WO1998008083A1 - Procede et appareil de detection de structures moleculaires predeterminees dans un echantillon - Google Patents
Procede et appareil de detection de structures moleculaires predeterminees dans un echantillon Download PDFInfo
- Publication number
- WO1998008083A1 WO1998008083A1 PCT/US1997/014372 US9714372W WO9808083A1 WO 1998008083 A1 WO1998008083 A1 WO 1998008083A1 US 9714372 W US9714372 W US 9714372W WO 9808083 A1 WO9808083 A1 WO 9808083A1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- pattern
- sample
- molecular structure
- binding sites
- predetermined molecular
- Prior art date
Links
- 238000000034 method Methods 0.000 title claims description 32
- 230000027455 binding Effects 0.000 claims abstract description 87
- 239000000523 sample Substances 0.000 claims abstract description 63
- 238000001514 detection method Methods 0.000 claims abstract description 43
- 239000013074 reference sample Substances 0.000 claims abstract description 9
- 230000001419 dependent effect Effects 0.000 claims description 15
- 230000007613 environmental effect Effects 0.000 claims description 3
- 238000002844 melting Methods 0.000 claims description 3
- 230000008018 melting Effects 0.000 claims description 3
- 239000002773 nucleotide Substances 0.000 description 25
- 125000003729 nucleotide group Chemical group 0.000 description 25
- 238000013459 approach Methods 0.000 description 16
- 108020004414 DNA Proteins 0.000 description 11
- 238000009396 hybridization Methods 0.000 description 9
- 230000000295 complement effect Effects 0.000 description 8
- 108090000623 proteins and genes Proteins 0.000 description 8
- 239000003298 DNA probe Substances 0.000 description 7
- 230000000875 corresponding effect Effects 0.000 description 7
- 230000005684 electric field Effects 0.000 description 6
- 108091034117 Oligonucleotide Proteins 0.000 description 5
- 102000053602 DNA Human genes 0.000 description 4
- 108020004682 Single-Stranded DNA Proteins 0.000 description 4
- 239000012634 fragment Substances 0.000 description 4
- 238000005286 illumination Methods 0.000 description 4
- 230000003287 optical effect Effects 0.000 description 4
- 241000894007 species Species 0.000 description 4
- 238000012360 testing method Methods 0.000 description 4
- 238000000018 DNA microarray Methods 0.000 description 3
- 238000003491 array Methods 0.000 description 3
- 230000006870 function Effects 0.000 description 3
- 108020003215 DNA Probes Proteins 0.000 description 2
- 208000034826 Genetic Predisposition to Disease Diseases 0.000 description 2
- 208000028782 Hereditary disease Diseases 0.000 description 2
- 208000024556 Mendelian disease Diseases 0.000 description 2
- JLCPHMBAVCMARE-UHFFFAOYSA-N [3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate Polymers Cc1cn(C2CC(OP(O)(=O)OCC3OC(CC3OP(O)(=O)OCC3OC(CC3O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c3nc(N)[nH]c4=O)C(COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3CO)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cc(C)c(=O)[nH]c3=O)n3cc(C)c(=O)[nH]c3=O)n3ccc(N)nc3=O)n3cc(C)c(=O)[nH]c3=O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)O2)c(=O)[nH]c1=O JLCPHMBAVCMARE-UHFFFAOYSA-N 0.000 description 2
- 230000002596 correlated effect Effects 0.000 description 2
- OPTASPLRGRRNAP-UHFFFAOYSA-N cytosine Chemical compound NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 description 2
- 238000002405 diagnostic procedure Methods 0.000 description 2
- 238000010586 diagram Methods 0.000 description 2
- UYTPUPDQBNUYGX-UHFFFAOYSA-N guanine Chemical compound O=C1NC(N)=NC2=C1N=CN2 UYTPUPDQBNUYGX-UHFFFAOYSA-N 0.000 description 2
- 238000010438 heat treatment Methods 0.000 description 2
- 230000009871 nonspecific binding Effects 0.000 description 2
- 230000035945 sensitivity Effects 0.000 description 2
- 230000009870 specific binding Effects 0.000 description 2
- 239000000758 substrate Substances 0.000 description 2
- RWQNBRDOKXIBIV-UHFFFAOYSA-N thymine Chemical compound CC1=CNC(=O)NC1=O RWQNBRDOKXIBIV-UHFFFAOYSA-N 0.000 description 2
- 229930024421 Adenine Natural products 0.000 description 1
- GFFGJBXGBJISGV-UHFFFAOYSA-N Adenine Chemical compound NC1=NC=NC2=C1N=CN2 GFFGJBXGBJISGV-UHFFFAOYSA-N 0.000 description 1
- 108020004635 Complementary DNA Proteins 0.000 description 1
- 239000013614 RNA sample Substances 0.000 description 1
- 241000255588 Tephritidae Species 0.000 description 1
- 229960000643 adenine Drugs 0.000 description 1
- 239000000427 antigen Substances 0.000 description 1
- 108091007433 antigens Proteins 0.000 description 1
- 102000036639 antigens Human genes 0.000 description 1
- 238000000149 argon plasma sintering Methods 0.000 description 1
- 238000003556 assay Methods 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
- 238000010804 cDNA synthesis Methods 0.000 description 1
- 239000002299 complementary DNA Substances 0.000 description 1
- 229940104302 cytosine Drugs 0.000 description 1
- 238000011161 development Methods 0.000 description 1
- 201000010099 disease Diseases 0.000 description 1
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 1
- 238000003384 imaging method Methods 0.000 description 1
- 230000010365 information processing Effects 0.000 description 1
- 238000007834 ligase chain reaction Methods 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 244000052769 pathogen Species 0.000 description 1
- 230000001717 pathogenic effect Effects 0.000 description 1
- 238000012545 processing Methods 0.000 description 1
- 230000002285 radioactive effect Effects 0.000 description 1
- 239000012488 sample solution Substances 0.000 description 1
- 239000004065 semiconductor Substances 0.000 description 1
- 238000012163 sequencing technique Methods 0.000 description 1
- 238000013179 statistical model Methods 0.000 description 1
- 229940113082 thymine Drugs 0.000 description 1
- 238000011269 treatment regimen Methods 0.000 description 1
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Substances O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
- C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
Definitions
- the present invention relates to methods and system for molecular detection.
- a molecular detection chip typically includes a substrate on which an array of binding sites is arranged. Each binding site, or hybridization site, has a respective molecular receptor which binds or hybridizes with a molecule having a predetermined structure.
- a sample solution is applied to the molecular detection chip, and molecules in the sample bind or hybridize at one or more of the binding sites. The particular binding sites at which hybridization occurs are detected, and one or more molecular structures within the sample are subsequently deduced.
- molecular detection chips for gene sequencing These chips, often referred to as DNA chips, utilize an array of selective binding sites each having respective single-stranded DNA probes.
- a sample of single- stranded DNA fragments referred to as target DNA, is applied to the DNA chip. The DNA fragments attach to one or more of the DNA probes by a hybridization process. By detecting which DNA probes have a DNA fragment hybridized thereto, a sequence of nucleotide bases within the DNA fragment can be determined.
- molecular detection chips One use of molecular detection chips is to perform medical diagnostics.
- a genomic sample from an individual is screened to determine if the individual has a genetically-inherited disease or a genetic predisposition to disease.
- medical diagnostics migrate to miniature devices capable of performing higher numbers of tests with greater sensitivity, there is a corresponding increase in the amount of information being generated, and in the demand for greater processing power to obtain test results .
- FIG. 1 is a flow chart of an embodiment of a method of detecting a predetermined molecular structure in a sample
- FIG. 2 is a flow chart of an embodiment of a method of generating the reference pattern
- FIG. 3 is a flow chart of another embodiment of a method of generating the reference pattern;
- FIG. 4 illustrates an array of binding sites on a molecular detection device used in the specific embodiment;
- FIG. 5 illustrates a reference pattern for detecting an a-c-g nucleotide sequence in a sample
- FIG. 6 illustrates a reference pattern for detecting an a-c-t nucleotide sequence in a sample
- FIG. 7 is an example of a pattern generated by a sample having an unknown molecular structure
- FIG. 8 is a flow chart of additional steps which can be utilized to detect the predetermined molecular structure
- FIG. 9 is a block diagram of an apparatus for detecting a predetermined molecular structure in a sample
- FIG. 10 is a flow chart of an embodiment of a method of gene discovery in accordance with the present invention.
- Embodiments of the present invention advantageously provide improved information processing approaches to detecting predetermined molecular structures using a miniaturized device having an array of biological sensors.
- a diagnostic device in accordance with the present invention is designed to perform one or more specific diagnostic tests.
- FIG. 1 is a flow chart of an embodiment of a method of detecting a predetermined molecular structure in a sample.
- the method can be utilized for detection of a variety of molecular structures in a variety of different types of samples. Examples of the different types of samples include, but are not limited to, medical samples, environmental samples, agricultural samples, and other samples applicable to diagnostics.
- the predetermined molecular structure can be any indication of a structure of molecules contained in the sample.
- the predetermined molecular structure can be indicative of a presence of a pathogen in an environmental sample such as water.
- the predetermined molecular structure can provide an indication of crop resistance, for example.
- a predetermined molecular structure can be indicative of a disease gene .
- a predetermined nucleotide base sequence in a sample from a living organism or a plant.
- the sample can include a DNA sample or an RNA sample, for example.
- the predetermined nucleotide base sequence can be associated with a genetically-inherited disease and/or a genetic predisposition to disease of the individual, for example. Detection of these types of molecular structures allow medical personnel to formulate an appropriate treatment strategy for the individual .
- a step of providing a molecular detection device is performed.
- Various types of molecular detection devices can be utilized. Such molecular detection devices include, but are not limited to, molecular detection chips, DNA chips, biosensor arrays, genosensor arrays, and the like.
- the molecular detection device typically includes a plurality binding sites or hybridization sites which are arranged as an array on a substrate. Each binding site has a respective molecular receptor which specifically binds or hybridizes with a molecule having a predetermined structure.
- Each molecular receptor typically includes a biological or synthetic molecule having a specific affinity to the molecule to be detected.
- a molecular receptor having a chain of at least one nucleotide to hybridize with a molecule having a complementary chain of at least one nucleotide.
- the molecular receptor can include a DNA probe for detecting a corresponding, complementary DNA sequence in the sample.
- the scope of the invention is not limited to sensing the hybridization of DNA molecules.
- embodiments of the present invention can be utilized to detect RNA hybridization and antibody- antigen binding events.
- the molecular detection device can include an array of detection sites, such as in the context of an oligonucleotide ligation assay (OLA) .
- OLA oligonucleotide ligation assay
- pairs of oligonucleotides are utilized to amplify a selected oligonucleotide sequence.
- a corresponding detection site is screened for full-length ligated oligonucleotides using any of the sensing approaches described herein.
- an optional step of tagging molecules within the sample is performed.
- Each molecule is tagged with a member which can be sensed by the molecular detection device.
- Such members are commonly referred to in the art as tags, markers, and labels. Examples of such members include, but are not limited to, radioactive members, optical members (such as fluorescent members, luminescent members, and light-scattering members) , charged members, and magnetic members.
- a step of applying the sample to the molecular detection device is performed. Thereafter, the sample is allowed to hybridize at one or more of the binding sites, as indicated by block 16.
- the sample specifically binds to at least one of the binding sites, and non-specifically binds to at least another one of the binding sites.
- specific binding it is meant that an intended target molecule is bound to a molecular receptor.
- nonspecific binding it is meant that an unintended target molecule is bound to a molecular receptor.
- the molecular receptor includes a chain of at least one nucleotide
- specific binding occurs with a molecule having a complementary chain of the at least one nucleotide.
- Non-specific binding with such a molecular receptor occurs with a molecule having at least one mismatching base.
- a local concentration of molecules in the sample can be increased at predetermined sites using electric field enhancements.
- each site has an electrode associated therewith for selectively generating an electric field thereby.
- the electric field is generated by applying an electric potential between an electrode at the site and a counter electrode.
- the polarity of the electric potential is selected to generate an electric field having a polarity opposite to the charge of the molecules.
- an optional step of removing unwanted molecules from the binding sites can be performed, as indicated by block 18.
- the step of removing unwanted molecules can be performed by generating an electric field having the same polarity as the charge of the unwanted molecules.
- the electric field acts to repel unwanted molecules from the binding sites.
- a thermally-assisted approach can be utilized to remove unwanted molecules.
- the temperature at the binding sites is raised, in dependence upon a melting temperature, to dissociate partially-bound molecules from the molecular receptors.
- the unwanted molecules to be dehybridized can include unbound molecules and partially-bound (i.e. non-specifically bound) molecules.
- the step of removing unwanted molecules does not remove all unwanted molecules from the binding sites. This step is beneficial, however, in improving the accuracy of detection as outlined in subsequent steps.
- the method includes a step of sensing a pattern in which the sample binds to an array of binding sites in a molecular detection device.
- the pattern can be sensed using a variety of approaches, including but not limited to, optical approaches, radioactive-sensing approaches, electronic approaches, and magnetic approaches. The specific approach utilized depends upon the type of tagging member attached to the molecules in the sample.
- the step of sensing the pattern includes sensing an intensity or a magnitude of binding at each of a plurality of the array of binding sites.
- Each intensity can be indicative of a number of molecules bound at a respective binding site, a binding strength at a respective binding site, and/or a melting temperature for the binding at a respective binding site.
- the step of sensing the pattern includes capturing at least one image of the pattern.
- the image is formed by luminescent light, fluorescent light or a scattering of light associated with a hybridization event.
- the image can be captured using a CCD camera, a confocal microscope, or other like imaging device.
- the image indicates an intensity or magnitude of binding at each of the binding sites by a measure of illumination.
- the measure of illumination at a binding site can be based on a gray scale or the like at the location of the binding site on the image.
- the intensity of binding at a binding site is based on an average illumination (e.g. an average gray scale) at the binding site.
- the method includes a step of comparing the pattern to a reference pattern to detect the predetermined molecular structure in the sample.
- the step of comparing includes determining a correlation between the pattern and the reference pattern.
- the predetermined molecular structure can be detected when a measure of the correlation is within a predetermined range.
- the step of comparing includes determining a difference between the pattern and the reference pattern.
- the predetermined molecular structure can be detected when a measure of the difference is within a predetermined range.
- the step of comparing includes a step of comparing at least one image of the pattern to an image of the reference pattern.
- the method optionally comprises a step of determining a confidence level of detecting the predetermined molecular structure in the sample.
- the confidence level indicates a degree of significance of the result obtained in the step of comparing in block 22.
- the steps indicated by blocks 22 and 24 can be repeated for a plurality of different reference patterns.
- a genomic sample can be screened to determine if it contains any of a plurality of predetermined base sequences .
- FIG. 2 is a flow chart of an embodiment of a method of generating the reference pattern. Typically, the reference pattern is generated prior to performing the steps indicated in FIG. 1.
- the method includes a step of providing a reference device having a like array of binding sites as the molecular detection device used for detection. If desired, the same molecular detection device can be utilized for generating the reference pattern and for subsequent detection of an unknown molecular structure in a sample. Typically, however, another like device is utilized.
- an optional step of tagging molecules in a reference sample is performed.
- the reference sample is selected to contain the predetermined molecular structure which is to be detected.
- a step of applying the reference sample to the reference device is performed.
- the reference sample is allowed to hybridize at one or more of the binding sites.
- a step of removing unwanted molecules from the binding sites is performed, as indicated by block 38.
- a step of sensing a pattern in which the reference sample binds to the like array of binding sites is performed.
- This pattern is utilized as the reference pattern for subsequent comparison.
- the reference pattern is sensed using the same approach as utilized for subsequent detection steps. It is further preferred that an intensity of binding at each of the binding sites in the like array be included in the reference pattern.
- an optional step of modifying a temperature at the binding sites is performed.
- the temperature is raised to dissociate weakly bound molecules from the binding sites.
- the step of sensing the pattern, indicated by block 40 is repeated.
- the temperature can be repeatedly raised to generate a plurality of temperature-dependent reference patterns.
- the reference device can be washed, and the steps indicated by blocks 32, 34, 36, 38, 40, and 42 can be repeated for another reference sample containing the same predetermined molecular structure.
- the steps indicated by blocks 30, 32, 34, 36, 38, 40, and 42 can be repeated to apply the same predetermined molecular structure to a number of like reference devices. Either approach may be utilized to provide a plurality of reference patterns for the same predetermined molecular structure.
- Sensed patterns formed by a sample having an unknown molecular structure can be compared to each of the above-described plurality of reference patterns, or a statistical model thereof, to detect the predetermined molecular structure in the sample.
- FIG. 3 is a flow chart of another embodiment of a method of generating the reference pattern.
- the method includes a step of determining an architecture of the array of binding sites of the molecular detection device. This step can include determining a layout of the binding sites, and determining the type of molecular receptor at each of the binding sites.
- the method includes a step of predicting a reference pattern in which the predetermined molecular structure binds to the array of binding sites.
- the reference pattern is predicted based upon the predetermined molecular structure and the architecture of the molecular detection device.
- the reference pattern includes a predicted intensity of binding at each of the binding sites. Regardless of the approach taken, the reference pattern acts as a novelty filter which is predictive of a successful or a desirable test result.
- FIGS. 4 to 7 illustrate the detection of a predetermined molecular structure in accordance with a specific embodiment of the present invention. In this simplified example, a predetermined sequence of nucleotide bases is detected in a genomic sample, such as a DNA sample.
- FIG. 4 illustrates an array of binding sites 60 on a molecular detection device used in the specific embodiment.
- the array of binding sites 60 contains all possible single-stranded DNA probes having a length of three bases. It is noted that molecular detection devices used in practice typically have more binding sites. For example, 256x256 arrays containing all possible 8-mer DNA probes are commonly utilized.
- the respective base sequence at each binding site is indicated using standard nucleotide abbreviations ("a” representing adenine, "c” representing cytosine, "g” representing guanine, and "t” representing thymine) .
- each DNA probe is utilized to detect molecules having a complementary sequence of nucleotide bases.
- FIG. 5 illustrates a reference pattern for detecting an a-c-g nucleotide sequence in a sample.
- the reference pattern indicates an intensity of binding at each of the binding sites by an intensity of illumination.
- darker sites are indicative of lower binding intensities, while brighter sites are indicative of higher binding intensities.
- a binding site 62 having a t-g-c sequence, which is complementary to the a-c-g sequence, has the greatest intensity of binding.
- Binding sites with no matching complementary bases, such as those indicated by reference numeral 68 have a low intensity of binding.
- FIG. 6 illustrates a reference pattern for detecting an a-c-t nucleotide sequence in a sample.
- the reference patterns in FIGS. 5 and 6 can be sensed using a reference sample, or can be predicted based on the number of mismatching bases at each binding site.
- FIG. 7 is an example of a pattern generated by a sample having an unknown molecular structure.
- the pattern is generated by applying a sample of tagged single-stranded DNA molecules to the molecular detection device, allowing the molecules to hybridize to the binding sites, and optionally removing unwanted molecules.
- the resulting pattern shows a high intensity of binding at a t-g-a site 70.
- the sample includes an a-c-t nucleotide sequence (i.e. the complement of t-g-a).
- the overall pattern is better correlated to the reference pattern for the a-c-g nucleotide sequence (in FIG. 5) than to the reference pattern for a-c-t (in FIG. 6) .
- the pattern is significantly correlated to the reference pattern in FIG. 5.
- the method of the present invention would conclude that the sample includes the a-c-g nucleotide sequence.
- the pattern in FIG. 7 can be compared to the reference patterns in FIG. 5 and FIG. 6 using any of a variety of correlation measures and/or difference measures.
- a difference measure can be formulated using intensity differences (between the pattern and the reference pattern) for each of the binding sites.
- the difference measure can be a sum of absolute differences, a maximum difference, a root-mean square difference, or any other suitable function of the intensity differences.
- a correlation measure can be formulated using a coefficient of correlation between the pattern intensities and the reference intensities. In general, any linear or nonlinear function of the pattern intensities and the reference intensities can be utilized to compare the pattern to the reference pattern.
- FIG. 8 is a flow chart of additional steps which can be utilized to detect the predetermined molecular structure. The steps illustrated here can be performed after performing the steps indicated by blocks 10, 12, 14, 16 and 18 in FIG. 1.
- a step of modifying a temperature at the binding sites is performed.
- the temperature is raised to dissociate weakly bound molecules from the binding sites .
- the temperature can be independently modified at selected binding sites, or can be modified for all of the binding sites.
- a step of sensing a pattern is performed.
- a plurality of temperature-dependent patterns is generated.
- a step of comparing at least one of the plurality of temperature-dependent patterns to a corresponding at least one of a plurality of temperature-dependent reference patterns is performed.
- each of the temperature-dependent patterns can be compared to a corresponding one of the temperature-dependent reference patterns.
- only selected ones of the temperature-dependent patterns can be compared to corresponding reference patterns.
- a correlation measure and/or a difference measure is computed based on this comparison.
- a predetermined molecular structure is detected when the measure is within a predetermined range.
- the temperature-dependent pattern having a greatest variability of intensity is selected for comparison.
- the variability of intensity is greatest at a temperature which dissociates many non-specifically-bound molecules, but does not significantly dissociate specifically- bound molecules.
- This pattern can be compared with a corresponding reference pattern to detect a predetermined molecular structure. It is noted that a variety of different measures of variability can be utilized, including but not limited to, sample variance and sample standard deviation.
- FIG. 9 is a block diagram of an apparatus for detecting a predetermined molecular structure in a sample.
- the apparatus includes an array of binding sites 90 each having a respective molecular receptor.
- a sensor 92 provides means for sensing the pattern in which the sample binds to the array of binding sites 90.
- Various types of sensors can be utilized, as described earlier.
- a memory 94 contains a library of at least one reference pattern.
- the memory 94 contains a library of a plurality of reference patterns so that the apparatus can be utilized for detecting any of a plurality of predetermined molecular structures in the sample.
- a processor 96 is operatively associated with the sensor 92 and the memory 94.
- the processor 96 provides means for comparing the pattern sensed by the sensor 92 to the reference patterns stored in the memory. Based on the comparison (s) , the processor 96 outputs an indication of which predetermined molecular structure is detected, and a confidence level therefor.
- the array of binding sites are operatively associated with the sensor 92 and the memory 94.
- the processor 96 provides means for comparing the pattern sensed by the sensor 92 to the reference patterns stored in the memory. Based on the comparison (s) , the processor 96 outputs an indication of which predetermined molecular structure is detected, and a confidence level therefor.
- the array of binding sites is operatively associated with the sensor 92 and the memory 94.
- the processor 96 provides means for comparing the pattern sensed by the sensor 92 to the reference patterns stored in the memory. Based on the comparison (s) , the processor 96 outputs an indication of which predetermined molecular structure is detected, and
- the above-described apparatus can be utilized to perform the steps described for FIGS. 1 and 8.
- one or more heating elements 98 can be incorporated in the device.
- the heating elements 98 are preferably controlled by the processor 96 to form a plurality of temperature-dependent patterns.
- FIG. 10 is a flow chart of an embodiment of a method of gene discovery in accordance with the present invention.
- the method includes a step of sensing a pattern of detection for a sample applied to a molecular detection device having a plurality of detection sites.
- the sample is taken from a first species having unknown genes to be discovered. Any of the various approaches described herein can be utilized for sensing the pattern.
- the method includes a step of determining an architecture of the plurality of detection sites of the molecular detection device.
- a step of reading a nucleotide sequence from a database is performed, as indicated by block 104.
- any nucleotide sequence can be read.
- the nucleotide sequence can include a gene from a fruit fly, -while the sample in which gene discovery is to be performed is from a human.
- the method includes a step of predicting a reference pattern which would be detected if the nucleotide sequence were applied to the molecular detection device. As indicated by block 108, a step of comparing the pattern to the reference pattern is performed to determine whether the nucleotide sequence is within the sample.
Landscapes
- Chemical & Material Sciences (AREA)
- Organic Chemistry (AREA)
- Life Sciences & Earth Sciences (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Microbiology (AREA)
- Biochemistry (AREA)
- Physics & Mathematics (AREA)
- Molecular Biology (AREA)
- Biotechnology (AREA)
- Biophysics (AREA)
- Analytical Chemistry (AREA)
- Immunology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Apparatus Associated With Microorganisms And Enzymes (AREA)
Abstract
Priority Applications (1)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
AU43276/97A AU4327697A (en) | 1996-08-20 | 1997-08-13 | Method and apparatus for detecting predetermined molecular structures in a sample |
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US70018296A | 1996-08-20 | 1996-08-20 | |
US08/700,182 | 1996-08-20 |
Publications (1)
Publication Number | Publication Date |
---|---|
WO1998008083A1 true WO1998008083A1 (fr) | 1998-02-26 |
Family
ID=24812499
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/US1997/014372 WO1998008083A1 (fr) | 1996-08-20 | 1997-08-13 | Procede et appareil de detection de structures moleculaires predeterminees dans un echantillon |
Country Status (2)
Country | Link |
---|---|
AU (1) | AU4327697A (fr) |
WO (1) | WO1998008083A1 (fr) |
Cited By (9)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO2000039580A1 (fr) * | 1998-12-23 | 2000-07-06 | University Of Sydney | Essai pour la detection d'un partenaire de liaison |
WO2003072817A3 (fr) * | 2002-02-28 | 2003-12-31 | Febit Ag | Augmentation de la sensibilite et de la specificite de tests d'hybridation avec des puces a acide nucleique |
US6720138B2 (en) | 1997-04-30 | 2004-04-13 | Diagenic As | Method of preparing a standard diagnostic gene transcript pattern |
DE10324912A1 (de) * | 2003-05-30 | 2005-01-05 | Siemens Ag | Verfahren zur Detektion von DNA-Punktmutationen (SNP-Analyse) sowie zugehörige Anordnung |
EP1947116A2 (fr) | 2003-02-10 | 2008-07-23 | TO-BBB Holding B.V. | Acides nucléiques exprimés par action différentielle dans la barrière hématoencéphalique sous des conditions inflammatoires |
WO2010087702A1 (fr) | 2009-01-30 | 2010-08-05 | Stichting Katholieke Universiteit | Gène tet2 en tant que marqueur pour diagnostiquer un syndrome myélodysplasique (mds) ou une leucémie myéloïde aiguë (aml) et déterminer le pronostic chez un sujet |
WO2011034421A1 (fr) | 2009-09-16 | 2011-03-24 | Stichting Het Nederlands Kanker Instituut | Gènes cibles fra-1 utilisés comme cibles médicamenteuses pour le traitement du cancer |
US8105773B2 (en) | 2004-06-02 | 2012-01-31 | Diagenic As | Oligonucleotides for cancer diagnosis |
WO2014007623A1 (fr) | 2012-07-03 | 2014-01-09 | Interna Technologies B.V. | Portefeuille de diagnostic et ses utilisations |
Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5532128A (en) * | 1991-11-19 | 1996-07-02 | Houston Advanced Research Center | Multi-site detection apparatus |
US5571639A (en) * | 1994-05-24 | 1996-11-05 | Affymax Technologies N.V. | Computer-aided engineering system for design of sequence arrays and lithographic masks |
US5605662A (en) * | 1993-11-01 | 1997-02-25 | Nanogen, Inc. | Active programmable electronic devices for molecular biological analysis and diagnostics |
-
1997
- 1997-08-13 WO PCT/US1997/014372 patent/WO1998008083A1/fr active Application Filing
- 1997-08-13 AU AU43276/97A patent/AU4327697A/en not_active Abandoned
Patent Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5532128A (en) * | 1991-11-19 | 1996-07-02 | Houston Advanced Research Center | Multi-site detection apparatus |
US5605662A (en) * | 1993-11-01 | 1997-02-25 | Nanogen, Inc. | Active programmable electronic devices for molecular biological analysis and diagnostics |
US5571639A (en) * | 1994-05-24 | 1996-11-05 | Affymax Technologies N.V. | Computer-aided engineering system for design of sequence arrays and lithographic masks |
Non-Patent Citations (2)
Title |
---|
PROC. NATL. ACAD. SCI. U.S.A., July 1995, Vol. 92, STIMPSON D.I., "Real-Time Detection of DNA Hybridization and Melting on Oligonucleotide Arrays by Using Optical Wave Guides", pages 6379-6383. * |
PROC. NATL. ACAD. SCI. U.S.A., May 1994, Vol. 91, PEASE A.C., "Light-Generated Oligonucleotide Arrays for Rapid DNA Sequence Analysis", pages 5022-5026. * |
Cited By (11)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US6720138B2 (en) | 1997-04-30 | 2004-04-13 | Diagenic As | Method of preparing a standard diagnostic gene transcript pattern |
WO2000039580A1 (fr) * | 1998-12-23 | 2000-07-06 | University Of Sydney | Essai pour la detection d'un partenaire de liaison |
US7560226B2 (en) | 1998-12-23 | 2009-07-14 | Medsaic Pty Limited | Assay to detect a binding partner |
WO2003072817A3 (fr) * | 2002-02-28 | 2003-12-31 | Febit Ag | Augmentation de la sensibilite et de la specificite de tests d'hybridation avec des puces a acide nucleique |
EP1947116A2 (fr) | 2003-02-10 | 2008-07-23 | TO-BBB Holding B.V. | Acides nucléiques exprimés par action différentielle dans la barrière hématoencéphalique sous des conditions inflammatoires |
DE10324912A1 (de) * | 2003-05-30 | 2005-01-05 | Siemens Ag | Verfahren zur Detektion von DNA-Punktmutationen (SNP-Analyse) sowie zugehörige Anordnung |
US7488578B2 (en) | 2003-05-30 | 2009-02-10 | Siemens Aktiengesellschaft | Method for detecting DNA point mutations (single nucleotide polymorphism (SNP) analysis) and associated arrangement |
US8105773B2 (en) | 2004-06-02 | 2012-01-31 | Diagenic As | Oligonucleotides for cancer diagnosis |
WO2010087702A1 (fr) | 2009-01-30 | 2010-08-05 | Stichting Katholieke Universiteit | Gène tet2 en tant que marqueur pour diagnostiquer un syndrome myélodysplasique (mds) ou une leucémie myéloïde aiguë (aml) et déterminer le pronostic chez un sujet |
WO2011034421A1 (fr) | 2009-09-16 | 2011-03-24 | Stichting Het Nederlands Kanker Instituut | Gènes cibles fra-1 utilisés comme cibles médicamenteuses pour le traitement du cancer |
WO2014007623A1 (fr) | 2012-07-03 | 2014-01-09 | Interna Technologies B.V. | Portefeuille de diagnostic et ses utilisations |
Also Published As
Publication number | Publication date |
---|---|
AU4327697A (en) | 1998-03-06 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
US20230204538A1 (en) | Methods and apparatus for measuring analytes using large scale molecular electronics sensor arrays | |
US6171793B1 (en) | Method for scanning gene probe array to produce data having dynamic range that exceeds that of scanner | |
US6926865B2 (en) | Method and apparatus for detecting DNA hybridization | |
JP4029921B2 (ja) | 光ファイバーバイオセンサ用高密度アレイの製造法と読出法 | |
US8241893B2 (en) | Method and device for separating molecular targets in a complex mixture | |
US20100270174A1 (en) | Biosensor cell and biosensor array | |
US20210350163A1 (en) | Equalization-Based Image Processing and Spatial Crosstalk Attenuator | |
Lennon | High-throughput gene expression analysis for drug discovery | |
Walt | Imaging optical sensor arrays | |
US20080215252A1 (en) | Method of Determining Base Sequence of Nucleic Acid and Apparatus Therefor | |
WO1998008083A1 (fr) | Procede et appareil de detection de structures moleculaires predeterminees dans un echantillon | |
Belosludtsev et al. | Organism identification using a genome sequence-independent universal microarray probe set | |
JP2000228999A (ja) | 個体の集団の多重遺伝子型 | |
US20080044821A1 (en) | Nucleic acid array having fixed nucleic acid anti-probes and complementary free nucleic acid probes | |
US20050266455A1 (en) | Method and microelectronic device for multi-site molecule detection | |
JP3944576B2 (ja) | マイクロアレイを用いたアプタマーの取得方法 | |
US20100056388A1 (en) | Nucleic acid array having fixed nucleic acid anti-probes and complementary free nucleic acid probes | |
JP2006506605A (ja) | mRNAの絶対量を測定する方法及びシステム | |
US6218116B1 (en) | Method and device for treatment by complexing of a liquid medium | |
JP2003310257A (ja) | 肺炎クラミジアのdnaマイクロアレイ、肺炎クラミジア感染の有無を検査する方法および薬物のスクリーニング方法 | |
US20050095595A1 (en) | Methods and systems for improving of polymer analysis | |
Leslie et al. | Differential display: a practical approach | |
US20080003589A1 (en) | Method of measuring repeat number of unit base | |
US20050226535A1 (en) | Method and system for rectilinearizing an image of a microarray having a non-rectilinear feature arrangement | |
EP3677690A1 (fr) | Méthode et dispositif pour l'analyse d'acides nucléiques |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
AK | Designated states |
Kind code of ref document: A1 Designated state(s): AL AM AT AU AZ BA BB BG BR BY CA CH CN CU CZ DE DK EE ES FI GB GE GH HU IL IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT UA UG US UZ VN YU ZW AM AZ BY KG KZ MD RU TJ TM |
|
AL | Designated countries for regional patents |
Kind code of ref document: A1 Designated state(s): GH KE LS MW SD SZ UG ZW AT BE CH DE DK ES FI FR GB GR IE IT LU MC NL |
|
121 | Ep: the epo has been informed by wipo that ep was designated in this application | ||
REG | Reference to national code |
Ref country code: DE Ref legal event code: 8642 |
|
NENP | Non-entry into the national phase |
Ref country code: JP Ref document number: 98510835 Format of ref document f/p: F |
|
122 | Ep: pct application non-entry in european phase | ||
NENP | Non-entry into the national phase |
Ref country code: CA |