Abstract: Disclosed is a method of amplifying a nucleic acid sequence, wherein the method comprises subjecting a reaction mixture to at least one amplification cycle, wherein the reaction mixture comprises a double-stranded nucleic acid and at least two primers capable of annealing to complementary strands of the double-stranded nucleic acid and amplifying at least one short tandem repeat (STR) using a Family A DNA polymerase in a Fast PCR protocol having a two-step amplification cycle in 25 seconds or less. Also disclosed are real-time PCR methods using the two-step protocol and kits for STR profiling using the Fast PCR protocol.

Abstract: A method for detecting rare genomic variants in a population of cells is disclosed. The method can detect de novo mutations in bacteria and analyze the impact of various physiological conditions on mutation rate, even though such effects would be too subtle to detect using other methods. The method can be used for detection of low-frequency subpopulations in the microbiome or in cancer.

Abstract: Through a novel primer design, multiplex pyrophosphorolysis activated polymerization uses multiple pairs of blocked primers to amplify multiple almost-sequence-identical templates located in one locus in a single reaction, greatly increasing the productivity of nucleic acid amplification.

Abstract: Provided are methods for high-throughput screening to determine locations of double-stranded DNA breaks (DSBs) and translocations in genomes caused by different agents, such as enzymes.

Abstract: A method for visualizing and discriminating between DNA/RNA fragment(s) of unknown length(s) and an internal marker(s) of known length in a sample that is disposed in a common electrophoresis gel laneway. The method comprises labeling the DNA/RNA fragment(s) with a first dye and labeling the internal marker(s) with a second dye. The first and second dyes have discrete fluorescent emission spectra, which may be used to visually discriminate the DNA/RNA fragment(s) and the internal marker(s).

Abstract: The present invention provides novel methods of diagnosing and determining treatment strategies for Lyme disease and other tick-borne illnesses.

Abstract: Methods and reagents for performing digital PCR for detection and quantification of mutant alleles and copy number variation are disclosed. In particular, the invention relates to methods using a nonspecific DNA-binding dye, which produces a fluorescent signal that increases in intensity according to the number of base-pairs present in the PCR amplicon product. The method utilizes mutant-specific and wild-type-specific primers having non-complementary “tail” sequences of different lengths. Accordingly, the amplicons for the wild-type and mutant alleles differ in length and can be distinguished based on the difference in the intensities of their fluorescent signals. The methods of the invention can be used to detect rare genetic events, including single nucleotide mutations, alterations of copy number, and deletions or insertions of nucleotides.

Abstract: The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.

Abstract: There is disclosed a process for in vitro synthesis and assembly of long, gene-length polynucleotides based upon assembly of multiple shorter oligonucleotides synthesized in situ on a microarray platform. Specifically, there is disclosed a process for in situ synthesis of oligonucleotide fragments on a solid phase microarray platform and subsequent, “on device” assembly of larger polynucleotides composed of a plurality of shorter oligonucleotide fragments.

Abstract: A method for high-throughput assay processing includes (a) modulating temperature of a plurality of samples disposed in a respective plurality of fluidic channels on an image sensor wafer, including a plurality of image sensors, by heating the image sensor wafer using a heating module thermally coupled with the image sensor wafer, to control reaction dynamics in the samples, and (b) capturing a plurality of fluorescence images of the samples, using the plurality of image sensors, to detect one or more components of the plurality of samples. A method for manufacturing a high-throughput fluorescence imaging system with sample heating capability includes (a) bonding a fluidic wafer, including a plurality of recesses, to an image sensor wafer including a plurality of image sensors, and (b) bonding a heating module, including a heater for generating heat, to the image sensor wafer to thermally couple the heater and the image sensor wafer.

Abstract: Provided are a target region enrichment method based on multiplex PCR, and a reagent, the method comprising: connecting a first linker and a second linker respectively at two ends of a nucleic acid segment containing target regions to be enriched so as to obtain a linker-connected product; performing a PCR amplification on the linker-connected product using a first primer specifically bound to the first linker and a second primer specifically bound to the second linker to obtain an amplified product, the first primer or the second primer having a first affinity label; capturing a single strand having the first affinity label in the amplified product using a solid phase carrier; performing single primer linear amplification using a third primer with the captured single strand as a template; performing exponential amplification using the third primer and the first primer, with the linearly amplified product as the template, to obtain a product containing the target regions.

Abstract: The present invention provides compositions and methods based on genetic polymorphisms that are associated with coronary heart disease (particularly myocardial infarction), aneurysm/dissection, and/or response to drug treatment, particularly statin treatment. For example, the present invention relates to nucleic acid molecules containing the polymorphisms, variant proteins encoded by these nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and variant proteins, and methods of using the nucleic acid molecules and proteins as well as methods of using reagents for their detection.

Abstract: This invention relates to prognostic signatures, and compositions and methods for determining the prognosis of cancer in a patient, particularly for colorectal cancer. Specifically, this invention relates to the use of genetic markers for the prediction of the prognosis of cancer, such as colorectal cancer, based on signatures of genetic markers. In various aspects, the invention relates to a method of predicting the likelihood of long-term survival of a cancer patient, a method of determining a treatment regime for a cancer patient, a method of preparing a treatment modality for a cancer patient, among other methods as well as kits and devices for carrying out these methods.

Abstract: Provided herein are a GeXP rapid detection primer set for simultaneously identifying gene HA of eight different human-infected subtypes of avian influenza virus, a kit, and use thereof. Disclosed are 9 pairs of specific primer and 1 pair of universal primer, for a GeXP rapid detection primer kit for simultaneously identifying gene HA of eight different human-infected subtypes of avian influenza virus. Eight different human-infected subtypes HA of avian influenza virus from the nine genes of M, H1, H2, H3, H5, H6, H7, H9 and H10 can be identified simultaneously with a sensitivity of 102 copies/?L.

Abstract: The disclosure provides methods and kits involving site-specific endonuclease guided rolling circle amplification (RCA). Nucleic acid substrates, optionally generated by hybridizing a guidance primer to a single stranded nucleic acid, are cleaved with a site-specific endonuclease. In the presence of the target site, endonuclease cleavage of the substrate generates a nucleic acid having a free 3?-hydroxyl end, which is allowed to hybridize to covalently closed circular DNA probe (“take-off probe”), and initiate a rolling circle amplification (RCA) reaction. The methods and kits may be used to detect the presence of a target nucleic acid sequence, including detection of single nucleotide polymorphisms, and may be used to assess methylation status of a desired sequence, assess zygosity and/or ploidy status. The methods and kits may also be used to detect nucleic acids associated or indicative of medical conditions or pathogenic organisms.

Abstract: A method for determining the integrity of the genome of a sample and/or the quality of a library of DNA sequences obtained by deterministic restriction site whole genome amplification can include (a) amplifying the library of DNA sequences to produce first, second, and third PCR products each of a different size from 50 bp to 1000 bp, by PCR using at least one first primer pair, one second primer pair and one third primer pair, the primer pairs each hybridizing to a DNA sequence of the library having a length from 1000 bp to 5000 bp and corresponding to a sequence of the genome located respectively on a first, second and third chromosome arm; (b) detecting the first, second and third PCR products; (c) correlating the presence of the first, second and third PCR products with the integrity of the genome of the sample and/or the quality of the library.

Abstract: Disclosed are methods and kits for identifying and characterizing polynucleotide sequences in a sample which may include a heterogeneous sample. Some of the methods and kits are directed to the identification and characterization of a virus in a sample, which may include HIV capable of cause AIDS or AIDS-like symptoms. The virus may be HIV-1, and may also include drug resistant mutations. The methods may include reacting a mixture that includes, in addition to nucleic acid isolated from the sample, at least one oligonucleotide capable of specifically hybridizing to HIV nucleic acid where the oligonucleotide includes at least one non-natural base.” fu addition, the methods may include detection of one or more mutations in HIV nucleic acid that are associated with drug resistance.

Abstract: A method for detecting a low-occurrence mutation in isolated DNA adds a blocking probe to reagents during amplification of the isolated DNA. The blocking probe is an oligonucleotide complementary to wild-type DNA corresponding to the sample. The blocking probe spans a site of a suspected mutation within a region of interest in the isolated DNA. After amplification, fragments of the amplified DNA is sequenced using next generating sequencing and an output is generated to display the sequenced fragments. In some embodiments, the blocking probe is locked nucleic acid (LNA).

Abstract: The present invention provides a corn plant designated MON88017 and DNA compositions contained therein. Also provided are assays for detecting the presence of the corn plant MON88017 based on a DNA sequence and the use of this DNA sequence as a molecular marker in a DNA detection method.

Abstract: Methods and compositions disclosed herein generally relate to determination of susceptibility to eosinophilic esophagitis, asthma, and/or allergic diseases, disorders, and/or pulmonary and/or upper gastrointestinal conditions arising therefrom and/or related thereto and the diagnosis, treatment, and/or management of eosinophilic esophagitis, asthma, and/or allergic diseases, disorders, and/or pulmonary and/or upper gastrointestinal conditions arising therefrom and/or related thereto. Embodiments of the invention relate to the association between genes and specific polymorphisms of genes with eosinophilic esophagitis. Embodiments of the invention can be used to determine and manage patient risk factors for development of eosinophilic esophagitis; this determination can then be used to diagnose eosinophilic esophagitis and to treat a patient diagnosed with eosinophilic esophagitis.