Abstract: The present teachings relate to the extraction of nucleic acid from solid materials. Provided are useful compositions, methods, and kits for obtaining nucleic acids from a solid biological sample or an adhesive material having a biological material adherent or embedded within the adhesive substrate. The extracted nucleic acid can be used in downstream applications such as genotyping, detection, quantification, and identification of the source of the biological material.

Abstract: Provided herein are methods of identifying genomic region(s) predictive of an outcome of treatment with a cell therapy and/or of a phenotype of function of the cells. In some embodiments, the methods include epigenetic and/or epigenomic analyses of the cells in connection with methods for preparing engineered cells for cell therapy and/or predicting response to a cell therapy, e.g., engineered cells for cell therapy. In some embodiments, the methods include steps to assess, characterize and analyze changes or modifications in an epigenetic property of gene region or regions, such as chromatin accessibility, nucleosome occupancy, histone modification, spatial chromosomal conformation, transcription factor occupancy and/or DNA methylation. In some embodiments, the epigenetic and/or epigenomic analysis includes determining the epigenetic properties of a cell, e.g., an engineered cell for cell therapy.

Abstract: Compositions and methods for isolating new variants of known gene sequences are provided. The methods find use in identifying variants, particularly homologs, in complex mixtures. Compositions comprise hybridization baits that hybridize to gene families of interest, particularly agricultural interest, in order to selectively enrich the polynucleotides of interest from complex mixtures. Bait sequences may be specific for a number of genes from distinct gene families of interest and may be designed to cover each gene of interest by at least 2-fold. Thus methods disclosed herein are drawn to an oligonucleotide hybridization gene capture approach for identification of new genes of interest from environmental samples.

Abstract: The present invention provides methods for non-invasive determination of sex in a fetus or of Y chromosomal frequency abnormalities—indicative of aneuploidy or sex mosaicisms in a fetus—by detecting and determining the relative contribution genetic sequences from the Y chromosome in view of the percent fetal contribution in a maternal mixed sample.

Abstract: The present invention relates to a method of identifying epigenetic reprogramming. Identifying epigenetic reprogramming comprises detecting large organized heterochromatin lysine (K)-9 modified domains (LOCKs) and large DNA hypomethylated blocks in a sample containing DNA from a subject having cancer, for example, PDAC.

Abstract: The present invention relates to methods to detect an amount of DNA that originates from cells of a given type, where the sample comprising such DNA in admixture with DNA that does not originate from such cells. Such methods are based on differential methylation, at certain regions, of the DNA that originates from the given type of cells compared to the admixed DNA. Such methods have particular application in the detection, from a biological fluid from a pregnant female, of cell free DNA that originates from a foetus or the placenta of a foetus, or the detection, from a biological fluid from an individual, of cell free DNA that originates from cells of a tumour.

Abstract: The present disclosure provides gene and gene sets, the expression of which is important in the classification and/or prognosis of cancer, in particular of renal cell carcinoma.

Abstract: Provided are the use of a detection reagent for detecting the methylation of genes associated with colorectal cancer, and a kit. The kit comprises the detection reagent for detecting the methylation of genes associated with colorectal cancer.

Abstract: A method of making a noninvasive molecular control and analysis is described. The method of making the noninvasive molecular control includes, predetermining a positive control for a condition of interest, selecting a cell line with a control marker for the condition of interest, amplifying release of cfDNA from the selected cell line, isolating the released cfDNA from the selected cell line, quantifying the control marker from the isolated cfDNA, determining a volume of the control marker for addition to an isolated control plasma, isolating the control plasma from a control sample, treating the isolated control plasma with a control stabilizer, determining a volume of the control plasma to add to the volume of control marker, combining the volume of the control marker with the isolated control plasma, and analyzing a sample against the noninvasive molecular control to determine the presence or absence of a condition of interest.

Abstract: Biomarkers and methods for identifying, verifying and confirming circulating serum-based microRNAs. The microRNAs (PrognomiRs) can be used to differentiate patient's suffering from rapid progressing Parkinson's disease (PD) from slow progressing PD patients.

Abstract: The present invention relates to a system for predicting prognosis and benefit from adjuvant chemotherapy for patients with stage II and III gastric cancer, and an algorithm that can predict prognosis and chemotherapy responsiveness using quantitative analysis results of mRNA expression levels of a prognosis or chemotherapy responsiveness-related marker gene group and a reference gene group in advanced gastric cancer is developed, and can be used as supplementary information to determine a method for treating a gastric cancer patient.

Abstract: A nucleic acid-based assay of pancreatic cyst fluid is provided for differentiating between high-grade and low-grade intraductal papillary mucinous neoplasms.

Abstract: A method for obtaining a single-cell mRNA sequence, including: (1) capturing mRNA of a cell by using a cell tag carrier, and performing reverse transcription to obtain cDNA having a cell tag; (2) obtaining multiple cDNA fragments having molecular tags by using a transposase complex and a molecular tag carrier; (3) performing high-throughput sequencing; (4) performing sequence assembly according to the molecular tags to obtain the sequence of each mRNA; and (5) obtaining the sequence of all mRNAs of each single cell according to the cell tags.

Abstract: The present disclosure describes a method of treating a sample comprising cells with a process of partial lysing. Cells are exposed to a process such as bead beating that lyses some cells in the mixture. The process generates a resultant sample mixture that is suitable for both cell morphology screening and genetic screening.

Abstract: Sequencing nucleic acids can identify variations associated with presence, susceptibility or prognosis of disease. However, the value of such information can be compromised by errors introduced by or before the sequencing process including preparing nucleic acids for sequencing. Blunting single-stranded overhangs on nucleic acids in a sample can introduce deamination-induced sequencing errors. The disclosure provides methods of identifying and correcting for such deamination-induced sequencing errors and distinguishing them from real sequence variations.

Abstract: In the field of transplant rejection, identified are SNPs wherein mismatches in variants present in a recipient and donor for such SNPs are predictive of transplant outcome, wherein the SNPs represent non-HLA loci newly implicated in rejection. By the invention, transplant outcomes such as elevated risk of antibody mediated rejection, elevated risk of T-cell mediated rejection, or low risk of rejection can be predicted by analyzing mismatches between donor and recipient for the enumerated SNPs. Certain SNPs enumerated are predictive of kidney transplant outcome. The compatibility of prospective donors can be assessed for a recipient, allowing for optimized donor-recipient pairing.

Abstract: High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduces sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are sequencing adapters comprising a nondegenerate or variable length molecular barcode and compositions comprising a plurality of sequencing adapters, which can be useful for sequencing nucleic acids. Further provided are methods of using the sequencing adapters, including methods of sequencing nucleic acids, methods of identifying an error in a nucleic acid sequence, and methods of determining the number of nucleic acid molecules in a library.

Abstract: Provided herein is technology for ovarian cancer screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of ovarian cancer and sub-types of ovarian cancer (e.g., clear cell ovarian cancer, endometrioid ovarian cancer, mucinous ovarian cancer, serous ovarian cancer).

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

Abstract: Provided are methods for determining a presence of an intracranial aneurysm in a subject suspected of having an intracranial aneurysm or at risk for developing an intracranial aneurysm, or a subject in need of aneurysm monitoring. The method involves analyzing a biological sample from the subject for expression of a combination of biomarkers that provide a signature of an aneurism.