Abstract: The present invention features methods, devices, and kits for detecting expression in a patient having cancer or determining responsive of a patient having cancer to a treatment, such as irofulven. The invention further includes methods of treating a patient having cancer by administering, e.g., irofulven.

Abstract: The present disclosure is related to methods and materials for depleting unwanted RNA species from a nucleic acid sample. In particular, the present disclosure describes how to remove unwanted rRNA, tRNA, mRNA or other RNA species that could interfere with the analysis, manipulation and study of target RNA molecules in a sample.

Abstract: A tracer particle is provided. The tracer particle includes: a core structure; a nucleic acid molecule immobilized on the core structure; and a shell layer covering the core structure and the nucleic acid molecule; wherein the core structure has a first porosity, the shell layer has a second porosity, and the first porosity is greater than the second porosity.

Abstract: The present disclosure relates to methods, processes and systems for enzymatic synthesis of oligonucleotide from a single-stranded, immobilized primer in the presence of a polymerase. Using the disclosed methods single-stranded oligonucleotides can be synthesized enzymatically from a single-stranded, immobilized primer in the presence of deoxyribonucleotide triphosphates or ribonucleotide triphosphates. Dideoxyribonucleotide triphosphates, deoxyribonucleotide triphosphates with reversible terminators, or ribonucleotide triphosphates with reversible terminators can be added enzymatically to the end of the primer or its extension products. According to the disclosed method, a single-stranded primer can bind to a template such that the thus-formed double-stranded structure can allow the polymerase to extend the primer at 3? end.

Abstract: The present technology provides polynucleotide compositions and methods of using the same to detect circulating tumor DNA (ctDNA) in a patient. Kits for use in practicing the methods are also provided.

Abstract: Disclosed herein is a method of quantifying a mutant allele burden of a target gene in a subject. The method includes providing a first plasmid that includes a mutant allele sequence and an internal control sequence, and a second plasmid that includes a wild-type allele sequence and the internal control sequence, and subjecting DNA of the subject to quantitative polymerase chain reaction to measure a mutant allele expression level of the target gene, so as to determine the mutant allele burden of the target gene in the subject based on a standard curve of the mutant allele burden of the target gene created by serial dilution of the first and second plasmids.

Abstract: The present invention relates to methods of joining two or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule of each pair share a region of sequence identity. The method allows the joining of a large number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest. Kits for performing the method are also disclosed. The methods of joining DNA molecules may be used to generate combinatorial libraries useful to generate, for example, optimal protein expression through codon optimization, gene optimization, and pathway optimization.

Abstract: The invention relates to a method of estimating a nucleic acid copy number after amplification comprising the steps of providing a sample comprising nucleic acids of a to be determined number of copies; attaching variable labels to said nucleic acids; amplifying said nucleic acids with the labels with a nucleic acid duplication procedure, preferably PCR; determining amounts of amplified nucleic acid copies with a label, each amount is determined for nucleic acid copies with a different label; and providing an estimation of the nucleic acid copy number in the sample based on the determined amounts of amplified nucleic acid copies; as well as computer program products adapted for performing such methods.

Abstract: The present invention relates to the detection of a target nucleic acid sequence by a PTOCE-E (PTO Cleavage and Extension-dependent Extension) assay. The PTOCE-E assay of the present invention can reduce the non-target signal and increase the target signal as compared with the conventional PTOCE and PCE-SH methods, thereby enabling more accurate detection of the target nucleic acid sequence.

Abstract: Methods and compositions for high-throughput, single cell analyses are provided. The methods and compositions can be used for analysis of genomes and transcriptomes, as well as antibody discovery, HLA typing, haplotyping and drug discovery.

Abstract: The disclosure is directed to kits and methods for amplifying and detecting human papilloma virus (HPV) of genotype 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and/or 68 in a sample, which comprises a variety of combinations of forward oligonucleotide primers, reverse oligonucleotide primers, and oligonucleotide probes.

Abstract: This disclosure provides oligomers, combinations of oligomers, compositions, kits, uses, and methods for detecting a C1orf43 nucleic acid, such as C1orf43 mRNA, such as human C1orf43 mRNA, in a sample.

Abstract: Methods and systems described herein involve using long cell-free DNA fragments to analyze a biological sample from a pregnant subject. The status of methylated CpG sites and single nucleotide polymorphisms (SNPs) is often used to analyze DNA fragments of a biological sample. A CpG site and a SNP are typically separated from the nearest CpG site or SNP by hundreds or thousands of base pairs. Finding two or more consecutive CpG sites or SNPs on most cell-free DNA fragments is improbable or impossible. Cell-free DNA fragments longer than 600 bp may include multiple CpG sites and/or SNPs. The presence of multiple CpG sites and/or SNPs on long cell-free DNA fragments may allow for analysis than with short cell-free DNA fragments alone. The long cell-free DNA fragments can be used to identify a tissue of origin and/or to provide information on a fetus in a pregnant female.

Abstract: The invention relates to the amplification of specific target nucleic acids. The invention provides methods, reagents, and kits for carrying out such amplification via the autoligation chain reaction (ACR).

Abstract: Provided herein is reagent mixture comprising multiplexed amplification reagents and flap assay reagents for detecting, in a single reaction, mutant copies of the KRAS gene that contain any of the 34A, 34C, 34T, 35A, 35C, 35T or 38A point mutations. Methods that employ the reagent mix and kits for performing the same are also provided.

Abstract: Described herein are methods and compositions that provide highly efficient nucleic acid amplification. In some embodiments, this allows a 3-fold or greater increase of amplification product for each amplification cycle and therefore increased sensitivity and speed over conventional PCR. Modified bases can be employed in primers to provide this base-3 or greater amplification with satisfactory PCR cycle times, which are improved, as compared to those observed in the absence of modified bases.

Abstract: A microfluidic device includes a plurality of reaction wells; and a plurality of solid supports, and each of the solid supports has a reagent attached thereto. The reagent is attached to the solid support via a labile reagent/support bond such that the reagent is configured to be cleaved from the support via a cleaving operation.

Abstract: The present disclosure provides compositions, methods and systems for quantifying target sequences and identifying target sequence variants.

Abstract: The present invention relates to improved methods for epigenetic blood and immune cell counting, and respective uses and kits.

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.