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  Methods and compositions for detecting targetsUSPTO Application #: 20070219364Title: Methods and compositions for detecting targets Abstract: The present invention relates to methods and kits for detecting the presence or absence of (or quantitating) target nucleic acid sequences using ligation and amplification. The invention also relates to methods, reagents, and kits that employ addressable portions and labeled probes. (end of abstract)
Agent: Mila Kasan, Patent Dept. Applied Biosystems - Foster City, CA, US Inventors: Mark R. Andersen, Michael W. Hunkapiller, Kenneth J. Livak, Eugene G. Spier, H. Michael Wenz USPTO Applicaton #: 20070219364 - Class: 536024300 (USPTO) Related Patent Categories: Organic Compounds -- Part Of The Class 532-570 Series, Azo Compounds Containing Formaldehyde Reaction Product As The Coupling Component, Carbohydrates Or Derivatives, Nitrogen Containing, Dna Or Rna Fragments Or Modified Forms Thereof (e.g., Genes, Etc.), , Probes For Detection Of Specific Nucleotide Sequences Or Primers For The Synthesis Of Dna Or Rna The Patent Description & Claims data below is from USPTO Patent Application 20070219364. Brief Patent Description - Full Patent Description - Patent Application Claims
CROSS REFERENCE TO RELATED APPLICATIONS [0001] This application is a divisional of U.S. application Ser. No. 10/665,671, filed Sep. 19, 2003, which claims a priority benefit under 35 U.S.C. .sctn. 119(e) from U.S. application No. 60/412,225, filed Sep. 19, 2002, the contents of each is incorporated herein by reference. FIELD OF THE INVENTION [0002] The invention relates to methods and compositions for the detection of targets in a sample. BACKGROUND [0003] The detection of the presence or absence of (or quantity of) one or more target sequences in a sample containing one or more target sequences is commonly practiced. For example, the detection of cancer and many infectious diseases, such as AIDS and hepatitis, routinely includes screening biological samples for the presence or absence of diagnostic nucleic acid sequences. Also, detecting the presence or absence of nucleic acid sequences is often used in forensic science, paternity testing, genetic counseling, and organ transplantation. [0004] An organism's genetic makeup is determined by the genes contained within the genome of that organism. Genes are composed of long strands or deoxyribonucleic acid (DNA) polymers that encode the information needed to make proteins. Properties, capabilities, and traits of an organism often are related to the types and amounts of proteins that are, or are not, being produced by that organism. [0005] A protein can be produced from a gene as follows. First, the DNA of the gene that encodes a protein, for example, protein "X", is converted into ribonucleic acid (RNA) by a process known as "transcription." During transcription, a single-stranded complementary RNA copy of the gene is made. Next, this RNA copy, referred to as protein X messenger RNA (mRNA), is used by the cell's biochemical machinery to make protein X, a process referred to as "translation." Basically, the cell's protein manufacturing machinery binds to the mRNA, "reads" the RNA code, and "translates" it into the amino acid sequence of protein X. In summary, DNA is transcribed to make mRNA, which is translated to make proteins. [0006] The amount of protein X that is produced by a cell often is largely dependent on the amount of protein X mRNA that is present within the cell. The amount of protein X mRNA within a cell is due, at least in part, to the degree to which gene X is expressed. Whether a particular gene is expressed, and if so, to what level, may have a significant impact on the organism. SUMMARY OF THE INVENTION [0007] In certain embodiments, methods are provided for detecting at least one target nucleic acid sequence in a sample. In certain embodiments, the methods comprise forming a ligation reaction composition comprising the sample and a ligation probe set for each target nucleic acid sequence. In certain embodiments, the probe set comprises: (a) at least one first probe, comprising a target-specific portion, a 5' primer-specific portion, wherein the 5' primer-specific portion comprises a sequence, and a first addressable portion located between the 5' primer-specific portion and the target-specific portion, wherein the first addressable portion comprises a sequence; and (b) at least one second probe, comprising a target-specific portion, a 3' primer-specific portion, wherein the 3' primer-specific portion comprises a sequence, and a second addressable portion located between the 3' primer-specific portion and the target-specific portion, wherein the second addressable portion comprises a sequence. In certain embodiments, the probes in each set are suitable for ligation together when hybridized adjacent to one another on a complementary target nucleic acid sequence. [0008] In certain embodiments, the methods further comprise forming a test composition by subjecting the ligation reaction composition to at least one cycle of ligation, wherein adjacently hybridizing complementary probes are ligated to one another to form a ligation product comprising the 5' primer-specific portion, the first addressable portion, the target-specific portions, the second addressable portion, and the 3' primer-specific portion. [0009] In certain embodiments, the methods further comprise forming an amplification reaction composition comprising: [0010] the test composition; [0011] a polymerase; [0012] a first labeled probe, wherein the first labeled probe has a first detectable signal value when it is not hybridized to a complementary sequence, and wherein the first labeled probe comprises the sequence of the first addressable portion or comprises a sequence complementary to the sequence of the first addressable portion; [0013] a second labeled probe, wherein the second labeled probe has a first detectable signal value when it is not hybridized to a complementary sequence, and wherein the second labeled probe comprises the sequence of the second addressable portion or comprises a sequence complementary to the sequence of the second addressable portion; and [0014] at least one primer set, the primer set comprising (i) at least one first primer comprising the sequence of the 5' primer-specific portion of the ligation product, and (ii) at least one second primer comprising a sequence complementary to the sequence of the 3' primer-specific portion of the ligation product. [0015] In certain embodiments, the methods further comprise subjecting the amplification reaction composition to at least one amplification reaction. In certain embodiments, the methods further comprise detecting a second detectable signal value from the first labeled probe and from the second labeled probe at least one of during and after the amplification reaction, wherein a threshold difference between the first detectable signal value and the second detectable signal value of the first labeled probe and a threshold difference between the first detectable signal value and the second detectable signal value of the second labeled probe indicates the presence of the target nucleic acid sequence, and wherein no threshold difference between the first detectable signal value and the second detectable signal value of the first labeled probe and no threshold difference between the first detectable signal value and the second detectable signal value of the second labeled probe indicates the absence of the target nucleic acid sequence. [0016] In certain embodiments, methods are provided for detecting at least one target nucleic acid sequence in a sample. In certain embodiments, the methods comprise forming a ligation reaction composition comprising the sample and a ligation probe set for each target nucleic acid sequence. In certain embodiments, the probe set comprises (a) at least one first probe, comprising a target-specific portion and a 5' primer-specific portion, wherein the 5' primer-specific portion comprises a sequence, and (b) at least one second probe, comprising a target-specific portion and a 3' primer-specific portion, wherein the 3' primer-specific portion comprises a sequence. In certain embodiments, the probes in each set are suitable for ligation together when hybridized adjacent to one another on a complementary target nucleic acid sequence. In certain embodiments, at least one of the at least one first probe and the at least one second probe further comprises: (a) a first addressable portion located between the primer-specific portion and the target-specific portion, wherein the first addressable portion comprises a sequence, and (b) a second addressable portion located between the primer-specific portion and the target-specific portion, wherein the second addressable portion comprises a sequence. [0017] In certain embodiments, the methods further comprise forming a test composition by subjecting the ligation reaction composition to at least one cycle of ligation, wherein adjacently hybridizing complementary probes are ligated to one another to form a ligation product comprising the 5' primer-specific portion, the first addressable portion, the second addressable portion, the target-specific portions, and the 3' primer-specific portion. [0018] In certain embodiments, the methods further comprise forming an amplification reaction composition comprising: [0019] the test composition; [0020] a polymerase; Continue reading... Full patent description for Methods and compositions for detecting targets Brief Patent Description - Full Patent Description - Patent Application Claims Click on the above for other options relating to this Methods and compositions for detecting targets patent application. ###  How KEYWORD MONITOR works... a FREE service from FreshPatents1. Sign up (takes 30 seconds). 2. Fill in the keywords to be monitored. 3. Each week you receive an email with patent applications related to your keywords. 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