Abstract: The disclosure provides a powerful new approach to dual-strand high-throughput next-generation sequencing that improves upon duplex sequencing. The method provides a novel multi-oligonucleotide adapter construct that is ligated to DNA fragments to be sequenced (e.g., genomic DNA fragments) library construction method that concatenates both strands of each DNA duplex into a linear sequence. By physically linking both strands, the products are self-sufficient to form duplex consensus. This strategy has the potential to provide 1,000-fold more accurate sequencing with minimal added cost, and could directly enhance existing products (WGS, WES, targeted panels) offered at the Genomics Platform.

Abstract: Disclosed herein are methods to improve the efficiency of absolute quantification of nucleic acid targets such as digital PCR and digital isothermal amplification, and/or reduce the amount of nucleic acid sample required to determine the absolute quantity of target sequences in the sample.

Abstract: The present disclosure provides methods for preparing a target mutant nucleic acid for subsequent enrichment relative to a wild-type nucleic acid using nucleases that have a substantially higher activity on double stranded DNA versus single stranded DNA or RNA. The present disclosure also includes methods for enriching a target mutant nucleic acid and for preparing unmethylated/methylated nucleic acids of interest for subsequent enrichment.

Abstract: Presently described are methods for enriching regions of a genome in a sample using ligation of fragmented genomic nucleic acid and amplification using repeat elements. The methods can be used for a number of applications, including genome-wide homopolymer indel detection, and enable increasing the amount of information obtained from a limited sample of genomic nucleic acid.

Abstract: The present disclosure provides methods for preparing a target mutant nucleic acid for subsequent enrichment relative to a wild type nucleic acid using nucleases that have a substantially higher activity on double stranded DNA versus single stranded DNA or RNA. The present disclosure also includes methods for enriching a target mutant nucleic acid and for preparing unmethylated/methylated nucleic acids of interest for subsequent enrichment.

Abstract: The disclosure provides novel methods, compositions, and kits that combine hybrid capture using short allele-specific probes with duplex molecular” barcoding and noise modeling within each sample to afford high accuracy sequencing of rare mutations at low cost.

Abstract: Presently described are compositions and methods for performing genome-wide enrichment of DNA microsatellites (e.g., homopolymers) containing deletions and facilitating their detection via sequencing or other downstream methodologies. Additionally, disclosed herein are compositions and methods for selecting the genomic fraction containing poly-adenine/poly-thymidine homopolymer repeats and other A:T-rich sequences of low melting temperature from the genome, so that very little sequencing is required to detect the enriched homo-polymer deletions.

Abstract: Provided herein are methods to determine the original abundance of mutant alleles of one or more barcoded target sequences following mutation enrichment and sequencing.

Abstract: The present invention is directed to methods, compositions and software for enriching low abundance alleles in a sample. It is directed in particular to the use of an excess amount of reference blocking sequence in an amplification reaction mixture in order to improve the enrichment efficiency, and reduce cycle time, of full COLD-PCR.

Abstract: This disclosure relates to compositions and methods for single-step, multi-stage amplification reactions that combine many stages of sample preparation process in a single tube reaction. The disclosed technology provides a mean of performing multiplexed nested PCR in a single vessel, without any need of purification steps, and is based on the use of three sets of primers: a pair of outer primers, a pair of inner primers that are nested within the pair of outer primers, and tail primers that are complementary to tails on the inner primers. By adjusting the temperature conditions, annealing temperatures of the primers, number of amplification cycles, and the concentrations of the outer, inner, and tail primers, it is possible to carry out multiplexed nested PCR in a single vessel.

Abstract: Disclosed herein are compositions and methods for isothermal amplification of dsDNA without the use of primers. The dis-closed compositions and methods may be used for the generation of probes used in hybrid-capture techniques that usually precede sequencing. Methods of using the probes for capturing target DNA are also provided.

Abstract: The present invention is directed to methods, compositions and reaction mixtures for multiplexing COLD-PCR/ice-COLD-PCR to enrich simultaneously several low abundance alleles (mutant target sequences) from a sample. The invention also involves COLD-PCR/ice-COLD-PCR amplification performed on DNA fragments that have different melting temperatures, and therefore different critical denaturation temperatures, in a graded temperature approach such that mutation enrichment is achieved on all diverse DNA fragments simultaneously (temperature-independent COLD-PCR or TI-COLD-PCR). The invention also involves methods for enabling identification of variant-sequence alleles in the presence of a large excess of non-variant alleles in nucleic acids without the complication of polymerase-introduced errors or other primer-introduced artifacts.

Abstract: Disclosed herein are methods to improve the efficiency of absolute quantification of nucleic acid targets such as digital PCR and digital isothermal amplification, and/or reduce the amount of nucleic acid sample required to determine the absolute quantity of target sequences in the sample.

Abstract: The present invention is directed to methods, compositions and reaction mixtures for conducting COLD-PCR, by controlling and varying a preferential denaturation time.

Abstract: This disclosure relates to compositions and methods for single-step, multi-stage amplification reactions that combine many stages of sample preparation process in a single tube reaction. The disclosed technology provides a mean of performing multiplexed nested PCR in a single vessel, without any need of purification steps, and is based on the use of three sets of primers: a pair of outer primers, a pair of inner primers that are nested within the pair of outer primers, and tail primers that are complementary to tails on the inner primers. By adjusting the temperature conditions, annealing temperatures of the primers, number of amplification cycles, and the concentrations of the outer, inner, and tail primers, it is possible to carry out multiplexed nested PCR in a single vessel.

Abstract: Compositions and methods for the radiological and immunotherapeutic treatment of cancer are provided. Metallic nanoparticles conjugated with an immunoadjuvant are dispersed within a biodegradable polymer matrix that can be implanted in a patient and released gradually. The implant may be configured as, or be a component of, brachytherapy spacers and applicators, or radiotherapy fiducial markers. The composition may be combined with marginless radiotherapy, allowing for lower doses of radiation and enhancing the immune response against cancer, including at non-irradiated sites.

Abstract: A method of detecting migration of tumor cells is provided by implanting in a region of tumor cells one or more implants having a matrix material of a biocompatible and biodegradable polymer, and a plurality of nanoparticles dispersed within the matrix material and functionalized to bind tumor cells. Nanoparticles bound to the tumor cells that have migrated out of the region can be detected by various imaging modalities. The implant can be in the shape of a brachytherapy spacer or radiotherapy fiducial maker or can be a coating on a brachytherapy spacer or fiducial marker. A method of treating cancer is provided by implanting one or more brachytherapy spacers or fiducial markers including the matrix material and an anti-cancer therapeutic agent dispersed within the matrix material.

Abstract: Provided herein are methods to determine the original abundance of mutant alleles of one or more barcoded target sequences following mutation enrichment and sequencing.

Abstract: The present invention is directed to methods, compositions and software for enriching low abundance alleles in a sample. It is directed in particular to the use of an excess amount of reference blocking sequence in an amplification reaction mixture in order to improve the enrichment efficiency, and reduce cycle time, of full COLD-PCR.

Abstract: Compositions and methods for the radiological and immunotherapeutic treatment of cancer are provided. Metallic nanoparticles conjugated with an immunoadjuvant are dispersed within a biodegradable polymer matrix that can be implanted in a patient and released gradually. The implant may be configured as, or be a component of, brachytherapy spacers and applicators, or radiotherapy fiducial markers. The composition may be combined with marginless radiotherapy, allowing for lower doses of radiation and enhancing the immune response against cancer, including at non-irradiated sites.