Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Abstract: Short tandem repeat (STR) markers are genetic elements that are frequently used in the fields of forensic analysis, paternity determination and detection of genetic diseases and cancers. Such analysis involves the amplification of STR loci. Technically, this can be challenging due to sequence variations in the flanking regions of the locus. In the case of SE33, previous amplification efforts have failed. The present invention describes a set of primers for the amplification of SE33 and a method for the analysis of the presence and/or level of SE33, also in combination with other STRs.

Abstract: The present disclosure relates to compositions and methods for detecting rare nucleic acid molecule mutations in a plurality of nucleic acid molecules. Also disclosed are methods for determining the size of a nucleic acid molecule using droplet digital PCR.

Abstract: In certain embodiments, the present invention provides a way of “digitally” marking different the alleles of different chromosomes by using a transposase to insert differently barcoded transposons into genomic DNA before further analysis. According to this method, each allele becomes marked with a unique pattern of transposon barcodes. Because each unique pattern of transposon barcodes identifies a particular allele, the method facilitates determinations of ploidy and copy number variation, improves the ability to discriminate among homozygotes, heterozygotes, and patterns arising from sequencing errors, and allows loci separated by uninformative stretches of DNA to be identified as linked loci, thereby facilitating haplotype determinations. Also provided is a novel artificial transposon end that includes a barcode sequence in two or more positions that are not essential for transposition.

Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Abstract: A method of inducing competence in cells, the method comprising contacting the cell with a composition comprising a quaternary ammonium compound including a silicon-containing functional group and a hydrocarbyl-saccharide compound.

Abstract: The present invention relates to a method for storage and subsequent lysis of a sample in which the sample is immobilized on a solid support. The solid matrix is embedded with a low concentration of both a chaotropic salt and a surfactant which act synergistically to efficiently store and lyse a biological sample.

Abstract: Provided are compositions and methods for detecting in a sample the presence or absence, and/or the amount, of a small nucleolar RNA (snoRNA) HBII-52, also known as SNORD115. The compositions and methods are useful in diagnosis, prognosis, therapy recommendations, therapy, and monitoring of therapy for individuals who have a disorder that is positively correlated with elevated HBII-52, such as cancer, and particularly for prostate cancer. Kits containing primers for detecting and/or amplifying HBII-52 from a biological sample are provided. The disclosure includes a method for monitoring an individual undergoing therapy for a disorder associated with HBII-52 expression, a method for identifying an individual as a candidate for therapy with an antagonist of 5-HT2cR, and a method for therapy by administering to a subject a therapeutically effective amount of an antagonist of 5-HT2cR.

Abstract: Illustrative embodiments of systems and methods for the identification of traits associated with DNA samples using epigenetic-based patterns detected via massively parallel sequencing (MPS) are disclosed. Illustrative embodiments may involve digesting a DNA sample with a methylation-dependent endonuclease, amplifying loci of the digested DNA sample (including a positive control locus that does not contain a restriction site for the methylation-dependent endonuclease) using a multiplex PCR to produce amplicons, sequencing the amplicons using an MPS instrument to generate sequence reads, determining a sequence count for each of the loci by comparing each of the sequence reads to reference sequences, normalizing the sequence count for each of the loci to the sequence count of the positive control locus, and identifying a trait associated with the DNA sample by applying a classification algorithm to the normalized sequence counts.

Abstract: Provided are a PCR method and a PCR kit each of which has higher detection accuracy and is more convenient. A PCR method of the present invention subjects a sample to a PCR reaction, the sample containing: a primer set including a first primer and a second primer; a template amplified by the primer set; a first probe which loses at least one bulge structure in a case where a double strand is formed by the first probe and the first primer and which forms the at least one bulge structure by being dissociated from the double strand formed by the first probe and the first primer; and a bulge structure-binding molecule which emits a signal by binding to the at least one bulge structure.

Abstract: The present invention provides a novel technology that involves improved primer design. These primer pairs have a wide range of applications and provide high sensitivity and specificity.

Abstract: The present invention provides a method for detecting interactions between or with any two of at least three target substrates, or any two of at least three features of a target substrate, or a combination of interactions and features of target substrates, by a multiplexed proximity ligation assay, said method comprising: a) for each of the at least three target substrates or features, providing a proximity probe comprising a binding moiety with affinity for the feature or binding site on said substrate, and a proximity probe oligonucleotide coupled on the binding moiety; wherein each of the proximity probe oligonucleotide carries a unique tag sequence; b) mixing the proximity probes with a sample, under a condition to allow binding of each proximity probe to its respective binding site or feature on each of said substrates through the binding moiety, c) simultaneous with, or following step b), forming circularized DNA molecules where any two proximity probes bind sufficiently close to each other on the subst

Abstract: Methods and compositions for the amplification of nucleic acids and generation of concatemers are disclosed. Amplification methods provided herein may be performed under isothermal conditions. Methods and compositions may include reagents such as nucleic acid polymerases and primers.

Abstract: The invention relates to methods and compositions for identifying specific bacterial species, which are sulfur and iron oxidizers and/or reducers, from wall board (e.g., dry wall) and/or a patient tissue or body fluid. The method comprises the steps of extracting and recovering DNA of the bacterial species from the wall board and/or the patient tissue or body fluid, amplifying the DNA, hybridizing a probe to the DNA to specifically identify the bacterial species, and specifically identifying the bacterial species. Kits and nucleic acids for use in the methods are also provided. Methods for eliminating the sulfur and iron oxidizing and/or reducing bacteria from wall board using a zeolite are also provided.

Abstract: The invention provides methods and materials that use observation of DNA characteristics to obtain information relating to the age of individuals. The instant disclosure identifies 88 sites in or near 80 genes for which the degree of cytosine methylation in epithelial and/or white blood cells is significantly correlated with age. In illustrative embodiments of the invention, cytosine methylation patterns the promoters of the EDARADD, TOMILI, and NPTX2 genes are used to predict the age of an individual with a high degree of accuracy.

Abstract: The compositions and methods described herein are designed to introduce functionalized microparticles into droplets that can be manipulated in microfluidic devices by fields, including electric (dielectrophoretic) or magnetic fields, and extracted by splitting a droplet to separate the portion of the droplet that contains the majority of the microparticles from the part that is largely devoid of the microparticles. Within the device, channels are variously configured at Y- or T junctions that facilitate continuous, serial isolation and dilution of analytes in solution. The devices can be limited in the sense that they can be designed to output purified analytes that are then further analyzed in separate machines or they can include additional channels through which purified analytes can be further processed and analyzed.

Abstract: Methods and devices for nasopharyngeal carcinoma screening are disclosed. The method comprises providing a nasopharyngeal sample from a subject, isolating DNA from the sample, amplifying and detecting at least one EBV target sequence from the DNA using real-time PCR, wherein a real-time PCR cycle threshold number of less than or equal to 31.5 is indicative of the subject having nasopharyngeal carcinoma or a risk of developing nasopharyngeal carcinoma. The device for obtaining a brush biopsy sample comprises a longitudinal shaft having a first end and a second end, wherein at least two brush heads extend from the second end of the shaft.

Abstract: Provided herein are methods and compositions for the fabrication of patterned arrays, such as nucleotide arrays. The methods and compositions are suited for the transfer and reorientation of array components.

Abstract: The present invention relates to a method for extracting circulating nucleic acids from a biological fluid. The method comprising the successive steps of providing the biological fluid supposed to contain the circulating nucleic acids. Then the biological fluid is contacted with a lysis solution comprising at least a chaotropic agent, a binding solution comprising at least a PEG derivative designed for cooperating with at least part of the circulating nucleic acids, wherein the binding solution is free of ethanol and isopropanol, and a solid support capable of capturing at least part of the circulating nucleic acid. Finally, the solid support is separated from the lysis solution, from the binding solution and from the biological fluid.

Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.