Abstract:
In some embodiments, the disclosure relates generally to methods, compositions, systems, apparatuses and kits for performing a first amplification reaction which includes a multiplex nucleic acid amplification reaction using a plurality of target-specific primers in the presence of polymerase under amplification conditions to produce a plurality of amplified target sequences, and sequencing at least some of the amplified target sequences using a gel electrophoresis procedure, for example Sanger sequencing.
Abstract:
The present invention provides methods, compositions, kits, systems and apparatus that are useful for determining copy number variation of one or more nucleic acids present in a sample. In some aspects, the method includes various target-specific primers that allow for the selective amplification of one or more target nucleic acids in the sample. In yet another aspect, the invention relates to determining copy number variation with respect to gene or chromosome representation of a nucleic acid in the sample. In some aspects, the method for determining copy number variation of different target nucleic acids in a sample using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including diagnosis, predictive therapeutic regimes or other therapeutic purposes.
Abstract:
A method of aligning a plurality of targets is provided. The method includes generating a plurality of targets. A third phase includes the plurality of targets. The method further includes combining a first phase, a second phase, and the third phase in a volume. The first phase, the second phase, and the third phase are substantially immiscible, and the third phase is in fluid communication with the first phase and the second phase, and the first phase, the second phase, and the third phase are operable to be in a configuration of the third phase between the first phase and the second phase in the volume.
Abstract:
The present disclosure relates generally to compositions and methods for the reuse of arrays, including microarrays. Specifically, the present disclosure discloses polynucleotide targets comprising nucleotide analogs that are not present within the probe polynucleotides immobilized on the array. The nucleotide-analog containing targets can be chemically modified to reduce their thermal stability and thus easier to remove from the array. In preferred embodiments, the disclosure relates to DNA probes hybridized to single-stranded deoxyribouridine-containing targets, the targets subsequently being chemically modified using a uracil DNA glycosylase and/or nuclease. Accordingly, the disclosure allows for the glycosylase treated, deoxyuridine-containing targets to be removed from the array by exposure to less stringent denaturing conditions than otherwise would have been required. Using less stringent denaturing conditions permits reuse of the array by reducing damage to the probe polynucleotides immobilized on the array during target removal.
Abstract:
The present disclosure describes oligonucleotide-tethered nucleotides, methods of making them, and methods of using them. The oligonucleotide-tethered nucleotides comprise, in some embodiments, a nucleotide linked to an oligonucleotide of from about 3 to about 100 nucleotides in length. These oligonucleotide-tethered nucleotides can be used to label a plurality of different types of nucleic acids in a plurality of different situations with a known oligonucleotide, which can serve as a barcode in some embodiments. The resulting oligonucleotide-labeled nucleic acids oligonucleotides can be used in a variety of nucleic acid sequencing methods.
Abstract:
The present invention provides methods, compositions, kits, systems and apparatus that are useful for isolating one or more target nucleic acid molecules from a sample. In particular, the methods generally relate to normalizing the amount of target nucleic acid molecules from a sample. In one aspect, the invention relates to purifying a primer extension product from a primer extension reaction mixture using a primer having a first primer sequence and a second primer sequence that are complementary at a first melting temperature and are not complementary at a second melting temperature. In some aspects, target nucleic acid molecules obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and template library preparation.
Abstract:
The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.
Abstract:
The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.
Abstract:
Efficient methods for production of targeted libraries from complex samples is desirable for a variety of nucleic acid analyses. Provided are methods of selectively blocking abundant targets present in a sample for preparing libraries of target nucleic acid sequences, thereby allowing for rapid production of highly multiplexed targeted libraries and analysis of low frequency sequences, including sequencing applications. Methods optionally include use of unique tag sequences. Methods comprise contacting a nucleic acid sample with a plurality of target specific primers or adapters capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; ligating the digested target amplicons or repairing the digested target amplicons; and amplifying the ligated or repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the reactions further comprise target specific primers that are not capable of completely processing the workflow, resulting in non-useful amplicon production and thereby blocking selected target sequences, e.g., those present in high abundance in the sample. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences, which are optimized for detection of low frequency target sequences.
Abstract:
Provided are methods for preparing a library of target nucleic acid sequences, as well as compositions and uses therefor. Methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; repairing the digested target amplicons; and amplifying the repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the plurality of adaptor compositions comprise a handle and a targeted nucleic acid sequence and optionally one or more tag sequences. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences. Resulting library compositions are useful for a variety of applications, including sequencing applications.