be amplified.
• the target sequence to be amplified is typically a subsequence within a larger polynucleotide, for example a 200 nucleotide region of a 500 nucleotide polynucleotide.
• the skilled person will understand that the requirement for a particular sequence identity, or amplification rate, applies only to this portion of the polynucleotide that is to be amplified, and the sequence of the flanking regions is largely irrelevant.
• the sequence of the first tuned competitor polynucleotide to be amplified comprises least 15% GC, or at least 25%, is at least 35%, is at least 55%, is at least 65%, is at least 75%, is at least 85%, or at least 85% GC.
• the difference in GC content of the first target polynucleotide portion to be amplified and the first competitor polynucleotide to be amplified is at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85% or at least 90% or 95%.
• the first target polynucleotide portion to be amplified may comprise a sequence that is 20% GC
• the first competitor polynucleotide to be amplified may comprise a sequence that is 25% GC, resulting a difference in GC content of 5%.
• Altering the length of the product to be generated i.e. the distance between the sites of hybridisation of the two primers used in any given amplification, can also be used (alone or in combination with other methods described here such as altering the GC content) to tune the amplification rate.
• the first tuned competitor product is at least 5 nucleotides longer than the first target product, optionally at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290 or at least 330 nucleotides longer than the first target product.
• the first tuned competitor product is at least 5 nucleotides shorter than the first target product, optionally at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290 or at least 330 nucleotides shorter than the first target product.
• the first tuned competitor product is at least 5 nucleotides longer than the first target product, optionally at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290 or at least 330 nucleotides longer than the first target product.
• any combination of one or all of the above parameters i.e. GC content, sequence identity and length of amplicon can be used to produce an appropriately tuned competitor polynucleotide.
• the amplification products are detected. In some instances it is sufficient to detect the presence or absence of a particular product. In other instances determination of the actual or relative abundance of a product is required.
• Various means are available to the skilled person to determine the presence or amount of an amplification product, including gel based electrophoresis assays, affinity-based capture of the amplification products for example on lateral flow strips, and fluorescence labelled probe based assays.
• the present invention is particularly powerful when used to determine the relative abundance of at least two target polynucleotides. Accordingly in some embodiments the one or more target products, optionally one or more target PCR products; and the one or more tuned competitor products, optionally one or more competitor polynucleotide PCR products are detected.
• each target product and each corresponding competitor product is detected.
• the detection involves the use of fluorescently labelled probes wherein no matter how many targets and competitors are detected, the detection only uses two different fluorophores. Summing the fluorescence from each probe (i.e. just a single reading of fluorescence from both fluorophores) produces a single overall value, i.e. which of the fluorescence labels is higher. In turn, this corresponds to a diagnosis or prognosis.
• the method comprises providing one or more probe groups, wherein each probe group comprises at least one probe polynucleotide labelled with a first label and at least one probe polynucleotide labelled with a second label, and wherein the first and the second label are different.
• the at least one probe labelled with the first label is capable of hybridising to the first target product; and the at least one probe labelled with a second label is capable of hybridising to the first tuned competitor product. In some embodiments neither probe is capable of hybridising to the first target product.
• the at least one probe labelled with the first label is capable of hybridising to the first tuned competitor product; and the at least one probe labelled with the second label is capable of hybridising to the second tuned competitor product. In some embodiments neither probe is capable of hybridising to the first target product.
• the above reflects the fact that some genes may be predictive or diagnostic when the expression level is increased as compared to a control (e.g. non-diseased) sample; and that some genes may be predictive or diagnostic when the expression level is decreased as compared to a control sample.
• the skilled person will be able to ensure that the correct label is assigned to the correct probe so that combining the total fluorescence takes into account the direction of gene expression.
• a key feature of the present invention is that it is the difference between labels that provides the information; which label provides the "positive" signal and which provides a "negative” signal is decided by the skilled person.
• a particular probe group represents a set of probes that are each labelled with one of only two different labels. It will be clear that as described above, the methods may be used to detect a number of different target products and competitor products. Accordingly, in some embodiments, within a single probe group there are at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or at least 100 different probes each labelled with the first label.
• probes there are at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or at least 100 different probes each labelled with the second label.
• the direct method described above will typically require one probe with one label that can hybridise to the target product, and a corresponding probe labelled with the second label that can hybridise to the corresponding competitor product, i.e. a 1: 1 ratio of probes (though the labels may be swapped as described above depending on the predictive relationship or differential gene regulation signature).
• the indirect method does not necessarily require this 1: 1 ratio, since for example a single target product may be associated with two or more competitor products.
• a single probe group there are: at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or at least 100 different probes each labelled with the first label; and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or at least 100 different probes each labelled with the second label.
• appropriate probes are as follows:
• the power in the methods comes at least from combining the detection of a number of different targets and competitors into two single readings (i.e. a reading of the first label and a reading of the second label, both of which can be done in one single reading), which themselves are combined into a single reading - how much first label versus how much second label.
• first probe group reading the first and second label, followed by how much first label versus how much second label
• second probe group reading the third and fourth label, followed by how much third label versus how much fourth label
• the overall reading of first:second:third:fourth label can be taken. This will all depend on the predictive relationship or differential gene regulation signature that is being employed.
• the method comprises providing at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or at least 100 different probe groups, wherein no particular label is used in more than one probe group.
• the method comprises providing a number of labelled probe polynucleotides such that each target product has a corresponding labelled target probe polynucleotide and each tuned competitor product has a corresponding labelled competitor probe, and wherein the labelled probes corresponding to the target product and the tuned competitor product are labelled with different labels.
• each probe is labelled with a single type of label.
• each probe is labelled only with HEX, or is only labelled with FAM, and is not labelled with both HEX and FAM. It will be clear to the skilled person however that each probe may be labelled with more than one molecule of the same label, for example may be labelled with 1, 2, 3, 4, 5 or more HEX molecules.
• the probes may be labelled with any type of detectable label for example an enzyme based label that results in a colour change.
• the label is a fluorophore.
• the first and second label are fluorophores.
• fluorophore labelled probes are "TaqMan" probes (that require degradation to release the fluorophore from proximity to a quencher), Hybeacons (which light up only when bound to the target), and Molecular Beacons (which physically distance two fluorophores when bound to an amplicon though the fluorophores remain tethered through the probe), and Scorpion probes.
• a fluorophore does not mean that a quencher may not also be present.
• the probes are labelled with a first and a second fluorophore.
• each probe may also be labelled with an appropriate quencher, as will be understood by the skilled person.
• one probe is labelled with FAM and the other with the hapten digoxigenin (DIG).
• DIG hapten digoxigenin
• a primer for each the target and the competitor is labelled with biotin; thus amplification produces some amplicons labelled at one end with biotin and at the other with FAM, as well as other amplicons labelled at one end with biotin and at the other with DIG.
• the amplicons are mixed with a solution of streptavidin-coated gold nanoparticles, which binds to the biotin to form na noparticle-amplicon complexes, then allowed to flow up a lateral flow strip.
• Anti-FAM and anti-DIG antibodies printed in separate lines on this strip act act as affinity purification agents, binding to the respective amplicons. This causes gold nanoparticles to be trapped at the printed lines, producing a dark red band visible to the naked eye.
• the relative intensity of these two bands provides the "signal" in the same manner as the relative intensity of two fluorophores described above.
• the skilled person understands what is required of a probe that functions via hybridisation to a nucleic acid target.
• the probe could have a sequence that is 100% identical to the relevant region of the target.
• the skilled person also understands that the sequences do not have to be 100% identical. Designing such hybridisation probes is entirely routine for the skilled person.
• a fluorophore is capable of identifying appropriate fluorophores or fluorophore pairs.
• the first and second fluorophore are chosen so that they have distinct emission spectra.
• Exemplary fluorophores are TAM, SUN, VIC, TET, JOE, the cyanine dyes (Cy3, Cy3.5, Cy5, Cy5.5), the Atto dyes, and the Alexa Fluors (see for example https://eu.idtdna.com/site/Catalog/modifications/dyes and https://www.trilinkbiotech.com/omi - Figure 7).
• FAM and HEX are considered to be FAM and HEX; CY3 and CY5; and any combination of FAM, HEX, TFT and Cy5.
• a particularly useful pair of fluorophores are FAM and HEX.
• the first label is FAM and the second label is HEX.
• the first label is HEX and the second label is FAM.
• the probe that binds to the target product and the probe that binds to the corresponding competitor product are labelled with different labels, so the relative amounts of each product can be either determined, or incorporated into an overall determination of the amount of different target products and different competitor products.
• the at least one probe that is capable of hybridising to the first target product; and the at least one probe that is capable of hybridising to the first tuned competitor product are labelled with different labels.
• the at least one probe that is capable of hybridising to the first tuned competitor product; and the at least one probe that is capable of hybridising to the second tuned competitor product are labelled with different labels.
• a group of genes are all predictive of the particular state (e.g. disease, prognosis) when the expression of the genes is increased relative to a control sample or control level, then it is appropriate that each probe that is capable of hybridising to the a target product is labelled with the same first label; and each probe that is capable of hybridising to a tuned competitor product are labelled with the same second label.
• some genes are predictive of a particular state when the gene expression is repressed. Since many predictive relationships or differential gene regulation signatures and networks involve an increased expression of some genes and a concomitant repression of other genes, it is important that this can be reflected in the simple output from the method. Accordingly in some embodiments at least one of the probes that are capable of hybridising to a target product is labelled with a first label, and at least one of the probes that are capable of hybridising to a tuned competitor product are labelled with the same first label.
• probes that are capable of hybridising to a target product that are labelled with a first label there will be probes that are capable of hybridising to a target product that are labelled with a second label, probes that are capable of hybridising to a competitor product that are labelled with a first label, and probes that are capable of hybridising to a competitor product that are labelled with a second label.
• each probe that is capable of hybridising to a target polynucleotide product that is associated with a positive predictive relationship or differential gene regulation signature of a particular state is labelled with the first label, and the corresponding probe that is capable of hybridising to the tuned competitor polynucleotide product is labelled with the second label; and/or wherein each probe that is capable of hybridising to a target polynucleotide product that is associated with a negative predictive relationship or differential gene regulation signature of the particular state is labelled with the second label, and the corresponding probe that is capable of hybridising to the tuned competitor polynucleotide product is labelled with the first label.
• the actual amount of each product detected by the first probe and the amount of product detected by the second probe is determined.
• each probe it is the relative amounts of each probe that are determined. For instance in some embodiments the relative amounts of each probe are compared to a standard curve to determine the relative probability of one or more states.
• Generating an appropriate standard curve is routine for the skilled person and will require calibration, either by the individual user or the manufacturer, to relate a raw signal (or, in this case, the difference between signals) to a prediction/diag nosis.
• An advantage of the present invention is that it allows the interrogation of a number of different expression patterns simultaneously, for example via multiplex PCR, and due to the use of only 2, or perhaps a small number for example 3, 4, 5, 6 different fluorophores, allows the abundance, or relative abundance, or each product to be condensed into a single reading, for example a single reading over multiple wavelengths (channels) to detect the amount of fluorescence from each probe label, or multiple readings performed in quick succession on the same sample.
• the methods described herein capture the state of a portion of a gene expression network, optionally as a single value.
• the target polynucleotide can be any nucleic acid from any source, provided that it is capable of being amplified.
• the target polynucleotide is RNA, optionally is an RNA transcript, optionally is an mRNA.
• the target polynucleotide is an miRNA, IncRNA or an siRNA.
• the target polynucleotide may also be DNA.
• the DNA may be a modified form of DNA.
• the sample may be any sample provided it comprises, or is expected to comprise, nucleic acid.
• the methods of the present invention have both medical uses and biotechnological/bioproduct uses.
• the sample may be selected from the group comprising or consisting of: tissue, biopsy, blood, plasma, serum, pathogens, microbial cells, cell culture and cell lysate.
• the sample may comprise any source of nucleic acid.
• the sample comprises any one or more of: cells, optionally white blood cells and/or red blood cells; exosomes; circulating tumour DNA (ctDNA); cell-free DNA (cfDNA); RNA; or pathogen nucleic acid.
• the cells may be of any cell type.
• the cells may be mammalian cells, bacterial cells, yeast cells or plant cells.
• the mammalian cells may be human cells or are derived from human cells.
• the cells may be cultured cells, optionally primary patient-derived cells or immortalized cell lines.
• the cells may be mammalian stem cells.
• the cells are engineered cells, optionally engineered cells used in the bioproduction of metabolites and compounds.
• the cells may be yeast cells, optionally wherein the yeast cells are used in brewing.
• the method of the invention is, in some preferred embodiments, for the amplification of at least a first and a second target polynucleotide.
• the method is for the amplification of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or at least 100 target polynucleotides.
• the present methods also include what is termed a "redundant" model, whereby at least two or more portions of the same physical target polynucleotide molecule are amplified.
• the first and the second target polynucleotides are target sequences within the same single polynucleotide.
• the method comprises amplification of a tuned competitor polynucleotide with at least one primer that is capable of hybridising to the first and to the second target polynucleotide and producing a first target product and a second target product.
• the method comprises amplification of two tuned competitor polynucleotides, wherein the method comprises: amplification of a first tuned competitor polynucleotide with at least one primer that is capable of hybridising to the first target polynucleotide; and amplification of a second tuned competitor polynucleotide with at least one primer that is capable of hybridising to the second target polynucleotide.
• detection of the product is indicative of any one or more of: i) the presence or absence; ii) a particular pre-determined starting concentration; iii) a starting concentration above or below a pre-determined level; and/or iv) starting concentrations falling within a pre-determined range, of one or more target polynucleotides.
• (i), (ii), (iii) and/or (iv) above is indicative of one or more of: a) the relative expression of a specific gene; b) the relative expression of two or more specific genes; c) expression of one or more housekeeping genes d) expression of a particular gene expression signature; e) expression of a particular allelic variant of a gene or genes; f) expression of a mutant version of a gene; g) expression of cell-free tumour DNA, wherein the target polynucleotide is selected from one or more portions of a known sequence of (a)-(g).
• the methods of the present invention can be used to determine whether a particular sample more likely to be in a particular state A rather than a particular state B.
• the states are the states on which the predictive relationship or differential gene regulation signature is based. In some instances the states may be "particular disease” vs "no disease” or vs “other disease” or vs "not particular disease”.
• Any of the methods provided by the invention can be for the diagnosis and/or prognosis of a disease or condition in a subject.
• the invention also provides a method for the diagnosis and/or prognosis of a disease or condition in a subject.
• to diagnose a disease or condition requires the assessment of the relative expression levels of at least two genes, optionally requires the assessment of the relative expression levels of at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or at least 100 genes.
• the disease or condition is selected from: human tuberculosis, human tuberculosis with HIV co-infection, human tuberculosis without HIV coinfection, cancer, optionally prostate cancer, sepsis, bloodstream candidiasis, bovine tuberculosis, bovine mastitis.
• the disease is tuberculosis.
• the disease is tuberculosis
• the differential gene regulation signature and/or predictive relationship or differential gene regulation signature is identified from the white blood cells of the subject.
• the degree of differential regulation of GBP6, ARG1 and TMCC1 contributes to an overall probability of having tuberculosis as compared to having some "other disease".
• the gene expression signature is upregulation of GBP6, and down regulation of ARG1 and TMCC1, compared to the levels of these genes in patients not having tuberculosis.
• ARG1 and TMCC1 contributes to an overall probability of having tuberculosis as compared to having some "other disease"
• examples of the primers and competitor sequences that can be used are shown in Figure 17.
• the WT sequence in each case is the target sequence.
• the F primer and R primer sequences are the sequences used to amplify the target and corresponding competitor sequences.
• the "Core” sequence is the sequence of the competitor between the two primer annealing sites, and the “Full seq” is the sequence of the full target or competitor oligonucleotide that is amplified by the two primers.
• target is TMCC1 and the target sequence is SEQ ID NO: 4
• appropriate competitor sequences used to determine the most optimum competitor are considered to be SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34 and 36.
• Appropriate primers for amplification of the target and competitors are shown in SEQ ID NO: 1 and 3.
• Appropriate probes for detection of this target's contribution are shown in SEQ ID NO: 77 and 78.
• target is ARG1 and the target sequence is SEQ ID NO: 40
• appropriate competitor sequences used to determine the most optimum competitor are considered to be SEQ ID NO: 42, 44, 46 and 48.
• Appropriate primers for amplification of the target and competitors are shown in SEQ ID NO: 37 and 39.
• Appropriate probes for detection of this target's contribution are shown in SEQ ID NO: 79 and 78.
• target is GBP6 and the target sequence is SEQ ID NO: 52
• appropriate competitor sequences used to determine the most optimum competitor are considered to be SEQ ID NO: 54, 56, and 58.
• Appropriate primers for amplification of the target and competitors are shown in SEQ ID NO: 49 and 51.
• Appropriate probes for detection of this target's contribution are shown in SEQ ID NO: 80 and 77.
• the disease is cancer, for example is prostate cancer or breast cancer, optionally prostate cancer.
• the primers and probes that can be used are as follows:
• the disease is cancer, and the relative expression of a mutant version of a gene, particular allelic variant and/or cell-free tumour DNA is detected.
• the target polynucleotides may comprise SNPs, SNVs (single nucleotide variants) indels or copy-number variants (CNVs) associated with a disease state, optionally associated with the presence of a tumour and/or cancer, for example may comprise snps, snvs or indels in cell-free tumour DNA.
• the target is EGFR, in particular a SNR in EGFR.
• the target sequence is SEQ ID NO: 62, and appropriate competitor sequences are SEQ ID NO: 64, 67 and 71. Appropriate primer sequences are SEQ ID NO: 68 and 70.
• a blocker oligonucleotide is used, wherein the blocker oligonucleotide cannot undergo extension of its 3' end, and wherein the blocker oligonucleotide is not complementary to the portion of the sequence in the at least one target polynucleotide containing the single-nucleotide polymorphism, optionally wherein the snp is a snv, but wherein the blocker oligonucleotide is complementary to the corresponding wild-type sequence and wherein the sequence in the target polynucleotide that comprises the sequence that is complementary to the blocker oligonucleotide overlaps with at least a portion of the sequence complementary to one of the primers.
• appropriate blocker sequences are SEQ ID NO: 75 and 76.
• the sample is obtained from a subject that is already suspected of having a particular disease or condition.
• the method may be used as part of a routine screening programme, in which case the target polynucleotide may be derived from a sample obtained from a subject not suspected of having a particular disease or condition.
• the subject may be considered to be at risk of a particular disease or condition, for example due to age or lifestyle.
• the present invention is useful in the field of bioengineering and industrial biotechnology.
• the detection of the relative expression of a specific gene or genes is indicative of the expression of specific natural and/or engineered genes in cells in culture and can for example allow the skilled person to determine whether a cell or system is behaving favourable or if culture parameters need to be optimised, for example.
• any means of amplification is suitable for use with the present invention.
• preferred methods of amplification include the polymerase chain reaction (PCR) or the recombinase polymerase reaction (RPA).
• the invention provides numerous methods for the amplification of one or more target polynucleotides.
• the invention provides: a method of translating the relative abundance of at least two oligonucleotides, for example the relative expression of at least two genes, or presence or absence of at least two mutations, in a sample into the relative probability of a particular state; a method of detecting the relative abundance of at least three oligonucleotides, for example the relative expression of at least three genes, or presence or absence of at least three mutations, in a sample using only two fluorophore labelled probes; a method of combining the relative abundance of at least two oligonucleotides, for example the relative expression of at least two genes, or presence or absence of at least two mutations, in a sample into a single value; a method of converting the predictive relationship, decision surface or differential target oligonucleotide pattern such as a differential gene regulation signature provided by the relative abundance of at least two oligonucleotide
• the method comprises the step of amplifying one or more target polynucleotides in a sample.
• the step of amplifying one or more target polynucleotides can be performed according to any of the methods of amplification described herein.
• the invention further provides a method of diagnosis or prognosis of a disease or condition in a subject wherein the method comprises any of the methods of amplification of the invention.
• the subject is diagnosed as having a disease or condition or prognosis of a disease or condition when the relative amounts of the first label and the second label indicate prognosis of disease or condition.
• the disease or condition may be selected from: human tuberculosis, human tuberculosis with HIV co-infection, human tuberculosis without HIV co-infection, cancer optionally prostate or breast cancer, sepsis, bloodstream candidiasis, bovine tuberculosis, bovine mastitis. Preferences for the disease or condition are as described elsewhere herein.
• the invention also provides various compositions and kits that can be used to put the methods of the invention into practice.
• the invention provides a composition comprising one or more of: a) At least one target polynucleotide as described herein; b) At least one tuned competitor polynucleotide as described herein; c) At least one primer, preferably at least two primers, as defined herein; d) At least one or more probe groups as defined herein, wherein each probe group comprises at least one probe polynucleotide labelled with a first label and at least one probe polynucleotide labelled with a second label.
• composition for nucleic acid amplification may comprise one or more standard amplification components, such as a polymerase enzyme; appropriate amounts of each of four nucleotides A, C, T and G; a recombinase enzyme; a single stranded binding protein; and/or appropriate amounts of each of the nucleotides A, C, T, G and U.
• standard amplification components such as a polymerase enzyme; appropriate amounts of each of four nucleotides A, C, T and G; a recombinase enzyme; a single stranded binding protein; and/or appropriate amounts of each of the nucleotides A, C, T, G and U.
• the invention also provides a tuned competitor polynucleotide as defined herein. Preferences for features of the tuned competitor polynucleotide are described elsewhere herein.
• the invention also provides a kit for carrying out any of the methods of the invention, for example wherein the kit comprises one or more of: a) One or more tuned competitor polynucleotides as described herein; b) One or more primers as described herein; c) A first probe polynucleotide labelled with a first label as described herein and a second probe polynucleotide labelled with a second label as described herein; d) Suitable buffers; e) Instructions for use.
• the kit comprises; a) One or more tuned competitor polynucleotides as described herein; b) One or more primers as described herein; c) A first probe polynucleotide labelled with a first label as described herein and a second probe polynucleotide labelled with a second label as described herein.
• the invention also provides a composition comprising any one or more of: a) One or more tuned competitor polynucleotides as described herein; b) One or more primers as described herein; c) A first probe polynucleotide labelled with a first label as described herein and a second probe polynucleotide labelled with a second label as described herein.
• the composition comprises: a) One or more tuned competitor polynucleotides as described herein; and b) One or more primers as described herein.
• the composition comprises: a) One or more tuned competitor polynucleotides as described herein; and c) A first probe polynucleotide labelled with a first label as described herein and a second probe polynucleotide labelled with a second label as described herein.
• the composition comprises: b) One or more primers as described herein; and c) A first probe polynucleotide labelled with a first label as described herein and a second probe polynucleotide labelled with a second label as described herein.
• the composition comprises: a) One or more tuned competitor polynucleotides as described herein; b) One or more primers as described herein; and c) A first probe polynucleotide labelled with a first label as described herein and a second probe polynucleotide labelled with a second label as described herein.
• kit or composition comprises any one more of the sequences shown in Figure 17.
• the kit or composition is for amplifying a portion of TMCC1 mRNA and comprises any one more of the competitor sequences of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34 and 36.
• the kit or composition also comprises appropriate primers for amplification of the target and competitors, such as those of SEQ ID NO: 1 and 3.
• the kit or composition is for, or is also for, amplifying a portion of ARG1 mRNA and comprises any one more of the competitor sequences of SEQ ID NO: 42, 44, 46 and 48.
• the kit or composition also comprises appropriate primers for amplification of the target and competitors, such as those of SEQ ID NO: 39 and 39.
• the kit or composition is for, or is also for, amplifying a portion of GBP6 mRNA and comprises any one more of the competitor sequences of SEQ ID NO: 54, 56, and 58.
• the kit or composition also comprises appropriate primers for amplification of the target and competitors, such as those of SEQ ID NO: 49 and 51.
• the kit or composition is for amplifying a portion of EGFR genomic DNA, for example genomic DNA that is in a sample of ctDNA, for example in order to distinguish between the wild-type allele and a particular mutation, such as the L858R SNP, and comprises any one more of the competitor sequences of SEQ ID NO: 64, 67 and 71.
• the kit or composition also comprises appropriate primers for amplification of the target and competitors, such as those of SEQ ID NO: 68 and 70.
• the invention also provides a collection or kit that comprises at least two tuned competitor polynucleotides as described herein, wherein the collection comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 25, 26, 28, 30, 32, 34, 35, 36, 38, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or at least 200 tuned competitor polynucleotides.
• the invention also provides a collection or kit that comprises at least two tuned competitor polynucleotides and at least two corresponding labelled probes.
• the invention also provides a collection or kit that comprises: at least two tuned competitor polynucleotides; at last two corresponding labelled probes; and at least two primers. Further, the invention provides a collection or kit that comprises: at least two tuned competitor polynucleotides as defined by any of the preceding claims; at last two corresponding labelled probes as defined by any of the preceding claims; and at least two primers as defined by any of the preceding claims.
• the invention also provides a method of tuning a first competitor polynucleotide that competes for hybridisation with at least a first primer with a first target polynucleotide and which results in amplification of a first target product and a first tuned competitor product, and wherein: a) a different proportion of target polynucleotides are amplified compared to the proportion of tuned competitor polynucleotides that are amplified; b) amplification of the first target polynucleotide approximates, reproduces or matches the predictive relationship or differential gene regulation signature of the target polynucleotide to a particular state; and/or c) the rate of amplification of the first target polynucleotide and optionally the rate of amplification of a second target polynucleotide approximates, reproduces or matches a pre-defined weighting, the method comprising optimising the sequence of the tuned competitor polynucleotide and/or length of tuned competitor amplification product with respect to the sequence of
• the method of tuning a competitor polynucleotide of the invention may also comprise: a second primer is used in said amplification that is capable of hybridising to the first target polynucleotide so that the first target product is produced by primer extension from two primers, optionally produced by PCR; a third primer is used in said amplification that is capable of hybridising to the first tuned competitor polynucleotide so that the first tuned competitor product is produced by primer extension from two primers, optionally produced by PCR; optionally wherein the second and the third primer have the same sequence.
• said optimising comprises producing two or more test tuned competitor polynucleotides that following amplification result in: a) a different proportion of target polynucleotides are amplified compared to the proportion of tuned competitor polynucleotides that are amplified; b) amplification of the first target polynucleotide approximates, reproduces or matches the predictive relationship or differential gene regulation signature of the target to a particular state; and/or c) the rate of amplification of the first target polynucleotide and optionally the rate of amplification of a second target polynucleotide approximates, reproduces or matches a pre-defined weighting, and selecting the tuned competitor that results in the most preferred amplification of the first target polynucleotide.
• said optimising comprises producing at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 different test tuned competitor polynucleotides.
• said optimising comprises performing at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 test amplification reactions with each test tuned competitor polynucleotide, optionally wherein at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 amplification reactions are performed using at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 different concentrations of target polynucleotide and/or number of target polynucleotide molecules.
• At least two replicates of five amplification reactions are performed, wherein each of the five amplification reactions employs a different tuned competitor polynucleotide.
• each test amplification using a particular test tuned competitor polynucleotide is performed using a different concentration and/or number of target polynucleotide templates.
• test amplification reactions are performed with a range of concentrations and/or number of target polynucleotide templates that span 100 copies/ pL to 10 s copies/pL.
• test tuned competitor polynucleotides are designed to have different GC contents.
• Also provided by the present invention is a method of optimising a competitive amplification reaction according to any of the preceding claims, wherein said optimising comprises: a) Increasing or decreasing the starting concentration of the synthetic nucleic acid sequence; and/or b) Increasing or decreasing the starting concentration of any of the nucleic acid primers.
• the invention also provides a method of multiplexed competitive amplification of at least two target polynucleotides wherein the method comprises at least one competitive polynucleotide and wherein the target amplification products are detected using probes labelled with the same label, optionally labelled with the same fluorophore, optionally wherein the competitive polynucleotide is a tuned competitive polynucleotide according to any of the preceding claims.
• the invention also provides a method of determining the transcriptional state of a system wherein the method comprises competitive amplification according to any method of the invention.
• the invention also provides a method of determining whether a system is in state A or in state B wherein the method comprises competitive amplification according to any method of the invention.
• the method also provides a method of simultaneous competitive amplification of at least two target polynucleotides in a sample wherein the method comprises providing a) a sample comprising polynucleotides; b) a first and a second tuned competitor polynucleotide; c) a first primer set, wherein the primer set comprises two primers capable of hybridising on opposite strands of a first target polynucleotide and the first competitive polynucleotide, so as to allow production of a first target amplification product and a first competitive amplification product; d) a second primer set, wherein the primer set comprises two primers capable of hybridising on opposite strands of a second target polynucleotide and the second competitive polynucleotide, so as to allow production of a second target product and a second competitive product; e) a first probe group, wherein the first probe group comprises a first labelled target probe capable of hybridising to the first target amplification product and a first
• the method comprises providing e) a further 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 primer sets and corresponding probe groups.
• one of the labelled target probes is labelled with the second label and the corresponding labelled competitor probe is labelled with the first label.
• the method further comprises simultaneously detecting the amount of the first label and the second label following multiplexed amplification.
• a method of combining the relative expression of at least two genes in a sample into a single value comprises the step of amplifying six target polynucleotides and six tuned competitor polynucleotides, wherein the six target amplification products are each probed with a different hybridisation probe labelled with HEX, and each of the six tuned competitor amplification products are probed each probed with a different hybridisation probe labelled with FAM;
• the method comprises a step of amplifying one or more target polynucleotides in a sample, wherein the method comprises: providing: a) a sample comprising polynucleotides b) a first tuned competitor polynucleotide c) at least a first primer wherein at least the first primer is capable of hybridising to: a first target polynucleotide in the sample; and the first tuned competitor polynucleotide; and initiating a primer extension reaction such that the target polynucleotide (if present in the sample) and the first tuned competitor polynucleotide are amplified, wherein amplification results in a first target product and a first tuned competitor product.
• a summary of the overall approach that may be taken by the skilled person to put the invention into practice for specific applications is as follows: a) The practitioner begins by performing regression, e.g. logistic regression, on patient data to determine both which gene transcripts to target as well as the appropriate relationship between expression level and diagnostic probability for each transcript. The skilled person may obtain pre-existing data on which the logistic regression may be performed. b) Next, the practitioner selects a CAN architecture, i.e., the number of competitor sequences and the arrangement of shared primers, for each target transcript. Exemplary methods of selecting the CAN architecture are described elsewhere herein.
• this statistical model can be used to propose new sequence designs which, in light of the newly-acquired data, are now the most likely to produce the desired amplification behavior. This process continues until suitable competitor sequences are found that allow recapitulation of the logistic regression results via the CAN reaction.
• Simulations were carried out to identify ideal parameters values describing optimal behaviour. Designing a competitor sequence which displays behaviour reflected by one or more of these parameter values is the goal of tuning. First, numerous amplicon sequences are designed and obtained with identical primer sequences and variable "core" sequences between the primers. These sequences are tested experimentally, and their behaviour analysed to derive values for the descriptive parameters. Assuming none of these sequences displayed ideal amplification behaviour, the data is used to rationally design a new sequence with the best chance of matching the target behaviour. To this end, performed regression is performed to determine how various sequence design parameters predicted the parameters of interest describing amplification behaviour.
• a Gaussian Process regressor can be trained to relate the length and GC-content of the "core" sequence to the "amplification rate” parameter. This, or any other such regressor, could then be used to predict the behaviour of a given designed amplicon as well as provide the sequence descriptors (length and GC content) most likely to achieve the desired objective. This process of simulation, design, experimentation, analysis, and regression is iterated for every sequence in the Competitive Amplification Network until a suitable sequence is found. Modifications of this approach include incorporating information on the primer sequences themselves within the regression. This allows determination of both a global relationship between design parameters and amplification parameters as well as the idiosyncrasies of that relationship specific to a given pair of primers.
• a method of detecting the relative abundance of at least three target oligonucleotides in a sample using only two fluorophore labelled probes 1.
• a method of amplifying one or more target polynucleotides in a sample comprises: providing: a) a sample potentially comprising one or more target polynucleotides b) a first tuned competitor polynucleotide c) at least a first primer wherein at least the first primer is capable of hybridising to: a first target polynucleotide in the sample; and the first tuned competitor polynucleotide; and initiating a primer extension reaction such that the target polynucleotide (if present in the sample) and the first tuned competitor polynucleotide are amplified, wherein amplification results in a first target product and a first tuned competitor product.
• the second primer is capable of hybridising to the first target polynucleotide, wherein the first and second primer hybridise on opposite strands of the target so as to result in the production of the first target product, optionally a first target polymerase chain reaction (PCR) product.
• PCR polymerase chain reaction
• the second primer is also capable of hybridising to the first tuned competitor polynucleotide, wherein the first and second primer hybridise on opposite strands of the first tuned competitor polynucleotide so as to result in the production of the first tuned competitor product, optionally first tuned competitor PCR product.
• the second primer is: a) capable of hybridising to the first tuned competitor polynucleotide, wherein the first and second primer hybridise on opposite strands of the first tuned competitor polynucleotide so as to result in the production of the first tuned competitor product, optionally first tuned competitor PCR product; and b) is capable of hybridising to the second tuned competitor polynucleotide and initiating a primer extension reaction such that the second tuned competitor polynucleotide is amplified so as to result in the production of the second tuned competitor product, optionally in combination with a further primer wherein the second and further primer hybridise on opposite strands of the second tuned competitor polynucleotide so as to result in the production of the second tuned competitor product, optionally a first target polymerase chain reaction (PCR) product, optionally wherein the second primer is not capable of hybridising to the first target polynucleotide.
• PCR target polymerase chain reaction
• the second primer is: a) capable of hybridising to the first target polynucleotide, wherein the first and second primer hybridise on opposite strands of the target so as to result in the production of the first target product, optionally a first target polymerase chain reaction (PCR) product; and b) is not capable of hybridising to the first or second tuned competitor polynucleotide and wherein the method comprises a third primer capable of hybridising to the first and to the second tuned competitor polynucleotide.
• PCR polymerase chain reaction
• the method comprises providing a fourth primer, wherein the fourth primer is capable of hybridising to the first target polynucleotide, wherein the first and fourth primer hybridise on opposite strands of the target so as to permit formation of the first target product, optionally a first target PCR product.
• the method comprises providing: a) a second primer capable of i) hybridising to the first target polynucleotide, wherein the first and second primer hybridise on opposite strands of the target so as to result in the production of the first target product, optionally a first target polymerase chain reaction (PCR) product; and ii) capable of hybridising to the first tuned competitor polynucleotide; and b) a third primer capable of i) hybridising to the first tuned competitor polynucleotide wherein the third and second primer hybridise on opposite strands of the first tuned competitor polynucleotide so as to result in the production of the first tuned competitor polynucleotide product, optionally a first tuned competitor polynucleotide polymerase chain reaction (PCR) product; and ii) capable of hybridising to the second tuned competitor polynucleotide; and c) a fourth primer capable of hybridising to the second tuned competitor polyn
• sequence of the first tuned competitor polynucleotide to be amplified comprises at least 15% GC, or at least 25%, is at least 35%, is at least 55%, is at least 65%, is at least 75%, is at least 85%, or at least 85% GC.
• the first tuned competitor product is at least 5 nucleotides longer than the first target product, optionally at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290 or at least 330 nucleotides longer than the first target product.
• the first tuned competitor product is: at least 5 nucleotides shorter than the first target product, optionally at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290 or at least 330 nucleotides shorter than the first target product; or at least 5 nucleotides longer than the first target product, optionally at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290 or at least 330 nucleotides longer than the first target product.
• each probe that is capable of hybridising to a target polynucleotide product that is associated with a positive predictive relationship of a particular state is labelled with the first label
• the corresponding probe that is capable of hybridising to the tuned competitor polynucleotide product is labelled with the second label
• each probe that is capable of hybridising to a target polynucleotide product that is associated with a negative predictive relationship of the particular state is labelled with the second label
• the corresponding probe that is capable of hybridising to the tuned competitor polynucleotide product is labelled with the first label.
• RNA optionally is an RNA transcript, optionally is an mRNA.
• RNA transcript optionally is an RNA transcript
• siRNA siRNA
• sample is selected from the group comprising or consisting of: tissue, biopsy, blood, plasma, serum, pathogens, microbial cells, cell culture and cell lysate.
• sample comprises any one or more of: cells, optionally white blood cells and/or red blood cells; exosomes; circulating tumour DNA (ctDNA); cell-free DNA (cfDNA); RNA; or pathogen nucleic acid.
• ctDNA circulating tumour DNA
• cfDNA cell-free DNA
• RNA or pathogen nucleic acid.
• the cells are: mammalian cells, bacterial cells, yeast cells or plant cells; cultured cells, optionally primary patient-derived cells or immortalized cell lines; mammalian stem cells; engineered cells, optionally engineered cells used in the bioproduction of metabolites and compounds; and/or yeast cells, optionally wherein the yeast cells are used in brewing.
• the method comprises amplification of two tuned competitor polynucleotides, wherein the method comprises: amplification of a first tuned competitor polynucleotide with at least one primer that is capable of hybridising to the first target polynucleotide; and amplification of a second tuned competitor polynucleotide with at least one primer that is capable of hybridising to the second target polynucleotide.
• detection of the amplification products is indicative of: i) the presence or absence; ii) a particular pre-determined starting concentration; Hi) a starting concentration above or below a pre-determined level; and/or iv) starting concentrations falling within a pre-determined range, of one or more target polynucleotides.
• diagnosis of the disease or condition requires the assessment of the relative expression levels of at least two genes, optionally requires the assessment of the relative expression levels of at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or at least 100 genes.
• invention 63 The method of embodiment 61 or 62, wherein the disease or condition is selected from: human tuberculosis, human tuberculosis with HIV co-infection, human tuberculosis without HIV co-infection, cancer, optionally prostate cancer, sepsis, bloodstream candidiasis, bovine tuberculosis, bovine mastitis.
• target polynucleotide(s) comprise snps, snvs (single nucleotide variants) indels or copy-number variatns (CNVs) associated with a disease state, optionally associated with the presence of a tumour and/or cancer.
• the method further comprises adding a blocker oligonucleotide, wherein the blocker oligonucleotide cannot undergo extension of its 3' end, and wherein the blocker oligonucleotide is not complementary to the portion of the sequence in the at least one target polynucleotide containing the single-nucleotide polymorphism, optionally wherein the snp is a snv, but wherein the blocker oligonucleotide is complementary to the corresponding wild-type sequence and wherein the sequence in the target polynucleotide that comprises the sequence that is complementary to the blocker oligonucleotide overlaps with at least a portion of the sequence complementary to one of the primers.
• a method of diagnosis or prognosis of a disease or condition in a subject wherein the method comprises the method of any one of embodiments 1-77.
• any of embodiments 78 or 79, wherein the disease or condition is selected from: human tuberculosis, human tuberculosis with HIV co-infection, human tuberculosis without HIV co-infection, cancer optionally prostate or breast cancer, sepsis, bloodstream candidiasis, bovine tuberculosis, bovine mastitis.
• composition comprising one or more of: a) At least one target nucleic acid sequence as defined in any one of embodiments
• each probe group comprises at least one probe polynucleotide labelled with a first label and at least one probe polynucleotide labelled with a second label, optionally as defined in any of embodiments 28-82.
• composition of embodiment 83 further comprising: d) A polymerase enzyme; e) Appropriate amounts of each of four nucleotides A, C, T and G.
• composition of embodiment 83 or 84 further comprising: f) A recombinase enzyme; g) A single stranded binding protein; h) A polymerase enzyme; i) Appropriate amounts of each of the nucleotides A, C, T, G and U.
• kits for carrying out the method of any one of embodiments 1-82 comprising one or more of: a) One or more tuned competitor polynucleotides as defined by embodiments 7- 82; b) One or more primers; c) A first probe group as defined in any one of embodiments 28-82; d) Suitable buffers; e) Instructions for use, optionally wherein the kit comprises at least 2, 3, 4, 5, 6, 7, 8, 9 or at least 10 different tuned competitor polynucleotides and/or at least 2, 3, 4, 5, 6, 7, 8, 9 or at least 10 different probe groups.
• a collection or kit of at least two tuned competitor polynucleotides wherein the collection comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 25, 26, 28, 30, 32, 34, 35, 36, 38, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or at least 200 tuned competitor polynucleotides, optionally wherein the tuned competitors polynucleotides are defined by any of embodiments 7-88. 90.
• a collection/kit comprising at least two tuned competitor polynucleotides and at least two corresponding labelled probes.
• a collection/kit comprising: at least two tuned competitor polynucleotides; at last two corresponding labelled probes; and at least two primers.
• a collection/kit comprising: at least two tuned competitor polynucleotides as defined by any of the preceding embodiments; at last two corresponding labelled probes as defined by any of the preceding embodiments; and at least two primers as defined by any of the preceding embodiments.
• a method of tuning a first competitor polynucleotide that competes for hybridisation of at least a first primer with a first target polynucleotide and which results in amplification of a first target product and a first tuned competitor product, and wherein: a) a different proportion of target polynucleotides are amplified compared to the proportion of tuned competitor polynucleotides that are amplified; b) amplification of the first target polynucleotide matches the predictive relationship of the target polynucleotide to a particular state; and/or c) the rate of amplification of the first target polynucleotide and optionally the rate of amplification of a second target polynucleotide matches a pre-defined weighting, the method comprising optimising the sequence of the tuned competitor polynucleotide and/or length of tuned competitor amplification product with respect to the sequence of the first target product and/or length of the first target product.
• a second primer is used in said amplification that is capable of hybridising to the first target polynucleotide so that the first target product is produced by primer extension from two primers, optionally produced by PCR
• a third primer is used in said amplification that is capable of hybridising to the first tuned competitor polynucleotide so that the first tuned competitor product is produced by primer extension from two primers, optionally produced by PCR; optionally wherein the second and the third primer have the same sequence.
• the method according to embodiment 93 or 94 wherein said optimising comprises producing two or more test tuned competitor polynucleotides that following amplification result in: a) a different proportion of target polynucleotides are amplified compared to the proportion of tuned competitor polynucleotides that are amplified; b) amplification of the first target polynucleotide matches the predictive relationship of the target to a particular state; and/or c) the rate of amplification of the first target polynucleotide and optionally the rate of amplification of a second target polynucleotide matches a pre-defined weighting, and selecting the tuned competitor that results in the most preferred amplification of the first target polynucleotide.
• test amplification reactions are performed with a range of concentrations and/or number of target polynucleotide templates that span 100 copies/ pL to 10 8 copies/pL.
• test tuned competitor polynucleotides are designed to have different GC contents.
• a method of optimising a competitive amplification reaction according to any of the preceding embodiments, wherein said optimising comprises: a) Increasing or decreasing the starting concentration of the synthetic nucleic acid sequence; and/or b) Increasing or decreasing the starting concentration of any of the nucleic acid primers.
• a method of multiplexed competitive amplification of at least two target polynucleotides wherein the method comprises at least one competitive polynucleotide and wherein the target amplification products are detected using probes labelled with the same label, optionally labelled with the same fluorophore, optionally wherein the competitive polynucleotide is a tuned competitive polynucleotide according to any of the preceding embodiments.
• a method of determining the transcriptional state of a system wherein the method comprises competitive amplification according to any of the preceding embodiments.
• a method of simultaneous competitive amplification of at least two target polynucleotides in a sample comprising providing a) a sample comprising polynucleotides; b) a first and a second tuned competitor polynucleotide; c) a first primer set, wherein the primer set comprises two primers capable of hybridising on opposite strands of a first target polynucleotide and the first competitive polynucleotide, so as to allow production of a first target amplification product and a first competitive amplification product; d) a second primer set, wherein the primer set comprises two primers capable of hybridising on opposite strands of a second target polynucleotide and the second competitive polynucleotide, so as to allow production of a second target product and a second competitive product; e) a first probe group, wherein the first probe group comprises a first labelled target probe capable of hybridising to the first target amplification product and a first labelled competitor
• the method according to 104 wherein the method comprises providing e) a further 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 primer sets and corresponding probe groups.
• the target sequence is SEQ ID NO: 4
• competitor sequences used to determine the most optimum competitor are SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34 and 36, optionally wherein primers for amplification of the target and competitors are shown in SEQ ID NO: 1 and 3
• the target is ARG1
• the target sequence is SEQ ID NO: 40
• competitor sequences used to determine the most optimum competitor are SEQ ID NO: 42, 44, 46 and 48, optionally wherein primers for amplification of the target and competitors are shown in SEQ ID NO: 37 and 39
• the target is GBP6
• the target sequence is SEQ ID NO: 52
• competitor sequences used to determine the most optimum competitor are SEQ ID NO: 54, 56, and 58, optionally wherein primers for amplification of the target and competitors are shown in SEQ ID NO: 49 and 51; and/or where the target is EGFR
• the target sequence is SEQ ID NO: 50
• a method of amplifying one or more target polynucleotides in a sample comprises: providing: a) a sample potentially comprising one or more target polynucleotides b) a first tuned competitor polynucleotide c) at least a first primer wherein at least the first primer is capable of hybridising to: a first target polynucleotide in the sample; and the first tuned competitor polynucleotide; and initiating a primer extension reaction such that the target polynucleotide (if present in the sample) and the first tuned competitor polynucleotide are amplified, wherein amplification results in a first target product and a first tuned competitor product.
• the method comprises providing: a second primer; a second competitor polynucleotide; and/or a second target polynucleotide.
• the second primer is capable of hybridising to the first target polynucleotide, wherein the first and second primer hybridise on opposite strands of the target so as to result in the production of the first target product, optionally a first target polymerase chain reaction (PCR) product.
• PCR target polymerase chain reaction
• the method comprises providing a second tuned competitor polynucleotide.6.
• the second primer is: a) capable of hybridising to the first tuned competitor polynucleotide, wherein the first and second primer hybridise on opposite strands of the first tuned competitor polynucleotide so as to result in the production of the first tuned competitor product, optionally first tuned competitor PCR product; and b) is capable of hybridising to the second tuned competitor polynucleotide and initiating a primer extension reaction such that the second tuned competitor polynucleotide is amplified so as to result in the production of the second tuned competitor product, optionally in combination with a further primer wherein the second and further primer hybridise on opposite strands of the second tuned competitor polynucleotide so as to result in the production of the second tuned competitor product, optionally a first target polymerase chain reaction (PCR) product, optionally wherein the second primer
• PCR target polymerase chain reaction
• the second primer is: a) capable of hybridising to the first target polynucleotide, wherein the first and second primer hybridise on opposite strands of the target so as to result in the production of the first target product, optionally a first target polymerase chain reaction (PCR) product; and b) is not capable of hybridising to the first or second tuned competitor polynucleotide and wherein the method comprises a third primer capable of hybridising to the first and to the second tuned competitor polynucleotide.
• PCR polymerase chain reaction
• the first tuned competitor product is: at least 5 nucleotides shorter than the first target product, optionally at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290 or at least 330 nucleotides shorter than the first target product; or at least 5 nucleotides longer than the first target product, optionally at least 10,
• the method comprises providing one or more probe groups, wherein each probe group comprises at least one probe polynucleotide labelled with a first label and at least one probe polynucleotide labelled with a second label, and wherein the first and the second label are different.
• probe groups 19. 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or at least 100 different probe groups, optionally wherein no particular label, optionally a fluorophore, is used in more than one probe group.
• first and second label are fluorophores, optionally wherein each probe comprises a quencher; and/or wherein the first label is FAM and the second label is HEX; or wherein the first label is HEX and the second label is FAM.
• each probe that is capable of hybridising to a target polynucleotide product that is associated with a positive predictive relationship of a particular state is labelled with the first label
• the corresponding probe that is capable of hybridising to the tuned competitor polynucleotide product is labelled with the second label
• each probe that is capable of hybridising to a target polynucleotide product that is associated with a negative predictive relationship of the particular state is labelled with the second label
• the corresponding probe that is capable of hybridising to the tuned competitor polynucleotide product is labelled with the first label.
• the method comprises amplification of two tuned competitor polynucleotides, wherein the method comprises: amplification of a first tuned competitor polynucleotide with at least one primer that is capable of hybridising to the first target polynucleotide; and amplification of a second tuned competitor polynucleotide with at least one primer that is capable of hybridising to the second target polynucleotide.
• nucleic acids are amplified using the polymerase chain reaction (PCR) or the recombinase polymerase reaction (RPA).
• PCR polymerase chain reaction
• RPA recombinase polymerase reaction
• a method of diagnosis or prognosis of a disease or condition in a subject wherein the method comprises the method of any one of embodiments 1-30.
• any of embodiments 31 or 32, wherein the disease or condition is selected from: human tuberculosis, human tuberculosis with HIV co-infection, human tuberculosis without HIV co-infection, cancer optionally prostate or breast cancer, sepsis, bloodstream candidiasis, bovine tuberculosis, bovine mastitis.
• the disease is tuberculosis
• the differential gene regulation signature and/or predictive relationship is identified from the white blood cells of the subject; and/or the degree of differential regulation of GBP6, ARG1 and TMCC1 contributes to an overall probability of having tuberculosis as compared to having some "other disease", optionally wherein the gene expression signature is upregulation of GBP6, and downregulation of ARG1 and TMCC1, compared to the levels of these genes in patients not having tuberculosis.
• diagnosis of the disease or condition requires the assessment of the relative expression levels of at least two genes, optionally requires the assessment of the relative expression levels of at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or at least 100 genes.
• composition comprising one or more of: a) At least one target nucleic acid sequence as defined in any one of embodiments
• each probe group comprises at least one probe polynucleotide labelled with a first label and at least one probe polynucleotide labelled with a second label, optionally as defined in any of embodiments 16-30.
• kits for carrying out the method of any one of embodiments 1-36 comprising one or more of: a) One or more tuned competitor polynucleotides as defined by embodiments 1- 30; b) One or more primers, optionally as defined in any one of embodiments 1-30; c) A first probe group as defined in any one of embodiments 16-30; d) Suitable buffers; e) Instructions for use, optionally wherein the kit comprises at least 2, 3, 4, 5, 6, 7, 8, 9 or at least 10 different tuned competitor polynucleotides and/or at least 2, 3, 4, 5, 6, 7, 8, 9 or at least 10 different probe groups.
• a method of tuning a first competitor polynucleotide that competes for hybridisation of at least a first primer with a first target polynucleotide and which results in amplification of a first target product and a first tuned competitor product and wherein: a) a different proportion of target polynucleotides are amplified compared to the proportion of tuned competitor polynucleotides that are amplified; b) amplification of the first target polynucleotide matches the predictive relationship of the target polynucleotide to a particular state; and/or c) the rate of amplification of the first target polynucleotide and optionally the rate of amplification of a second target polynucleotide matches a pre-defined weighting, the method comprising optimising the sequence of the tuned competitor polynucleotide and/or length of tuned competitor amplification product with respect to the sequence of the first target product and/or length of the first target product.
• a second primer is used in said amplification that is capable of hybridising to the first target polynucleotide so that the first target product is produced by primer extension from two primers, optionally produced by PCR
• a third primer is used in said amplification that is capable of hybridising to the first tuned competitor polynucleotide so that the first tuned competitor product is produced by primer extension from two primers, optionally produced by PCR; optionally wherein the second and the third primer have the same sequence.
• a method of simultaneous competitive amplification of at least two target polynucleotides in a sample comprising providing a) a sample comprising polynucleotides; b) a first and a second tuned competitor polynucleotide; c) a first primer set, wherein the primer set comprises two primers capable of hybridising on opposite strands of a first target polynucleotide and the first competitive polynucleotide, so as to allow production of a first target amplification product and a first competitive amplification product; d) a second primer set, wherein the primer set comprises two primers capable of hybridising on opposite strands of a second target polynucleotide and the second competitive polynucleotide, so as to allow production of a second target product and a second competitive product; e) a first probe group, wherein the first probe group comprises a first labelled target probe capable of hybridising to the first target amplification product and a first labelled competitor probe
• the first labelled target probe and the second labelled competitor probe are labelled with the same first label; and wherein the first labelled competitor probe and the second labelled target probe are labelled with the same second label and allowing the first and second primer sets to hybridise to the target and competitive polynucleotides.
• Figure 1 Mechanism of traditional PCR.
• Figure 3 Target design for direct competitive PCR.
• the synthetic REF sequence competes with the WT sequence for the same primers, but the two are targeted by distinct probes with different labels.
• FIG. 4 Direct Competitive Amplification endpoints.
• the WT sequence from Figure 3 was amplified in the same reaction as the indicated REF sequence.
• the difference between WT (FAM) and REF (HEX) fluorescence after 45 PCR cycles is shown as a function of WT starting quantity.
• the initial concentration of the respective REF sequence is indicated in each plot by the vertical grey line.
• the dose-response relationships are fit with sigmoid curves (black curves, grey curve reflects ISO fit).
• the inset numbers indicate the sigmoid exponent; a higher number indicates a steeper curve. Reactions with a fast competitor sequence (shorter sequences and those with low GC content) displayed sharp transitions, while slow competitor sequences led to gradual curves.
• Figure 5 Indirect CAN principle.
• FIG. 6 Simulated outputs for various Indirect CAN architectures.
• Indirect CANs can be tuned by adjusting parameters of individual components (amplification rate, concentration) or by modifying the connectivity between components.
• indirect CANs can achieve a wide range of dynamic ranges (DR), defined as the WT concentration range between 10% and 90% maximum signal difference.
• Figure 8 Three-pair direct CAN for diagnosing tuberculosis.
• the CAN consists of three direct competitive pairs, one for each transcript in the gene expression signature. Each pair is designed to exhibit a signal response to various concentrations of the natural target that mimics the respective marginal log-odds from logistic regression (Figure 6). Simulated reaction results are shown here.
• Figure 9 Indirect CAN principle.
• FIG. 10 Higher-order CANs can be designed to approximate Boolean logic. Indirect competition can recognize combinatorial comprised of patterns of multiple targets.
• CAN motifs act as Boolean gates, signalling teal/high when the specified condition is true and orange/low when it is false.
• the "half" XOR is an exception, producing signal parity when false.
• the full XOR shown here is imperfect, needing further tuning, but demonstrates the rich behaviour possible from higher-order CANs. Tuning network parameters can determine the abruptness and location of the transition regime. Note that the inverse gates, NAND, NOR, and XNOR, can all be obtained by simply swapping the probe labels. Simulated results, all targets are assumed to have a 0.9 amplification rate.
• Figure 11 Logistic regression on digital PCR data.
• Figure 12 Simulated outputs for various indirect CAN architectures.
• Indirect CANs can be tuned by adjusting parameters of individual components (amplification rate, concentration) or by modifying the connectivity between components. As shown here, indirect CANs can achieve a wide range of dynamic ranges (DR), defined as the WT concentration range between 10% and 90% maximum signal difference.
• DR dynamic ranges
• Figure 13 CAN system for detection of trace cancerous SNPs in ctDNA.
• a blocker oligo (dark purple), which cannot be extended by the polymerase, inhibits replication of the corresponding WT strand owing to its greater affinity for the WT allele than the SNR variant. The ratio of the final colour intensities corresponds to the amount of SNR, even at high WT concentration.
• FIG 14 Higher-order CANs can be designed to approximate Boolean logic. Indirect competition can recognize combinatorial comprised of patterns of multiple targets.
• CAN motifs act as Boolean gates, signalling teal/high when the specified condition is true and orange/low when it is false.
• the "half" XOR is an exception, producing signal parity when false.
• the full XOR shown here is imperfect, needing further tuning, but demonstrates the rich behaviour possible from higher-order CANs. Tuning network parameters can determine the abruptness and location of the transition regime. Note that the inverse gates, NAND, NOR, and XNOR, can all be obtained by simply swapping the probe labels. Simulated results, all targets are assumed to have a 0.9 amplification rate.
• Figure 15 Redundant targeting allows design of a CAN that reports the relative concentration of two targets, agnostic to their absolute concentrations.
• Gene transcripts are typically thousands of nucleotides long, which PCR targets are on the order of one hundred nucleotides, implying that multiple PCR targets can be derived from a single transcript. This allows design of independent CAN motifs that each target different regions of the same sequence, such as to compare the concentration of a gene of interest (TMCC1) to a classical "housekeeping" gene (GAPDH).
• TMCC1 concentration of a gene of interest
• GPDH classical "housekeeping" gene
• Figure 16 A) Measured amplification rate and estimated trend across length and GC content for probe-targeted reactions by primer pair. Titles on top row indicate forward and reverse primers used, circles indicate measured values for specific targets at 10 A 8 copies/ reaction. B) Measured amplification rate and estimated trend across length and GC content for dye-targeted reactions by primer pair. Titles on top row indicate forward and reverse primers used, circles indicate measured values for specific targets at 10 A 8 copies/ reaction.
• FIG. 17 Sequence information.
• Figure 18 Combining CANs leads to additive behavior.
• 10 A 3 copies of S056.2.2 and 10 A 3 copies of synthetic competitor S056.4.2 were included in every reaction, and two targets S056.2.10 and S056.4.10 were included at the indicated concentration.
• 5056.2.10 shares primers with S056.2.2 and S056.4.10 with S056.4.2; S056.2.10 and
• Figure 19 The endpoint response profile of a CAN is tunable by adjusting various components. Shown here are the response profiles of single-competitor CANs. The sharpness of the response can be varied through choice of competitor and wild type sequences. Adjusting the concentration of the competitor shifts the center point of the response profile. Finally, the minimum and maximum extent of the signal response can be constrained through reducing the concentration of the primers.
• Figure 20 The process of designing a CAN for a specific application.
• the practitioner begins by performing regression, e.g. logistic regression, on patient data to determine both which gene transcripts to target as well as the appropriate relationship between expression level and diagnostic probability for each transcript.
• regression e.g. logistic regression
• the practitioner selects a CAN architecture, i.e., the number of competitor sequences and the arrangement of shared primers, for each target transcript.
• the practitioner then computationally determines the ideal components of each CAN module that will optimally recapitulate the patient data regression results, specifically the concentration of each oligonucleotide and the desired amplification behavior.
• design parameters length and GC content
• a regression surface (far left) is generated, for example through Gaussian Process regression, that relates the two competitor design parameters of length (BP, in nucleotides) and GC content (in percent) to the observed amplification rate, along with the uncertainty in that relationship.
• observed points i.e., competitor sequences which have been designed and experimentally tested
• Filled contours represent the expected amplification rate at each point determined by the regression algorithm
• dashed lines represent iso-uncertainty contours (the square root of the variance returned by the regressor), indicated as a multiple of the standard deviation of all observed r values thus far.
• a metric such as Expected Improvement can be calculated that indicates a new design likely to display the desired target amplification rate. Shown here are the Expected Improvement surfaces for different targets, lighter shades indicating a higher likelihood of achieving the goal.
• the practitioner can iteratively tune the competitor sequences to achieve the desired amplification rate: i) regression is performed on data obtained thus far, ii) a new design is proposed which has high likelihood of achieving the desired rate, iii) a new sequence based on this design is obtained and experimentally tested, iv) if observed behavior is suboptimal, the regression surface can be updated to incorporate this data, and v) yet another design can be proposed.
• the competitor is kept at a fixed concentration and the WT is tested at a range of concentrations between 10 ⁇ 2 and 10 ⁇ 8 copies per reaction.
• the WT is targeted by a probe with the FAM fluorophore; the intensity of this signal is shown on the top half of each panel.
• the competitor amplicons are targeted by a probe with the HEX fluorophore; the intensity of this signal is shown inverted on the bottom half of each panel.
• the reactions are color-coded by the log of the relative concentration of the competitor and the WT.
• a “log 10 Ratio” of 3 indicates that there is 1000-fold more WT in the reaction than the respective competitor, and a “loglO Ratio” of -5 implies there is 100000-fold more competitor in the reaction than WT. Note that the BP15 competitor was too short to permit a probe region, so no HEX signal is observed, but the dose-dependent change in endpoint fluorescence signal is still observed. The difference in FAM and HEX signal intensities for each reaction shown here are summarized in Figure 4.
• SEQ ID NOs: 1-80 are as set out in Figure 17.
• SEQ ID NOs: 81-287 are set out in Table 1 below and relate to the oligonucleotides described in Figure 23.
• the core technology is a system of at least three naturaltarget or competitor polynucleotides,usedinanucleicacidamplificationreactionforevaluationofacertain combination ofone ormore sequencesofinterest.Asthe sequencesare replicated, they compete for these shared primers, conferring unique characteristics to the resultingreadout.Forexample,takeasetofnaturalgenetranscripts,eachpairedwith anengineered syntheticcompetitor( Figure 8).Anamplification reaction isrunwitha fixed amountofeach competitorand variousamountsofeach naturaltarget.Asthe naturalsequence in each competitive pairreplicates,itproducesa greenfluorescent signal;each corresponding syntheticsequence producesan orange signal.Since all greensignalsandallorangesignalsstacariopofoneanother,lookingattherelative strength oforange and green atthe end ofthe reaction tells you how close,on aggregate,the concentration ofallthe transcripts are to the concentration oftheir respective competitors. Each competitor sequence can be designed to reflect the concentration range of
• the "direct” competitive amplification network described above comprising multiple pairs of natural and synthetic targets each competing for both primers, constitutes the simplest embodiment of this invention.
• the same competition principle applies to more complex networks.
• a natural target could share one of its primers with one synthetic target, which in turn shares its other primer with a second synthetic target, making an "indirect” CAN ( Figure 9).
• Primers can be shared between multiple synthetic targets, and fully connected networks can be designed to include multiple natural targets, creating the possibility of performing non-linear operations (Figure 10).
• a single natural sequence can be independently targeted at multiple locations on the same oligo, creating a "redundant" system with powerful properties (Figure 11).
• a competitor polynucleotide (REF) is included as a reference alongside the target (denoted in the figures as WT)( Figure 3).
• This competitor sequence is designed to share the same primer sequences as the WT but contains a different probe sequence.
• a probe with one fluorophore e.g., fluorescein, or FAM, which produces a green colour
• FAM fluorescein
• HEX hexachlorofluorescein
• HEX hexachlorofluorescein
• the target and the competitor When the target and the competitor are amplified in the same PCR reaction, they compete for the primers. Since primers are consumed by each replication of a target or competitor strand, the amplification of both sequences stops as soon as the primer pool is exhausted. The quantity of each amplification product at the end of the reaction depends on the relative starting quantity of the two targets. This is reflected in the resulting fluorescent signal ( Figure 4). For a target and competitor with the same amplification rate (such as the WT and the ISO from Figure 2) that begin at the same concentration, the fluorescent signal derived from each will be the same at the end of the reaction. If there is more WT than REF at the start of the reaction, the WT fluorophore will be more intense at the end, and vice versa. The sharpness of this transition from pure WT signal to pure REF signal can be tuned by adjusting the amplification rate of the competitor.
• Figure 4 shows competitive amplification of a WT sequence with various competitors (REFs), demonstrating the breadth of accessible behaviours, from very broad transitions (BP240, GC85) to very sharp (BP30).
• the midpoint of the response curve can be shifted to higher or lower WT concentrations by adjusting the initial concentration of the REF.
• Using gel electrophoresis we can directly measure the final concentration of the amplicons in each reaction, confirming the dynamics observed in the fluorescent signal. In essence, this system is reporting on how close the expression of the gene of interest is to a pre-determined concentration. We can define this concentration, as well as the range over which we are interested, by choosing the appropriate design of the REF and its initial concentration.
• Logistic regression models the probability of being in one group (infected with tuberculosis) compared to another (having some other disease, OD) by looking at the individual contributions of various determining factors (expression levels of various genes). It assumes that the log-odds, or relative probability, is given by a (linear) weighted sum of these factors:
• a patient may have 103 copies of GBP6, contributing a marginal log-odds of +0.25.
• the same patient might have 104 and 104 copies of ARG1 and TMCC1, respectively, contributing -0.5 and -0.2.
• a suitable target sequence be identified a priori (due to external constraints), its amplification parameters measured, then using the curve-fitting algorithm to select only competitor amplification parameters which produce a nearly- optimal response when simulated along with the measured parameters.
• the simulation of the amplification behavior is described above; supplied with the suitable equations for simulation, the skilled person would be able to perform any of several optimization techniques and algorithms, including Gradient Descent, Stochastic Gradient Descent, and Quasi-Newton optimization, among others.
• an unprobed target can simply mediate the competition between competitor polynucleotides. Because both primers are necessary for exponential amplification of a given target, replication can be arrested by depletion of only one primer. So, we can design a synthetic target, REFH, that shares one primer with a natural sequence, WT, and its second primer with a second synthetic target, REFF ( Figure 12). If all components have equal amplification rate and the two REFs start at equal concentration, without any WT present the HEX and FAM signals will amplify equally. However, increasing WT begins to outcompete REFH, dampening the HEX signal.
• a promising avenue of early cancer diagnosis or monitoring of cancer treatment is through detection of tumor-derived DNA in the bloodstream (circulating tumour DNA, ctDNA), chromosomal fragments shed by the cells as they die. This is distinguishable from the ordinary milieu of cell-free DNA (cfDNA) through specific mutations, such as single nucleotide polymorphisms (SNPs) or insertion-deletions (indels).
• SNPs single nucleotide polymorphisms
• indels insertion-deletions
• Blocker Displacement Amplification (Wu et al., 2017), a published approach for preferentially amplifying variant alleles over the corresponding wild-type ( Figure 13).
• BDA Blocker Displacement Amplification
• a short oligo is designed to overlap the SNP site but bind more strongly to the WT sequence.
• This "blocker” is chemically modified to prevent extension by the polymerase.
• This system can be coupled into an indirect CAN tuned such that one signal quickly dominates as the SNP concentration increases, even at high variable allele frequency (VAF). Designing one such CAN for several different targets allows for multiplexed surveillance, where the total signal reflects the total mutation burden in the ctDNA.
• VAF variable allele frequency
• Figure 14 shows CAN motifs that approximate AND, OR, and XOR logic from Boolean logic. Redundant Competitive Networks
• the CANs shown above are limited in their response to a given target; the output is always monotonic or at least unimodal with regards to the target concentration.
• Biosensing faces a bit of a paradox: variation in the concentration of a biomolecule is used to infer disease state, yet there are many non-biological reasons a sample could vary in the concentration of targets. The patient could be more or less hydrated than expected, the sample volume could be inaccurate, or simple statistics could lead to variation in the number of cells obtained.
• a classic approach to accommodate these uncertainties is the use of an internal standard, something innate to the sample that shouldn't vary with disease condition.
• this internal standard is typically a "housekeeping" gene, a transcript so fundamental to growth of a cell (controlling cytoskeleton or cell membrane metabolism, for example) that its concentration reflects only the number of cells analysed rather than their state.
• the concentration of truly interesting gene transcripts can be compared to the housekeeping gene(s) to produce a more reliable measure of their deviation from normality.
• these are either separate PCR reactions performed in parallel or multiple probes within a single reaction; in either case, this becomes very time-, resource-, and sample-intensive if, say, 16 genes of interest and 5 housekeeping genes are needed, with extensive post-processing required.
• Redundant targeting of indirect CANs offers a way to perform this calculation explicitly, on the molecular level, so the reported signal reflects the relative concentrations of two genes regardless of their absolute concentrations (Figure 15).
• the CAN platform could also solve a problem in bioprocessing, the industrial use of synthetic cells to produce a product such as a drug or to break down a material, such as petrochemicals or greenhouse gases. This involves coordination of several synthetic and natural gene systems and may involve more than one population of engineered cells grown simultaneously. Currently, system performance is verified through RNA- seq or microarrays, which are expensive and time consuming. Alternatively, engineers include genes that produce "reporter" in conjunction with the desired product. However, doing so consumes raw materials that otherwise could be used for production of the desired compound while putting greater stress and uncertainty on the engineered cells.
• the CAN architecture would provide a way to get a snapshot of the transcriptional activity of all relevant genes simultaneously. A CAN could be designed to produce one colour if all genes are operating within a pre-specified window, but if any gene is above or below that window a different colour is produced.

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• 2020
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• 2021
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  • 2021-10-07 EP EP21794924.7A patent/EP4225938B1/en active Active
  • 2021-10-07 CN CN202180082204.2A patent/CN117321223A/zh active Pending
  • 2021-10-07 CA CA3195034A patent/CA3195034A1/en active Pending
  • 2021-10-07 WO PCT/GB2021/052594 patent/WO2022074392A1/en not_active Ceased
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  • 2021-10-07 JP JP2023521681A patent/JP7618028B2/ja active Active
  • 2021-10-07 US US18/248,285 patent/US20230366016A1/en active Pending
• 2024
  • 2024-09-13 JP JP2024159321A patent/JP2025000698A/ja active Pending

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