Abstract: One embodiment of the present invention provides for a method for amplifying a template of nucleic acid target sequence contained in a sample. The method includes contacting the sample with an amplification reaction mixture containing a primer complementary to the template of nucleic acid target sequence. A temperature of the reaction is oscillated between an upper temperature and a lower temperature wherein the change in temperature is no greater than about 20° C. during a plurality of temperature cycles. The template of nucleic acid target sequence is amplified.

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: Analytical standards can allow one to detect and/or measure sampling, processing, and/or amplification errors in a sample that includes a plurality of polynucleotide molecules. The analytical standards can provide an internal control to detect errors in the representation of the original sample reflected in data obtained after manipulating and/or processing of sample molecules.

Abstract: The present disclosure describes a method of adapter ligation to the ends of fragmented double-stranded DNA molecules.

Abstract: Compositions and methods for amplifying selected polynucleotides, including DNA and RNA, particularly in multiplex amplification reactions using common primers amplification. Generally, methods of the invention employ multiple steps such as template-specific hybridization, a linear amplification, partial degradation of nucleic acid, and ligation. At the end of the process the sequences of selected polynucleotides are flanked by the common sequences which can be used for exponential amplification using common primers. In some aspects the polynucleotides are associated with a barcode and the presence of the barcode is detected to measure the amount of the polynucleotide.

Abstract: The present disclosure is drawn to methods for detection, quantitation and analysis of nucleotides of interest, for example SNPs, in nucleic acid sequences of interest using universal FRET-based reporter primers.

Abstract: Disclosed are composition and methods for treating immune disorders. Also disclosed are diagnosis methods and prognosis methods.

Abstract: The present invention relates to markers for diagnosing the difference in effects of renal cancer treatment or the prognosis of renal cancer patients, according to the gender of renal cancer patients. The survival rate and recurrence rate of renal cancer of a particular gender respectively relate to the mutation of genes, of the present invention, in renal cancer patients, and thus the mutated genes of the present invention can be used as markers in predicting, on the basis of gender, the difference in effects of renal cancer treatment or the prognosis of renal cancer patients.

Abstract: Methods, compositions, and kits are provided for quantification of genome editing.

Abstract: This invention relates to a prognostic method for determining the risk of an asymptomatic human subject with latent tuberculosis (TB) infection or apparent latent TB infection and/or after suspected exposure to TB progressing to active tuberculosis disease comprising the steps of quantifying and computationally analysing relative abundances of a collection of pairs of gene products (“TB biomarkers”) derived from a sample obtained from the subject. The invention further relates to a collection of TB biomarkers that generates a transcriptomic signature of risk for prediction of the likelihood of an asymptomatic human subject with latent TB infection and/or after suspected exposure to TB progressing to active tuberculosis disease. Furthermore, a kit comprising gene-specific primers or oligonucleotide probes for the detection of pairs of TB biomarkers that generates a prognostic signature of risk for use with the method of the invention is described.

Abstract: Method and apparatus to facilitate separation of solution-phase components surrounding an immobilized multicomponent complex while stabilizing association of the components within the complex. The technique can be used for reducing background signal arising from the presence of non-complexed components harboring detectable labels, thereby enhancing signal-to-background ratios and allowing enhanced detection of the multicomponent complex.

Abstract: Devices and methods are provided for collecting and handling difficult sample types.

Abstract: The present invention relates to a method for concentrating a biological sample containing nucleic acids by using magnetic chitosan microparticles and subsequently performing a PCR reaction on the nucleic acids captured on the microparticles. The chitosan microparticles added to the biological sample at a PCR compatible pH are mechanically agitated to provide for cell lysis and simultaneous DNA capture, and then serve as a solid support for the nucleic acid template during the PCR reaction. As the chitosan microparticles are utilized for lysis and the nucleic acids do not need to be removed from the microparticles before PCR, the ease of the sample preparation procedure is dramatically improved.

Abstract: Provided herein are reagents for improving PCR accuracy.

Abstract: The invention relates to methods, compositions, devices, systems and kits as described including, without limitation, reagents and mixtures for determining the identity of nucleic acids in nucleotide sequences using, for example, sequencing by synthesis methods. In particular, the present invention contemplates the use of photoprotective mixture of compounds as imaging reagents to improve stability and storage of fluorescent compounds, including but not limited to, nucleotides with fluorescent labels.

Abstract: Provided is a method for detecting a variation of a reference sequence in a target nucleic acid region, the method comprising the steps of: performing a template-dependent nucleic acid amplification reaction for amplifying a region containing the reference sequence using, as a template, a nucleic acid containing the target nucleic acid region, in the presence of a 10 to 200 nucleotide single-stranded nucleic acid capable of hybridizing with the reference sequence in the target nucleic acid region, and examining the presence or absence of an amplified product, wherein the single-stranded nucleic acid is RNA or a chimeric nucleic acid composed of RNA and one or more different nucleic acids, wherein the single-stranded nucleic acid contains a sequence complementary to the reference sequence, and wherein the single-stranded nucleic acid has a higher complementarity to the reference sequence than to a variant sequence having a variation of the reference sequence.

Abstract: A method of sequencing a target nucleic acid polymer by (a) modifying a target nucleic acid polymer to produce a modified nucleic acid polymer; (b) producing fragments of the modified nucleic acid polymer, wherein the fragments are attached to locations on a solid support surface (c) determining nucleotide sequences from the fragments at the locations; and (d) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the relative distances between the locations on the solid support surface.

Abstract: The invention provides methods of isolating a target nucleic acid in a sample. A primer is hybridized to the target. A polymerase and modified nucleotide resistant to nuclease degradation are used to extend the primer to create a modified polynucleotide. The sample is exposed to a nuclease, thereby isolating the modified polynucleotide. Optionally, the target nucleic acid may be further protected by binding a protein in a sequence specific manner to one end of the target nucleic acid to create a protected target nucleic acid resistant to nuclease degradation. Thus, after exposing the sample to a nuclease, the modified polynucleotide and protected target nucleic acid are isolated.

Abstract: Provided herein are methods for the collection and amplification of circulating nucleic acids from a non-celluar fraction of a biological sample. Circulating nucleic acids are extracted from the non-cellular fraction and are circularized to generate single-stranded nucleic acid circles, which are then subsequently amplified by rolling circular amplification using random primers to produce an amplified library. Devices for the collection of a non-cellular fraction from a biological sample are also provided. The device includes a filtration membrane and a dry solid matrix, which is in direct contact with the filtration membrane.

Abstract: The disclosure is directed to methods, kits, and compositions for amplifying and detecting a human immunodeficiency virus-1 (HIV-1) in a sample, which comprises a variety of combinations of forward oligonucleotide primers, reverse oligonucleotide primers, and oligonucleotide probes.