Abstract: The present disclosure provides methods and systems for various uses of cell-free nucleic acid (cfNA). Functional typing of cfNA fragmentation patterns may be utilized in the non-invasive detection, diagnosis, and monitoring of disease. One embodiment may determine a stage of cancer in a subject, the progression of cancer in a subject, or the responsiveness to treatment of a cancer in a subject. Another embodiment disclosed herein may include sequencing-free diagnostic methods.

Abstract: The disclosure describes novel systems, methods, and compositions for the manipulation of nucleic acids in a targeted fashion. The disclosure describes non-naturally occurring, engineered CRISPR systems, components, and methods for targeted modification of nucleic acids such as DNA. Each system includes one or more protein components and one or more nucleic acid components that together target nucleic acids.

Abstract: Disclosed herein is a clear cell renal cell carcinoma (ccRCC) biomarker set. Also disclosed herein is a detection system using the biomarker set disclosed herein, methods of determining whether a subject has or shows recurrence of clear cell renal cell carcinoma, method of determining whether a renal mass sample is benign or malignant, method of detecting response of a subject to systemic treatment, and a kit for carrying out the same.

Abstract: Methods, compositions and kits are provided to amplify an amount of genomic methylated DNA that can be subsequently analyzed and/or sequenced. It has particular use with small amounts of DNA, including, but not limited to cell free DNA samples. In some embodiments, the ratio of polymerase and methyltransferase is controlled in order to provide maximum yields. In some embodiments, a dual primase/polymerase is used.

Abstract: Disclosed are gene signatures and methods for predicting the recurrence of prostate cancer in prostatectomized subjects. Other objectives of the invention are assay devices and kits for determining the expression levels of specific gene sets correlated to prostate cancer recurrence.

Abstract: The present invention provides detection systems and methods for detection of loci and genomic regions in a sample, including mixed samples, using hybridization to an array.

Abstract: The present invention is directed to kits for identifying the presence of one or more target nucleotide sequences in a sample that involve a ligation and/or polymerase reaction. In some embodiments, the ligation products formed in the ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more target nucleotide sequences in the sample is identified based on the detection.

Abstract: The present invention relates to the selection of patients with enhanced antipsychotic treatment efficacy with iloperidone based on a patient's genotype at one or more single nucleotide polymorphism (SNP) loci and to treatment of such patients based upon the identification of their genetic information.

Abstract: Methods of detecting a leak from a subarray of a microarray chip, kits of components that facilitate leak detection, and microarray chips configured for leak detection are disclosed herein. The methods include positioning, within the given subarray, a sample solution, which includes dissolved sample molecules (DSMs) that define a dissolved sample oligonucleotide sequence and dissolved leak detection molecules (DLDMs) that define a predetermined dissolved leak detection oligonucleotide sequence. The methods also include detecting the DLDMs within a region of the microarray chip that is external the given subarray. The kits of components include the microarray chip and DLDMs. The microarray chips includes a plurality of subarrays and a leak detection region that is at least partially external the plurality of subarrays.

Abstract: Provided herein, inter alia, are improved methods for detecting analytes, including proteins and nucleic acids. In some instances, the analytes are detected in complex matrices such as serum.

Abstract: Methods are provided for evaluating tumor cell spheroids in a three-dimensional microfluidic device by determining changes in the relative levels of live cells and dead cells in aliquots cultured under different conditions. Methods are also described for allowing ex vivo recapitulation of the tumor microenvironment such that the in vivo effectiveness of a test compound in treating tumor tissue may be predicted.

Abstract: The present disclosure provides methods and systems for various uses of cell-free nucleic acid (cfNA). Functional typing of cfNA fragmentation patterns may be utilized in the non-invasive detection, diagnosis, and monitoring of disease. One embodiment may determine a stage of cancer in a subject, the progression of cancer in a subject, or the responsiveness to treatment of a cancer in a subject. Another embodiment disclosed herein may include sequencing-free diagnostic methods.

Abstract: Provided herein are methods, compositions, and kits for the detection of immune cell clonotypes and immune cell analytes within a biological sample.

Abstract: Disclosed are extended and/or branched oligonucleotide capture probe assemblies for use in spatial transcriptomics systems, and methods for making the capture probe assemblies.

Abstract: A method for identifying a group of single-stranded oligonucleotides for self-assembly into a double-stranded polynucleotide, the group comprising a plurality of overlapping complementary oligonucleotides, wherein each overlap between complementary oligonucleotides is selected to have a melting temperature (Tm) that differs from the melting temperatures of all other overlapping complementary oligonucleotides in the group.

Abstract: The invention is a method of predicting response to therapy in a colorectal cancer patient, the method comprising measuring tumor genetic heterogeneity via analysis of circulating tumor DNA from a patients sample.

Abstract: Kits for detecting analyte polynucleotides and an internal control in a sample. Included in the kit are an internal control polynucleotide and amplification reagents to co-amplify a first analyte polynucleotide and the internal control. Also included are first and second hybridization probes, each having a label indistinguishable from the other. The probes are respectively capable of hybridizing with a first analyte amplicon and an internal control amplicon. The first and second labels are indistinguishable homogeneous labels.

Abstract: Methods and systems are provided for differentiating between cancer variants and somatic variants originating from hematopoietic cells in a cell free DNA sample. In some embodiments, the cancer variants can be distinguished from somatic variants originating from hematopoietic cells based on fragment size distribution.

Abstract: A method of ctDNA library construction and sequencing data analysis for simultaneously detecting multiple common mutations in liver cancer. The library construction method and sequencing data analysis process have the following advantages: 1. Simultaneous detection of multiple mutation forms in liver cancer without capturing; 2. Suitable for efficient capture of ultra-small target regions; 3. The library may support 10-20 tests; 4. Ligate the DNA barcode to the starting ctDNA molecule during the library construction process, and cooperate with the biological information analysis process to achieve high specific detection of low-frequency mutations in ctDNA; 5. The library is usable for PCR hot spots detection and sequencing by a capture method at the same time, the added DNA barcode may effectively filter out false positive mutations and achieve high-specificity sequencing based on duplex.

Abstract: The invention relates in particular to a method for detecting and/or quantifying cell-free DNA from a sample of biological fluid of a patient of interest, comprising at least: (i) a step of extracting cell-free DNA from a sample of biological fluid to which at least one effective quantity of a first exogenous DNA fragment having 50-2000 base pairs, preferably 50-200 base pairs, preferably 60-160 base pairs, even more preferably 70-150 base pairs and better still 80-140 base pairs (ICE), is added; (ii) a step of amplifying and quantifying the cell-free DNA extracted in step (i) and the exogenous DNA fragment ICE; and (iii) a step of standardising the amount of cell-free DNA extracted, comprising the calculation of a first ratio (Grewis) of the number of copies of cell-free DNA to the number of copies of the first fragment of exogenous DNA (ICE), and the uses thereof for the purpose of diagnosis, prognosis or theragnosis, or for monitoring the progress of a specific physiological state of a patient of interest