Abstract: Disclosed herein are methods and compositions for evaluating genomic content using encoded particles to evaluate multiple samples in parallel.

Abstract: Encoded bead multiplex assays for chromosomal gains and losses are provided that provide the benefits of complex, large template DNA sources, such as BAC DNA, as the probe material without bead networking or other assay performance problems. Reagents for assaying DNA are described herein which include a plurality of encoded particles having attached amplicons amplified from a template DNA sequence. Each individual attached amplicon includes a nucleic acid sequence identical to a random portion of the template DNA sequence, wherein the amplicons together represent substantially the entire template DNA and wherein the nucleic acid sequence identical to a random portion of the template DNA sequence of each individual amplicon is shorter than the entire template DNA.

Abstract: Methods of determining the length of a multinucleotide repeat region in a target nucleic acid are provided herein which include labeling amplified target nucleic acids with a target detection label independent of the number of multinucleotide repeats and a repeat-detection label proportional to the number of multinucleotide repeats, wherein the two types of labels are each independently incorporated in the amplified target nucleic acids during the amplifying or after the amplifying; binding the amplified target nucleic acids to a capture probe specific for the amplified target nucleic acids; detecting the target detection label associated with the capture probe to produce a first signal; detecting the repeat-detection label associated with the capture probe to produce a second signal; and determining a ratio of the first signal and the second signal, wherein the ratio is indicative of the length of the multinucletotide repeat region in the target nucleic acid.

Abstract: Methods of determining the length of a multinucleotide repeat region in a target nucleic acid are provided herein which include labeling amplified target nucleic acids with a target detection label independent of the number of multinucleotide repeats and a repeat-detection label proportional to the number of multinucleotide repeats, wherein the two types of labels are each independently incorporated in the amplified target nucleic acids during the amplifying or after the amplifying; binding the amplified target nucleic acids to a capture probe specific for the amplified target nucleic acids; detecting the target detection label associated with the capture probe to produce a first signal; detecting the repeat-detection label associated with the capture probe to produce a second signal; and determining a ratio of the first signal and the second signal, wherein the ratio is indicative of the length of the multinucleotide repeat region in the target nucleic acid.

Abstract: Encoded bead multiplex assays for chromosomal gains and losses are provided that provide the benefits of complex, large template DNA sources, such as BAC DNA, as the probe material without bead networking or other assay performance problems. Reagents for assaying DNA are described herein which include a plurality of encoded particles having attached amplicons amplified from a template DNA sequence. Each individual attached amplicon includes a nucleic acid sequence identical to a random portion of the template DNA sequence, wherein the amplicons together represent substantially the entire template DNA and wherein the nucleic acid sequence identical to a random portion of the template DNA sequence of each individual amplicon is shorter than the entire template DNA.

Abstract: Compositions and methods are provided for detecting genomic DNA gain and loss. Embodiments of inventive compositions and methods include composite nucleic acid probes which specifically hybridize to two or more genomic loci in a genomic region of a reference genome for detection of genomic gain and/or loss in a subject genome. In some embodiments, a substrate-attached composite nucleic acid probe is provided which includes a mixture of separate populations of beads having attached DNA probes wherein all of the beads are identically encoded and wherein each individual bead has exclusively DNA derived from one source, such as a particular large insert vector containing chromosomal DNA, or amplicons generated by amplification of DNA derived from a large insert vector containing chromosomal DNA.

Abstract: Encoded bead multiplex assays for chromosomal gains and losses are provided that provide the benefits of complex, large template DNA sources, such as BAC DNA, as the probe material without bead networking or other assay performance problems. Reagents for assaying DNA are described herein which include a plurality of encoded particles having attached amplicons amplified from a template DNA sequence. Each individual attached amplicon includes a nucleic acid sequence identical to a random portion of the template DNA sequence, wherein the amplicons together represent substantially the entire template DNA and wherein the nucleic acid sequence identical to a random portion of the template DNA sequence of each individual amplicon is shorter than the entire template DNA.

Abstract: Methods of determining the length of a multinucleotide repeat region in a target nucleic acid are provided herein which include labeling amplified target nucleic acids with a target detection label independent of the number of multinucleotide repeats and a repeat-detection label proportional to the number of multinucleotide repeats, wherein the two types of labels are each independently incorporated in the amplified target nucleic acids during the amplifying or after the amplifying; binding the amplified target nucleic acids to a capture probe specific for the amplified target nucleic acids; detecting the target detection label associated with the capture probe to produce a first signal; detecting the repeat-detection label associated with the capture probe to produce a second signal; and determining a ratio of the first signal and the second signal, wherein the ratio is indicative of the length of the multinucleotide repeat region in the target nucleic acid.

Abstract: Compositions and methods are provided for detecting genomic DNA gain and loss. Embodiments of inventive compositions and methods include composite nucleic acid probes which specifically hybridize to two or more genomic loci in a genomic region of a reference genome for detection of genomic gain and/or loss in a subject genome. In some embodiments, a substrate-attached composite nucleic acid probe is provided which includes a mixture of separate populations of beads having attached DNA probes wherein all of the beads are identically encoded and wherein each individual bead has exclusively DNA derived from one source, such as a particular large insert vector containing chromosomal DNA, or amplicons generated by amplification of DNA derived from a large insert vector containing chromosomal DNA.

Abstract: Compositions and methods are provided for detecting genomic DNA gain and loss. Embodiments of inventive assays include using a substrate-attached composite nucleic acid probe which specifically hybridizes to two or more genomic loci in a genomic region of a reference genome. The genomic region is characterized by a first terminus and a second terminus and has an intermediate region disposed between the first terminus and second terminus of at least 400 kilobases. The composite nucleic acid probe includes nucleic acid sequences which specifically hybridize to substantially an entire first genomic locus including the first terminus and to substantially an entire second genomic locus including the second terminus. Methods and compositions are provided which include assessment of two or more genomic DNA references.

Abstract: A method for enhancing the conversion of a phenol substrate to a product by a peroxidase enzyme comprises the steps of reacting a conjugate comprising a detectably labeled phenol-containing molecule with a peroxidase enzyme in the presence of an enhancing reagent, the enhancing reagent comprising an organic compound having the structure wherein each R is independently selected from the group consisting of: hydrogen and a C1-12 substituent; where V, W, Y and Z are each independently selected from the group consisting of: H, halogen, the C1-12 substituent, NR2, OR and SR; and where X is selected from the group consisting of: H, Br, Cl, F, the C1-12 substituent, NR2, OR and SR; or synergistic mixtures of an inorganic salt and the organic compound. The C1-12 substituent is linear, branched or cyclic. The C1-12 substituent is alkyl, alkenyl, alkynyl, heteroatom substituted alkyl, heteroatom substituted alkenyl, heteroatom substituted alkynyl, aryl, arylalkyl, arylalkenyl or arylalkynyl.

Abstract: A method for enhancing the conversion of a phenol substrate to a product by a peroxidase enzyme comprises the steps of reacting a conjugate comprising a detectably labeled phenol with a peroxidase enzyme in the presence of an enhancing reagent, the enhancing reagent comprising an inorganic salt, an organic compound having the formula wherein when X is B(OH)2, Y is I, or wherein when X is OH, Y is a halogen, or Q-R wherein Q is a linear or branched 1-12 heteroatom alkyl wherein tie heteroatoms are selected from C, N, O, and S, wherein the bonds connecting the heteroatom alkyl chain are single or double, wherein any carbon atom in the heteroatom alkyl chain optionally includes a substituent selected from —OH, —COOH, —NH2, and —SH, and wherein R is selected from —OH, —COOH, —NH2, and —CH3; or mixtures of the inorganic salt and the organic compound.

Abstract: A method for enhancing the conversion of a phenol substrate to a product by a peroxidase enzyme comprises the steps of reacting a conjugate comprising a detectably labeled phenol-containing molecule with a peroxidase enzyme in the presence of an enhancing reagent, the enhancing reagent comprising an organic compound having the structure 1

Abstract: The present invention concerns an array-based analytical system and method having an enhanced sensitivity which allows for simple and rapid analysis of relative unmodified samples which comprises an analytical system of the type having a plurality of different first members of a specific binding pair affixed in an array thereupon, a mixture including at least one second member of a specific binding pair capable of binding to one of the first members so as to form a specific binding pair which is affixed to the support member, and a reporter system that produces a detectable signal indicative of the presence of the specific binding pair on the support member and wherein the reporter system includes an amplified reporter system that is independent of layering.

Abstract: The present invention concerns an array-based analytical system and method having an enhanced sensitivity which allows for simple and rapid analysis of relative unmodified samples which comprises an analytical system of the type having a plurality of different first members of a specific binding pair affixed in an array thereupon, a mixture including at least one second member of a specific binding pair capable of binding to one of the first members so as to form a specific binding pair which is affixed to the support member, and a reporter system that produces a detectable signal indicative of the presence of the specific binding pair on the support member and wherein the reporter system includes an amplified reporter system that is independent of layering.

Abstract: A method for enhancing the conversion of a phenol substrate to a product by a peroxidase enzyme comprises the steps of reacting a conjugate comprising a detectably labeled phenol with a peroxidase enzyme in the presence of an enhancing reagent, the enhancing reagent conmprising an inorganic salt, an organic compound having the formula wherein when X is B(OH)2, Y is I, or wherein when X is OH, Y is a halogen, or Q-R wherein Q is a linear or branched 1-12 heteroatom alkyl wherein the heteroatoms are selected from C, N, O, and S, wherein the bonds connecting the heteroatom alkyl chain are single or double, wherein any carbon atom in the heteroatom alkyl chain optionally includes a substituent selected from —OH, —COOH, —NH2, and —SH, and wherein R is selected from —OH, —COOH, —NH2, and —CH3; or mixtures of the inorganic salt and the organic compound.

Abstract: A method for enhancing the conversion of a phenol substrate to a product by a peroxidase enzyme comprises the steps of reacting a conjugate comprising a detectably labeled phenol with a peroxidase enzyme in the presence of an enhancing reagent, the enhancing reagent comprising an inorganic salt, an organic compound having the formula 1