The invention relates generally to the THAP1 gene and mutations in this gene, as well as the THAP1 protein and mutations in this protein, that are associated with dystonia. The invention relates to the identification, isolation, cloning and characterization of the DNA sequence corresponding to the wild type and mutant THAP1 genes, as well as isolation and characterization of their transcripts and gene products. The invention further relates to methods and kits useful for detecting mutations in THAP1 that are associated with dystonia, as well as to methods and kits useful for diagnosing dystonia. The present invention also relates to therapies for treating dystonia, including gene therapeutics and protein/antibody based therapeutics.

The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.

The present invention provides compositions and methods based on genetic polymorphisms that are associated with cardiovascular diseases, particularly coronary heart disease (especially myocardial infarction) or hypertension. For example, the present invention relates to nucleic acid molecules containing the polymorphisms, variant proteins encoded by these nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and variant proteins, and methods of using the nucleic acid molecules and proteins as well as methods of using reagents for their detection.

A method is provided for probabilistically assigning a tissue of origin to a nucleic acid in a sample, e.g., DNA in a cell-free fluid sample obtained from a human subject. A hydroxymethylation profile is generated for the sample DNA and then compared across a reference data set of hydroxymethylation profile vectors, where each hydroxymethylation profile vector identifies the hydroxymethylation profile at a specific reference locus, the tissue-specific gene associated with the reference locus, and the tissue with which the gene and reference locus are associated. A tissue of origin can be probabilistically assigned to the sample nucleic acid using the results of the comparison. Other methods of use are also provided.

The invention generally relates to droplet based digital PCR and methods for analyzing a target nucleic acid using the same. In certain embodiments, methods of the invention involve forming sample droplets containing, on average, a single target nucleic acid, amplifying the target in the droplets, excluding droplets containing amplicon from the target and amplicon from a variant of the target, and analyzing target amplicons.

The present invention relates to a DNA classification method, comprising calculating the MHL value of a DNA methylation haplotype block and/or the DNA copy number variation data of a sample of interest; calculating the similarity between the MHL value of the DNA methylation haplotype block of the sample of interest DNA and the MHL value of a DNA methylation haplotype region of a respective classification label, and/or the similarity between the copy number variation data of the sample of interest DNA and the DNA copy number variation data of a respective classification label; and determining a classification for the DNA in the sample of interest by using a classifier model and based on the similarity. The present invention provides new means with good specificity and sensitivity for detection of tumors in the urogenital system.

Methods and compositions disclosed herein generally relate to methods of improving clinical and economic outcomes to address adverse effects related to anesthesia, analgesics, opioids, and inadequate pain relief. Embodiments of the invention relate to the association between genes, specific polymorphisms of genes, and non-genetic factors with inadequate pain relief and anesthesia-, analgesic, and/or opioid-related adverse effects. Embodiments of the invention can be used to determine and manage patient risk factors for development of adverse perioperative effects and can allow for personalized anesthesia and pain management for improvement of pain control and reduction of anesthesia-, analgesic-, and opioid-related adverse outcomes. These methods and compositions apply to non-surgical pain management with opioids. Therefore, patients who are genetically predisposed to risk of inadequate pain relief and/or serious side effects from anesthesia, analgesics, and/or opioids can be identified and individualized treatment plans developed for implementation by the clinician to improve clinical and economic outcomes.

Provided is a method of analyzing microhaplotypes by using a next generation sequencing (NGS). The method of analyzing microhaplotypes by using the NGS includes: (a) performing a multiplex PCR for simultaneously amplifying the microhaplotypes; (b) performing an indexing PCR by using a product of the multiplex PCR; and (c) performing the NGS by using a product of the indexing PCR.

This application provides methods and systems for paternity determination. In some embodiments, the method is a non-invasive prenatal paternity determination method, which comprises obtaining genotypes for one or more polymorphic nucleic acid targets in a genomic DNA sample obtained from an alleged father, isolating cell-free nucleic acids from a biological sample obtained from the pregnant mother comprising fetal nucleic acids. The amount of each allele of one or more polymorphic nucleic acid targets in cell-free nucleic acids are determined and informative polymorphic nucleic acid targets are identified. Next, the allele frequency of each allele of the selected informative polymorphic nucleic acid targets is measured and fetal genotypes for each selected informative polymorphic nucleic acid targets are determined based on the allele frequency. Finally, the paternity status of the fetus are determined based on the genotypes of the mother, alleged father and the fetus for the informative nucleic acid targets.

The presently disclosed subject matter relates to using a haploid inducing line (whether existing or created) and transforming the haploid line so that it encodes cellular machinery capable of editing genes. The transformed haploid inducing line is used as a parent in a cross between two plants. During pollination, the parental gametes fuse to form an embryo; and the gene editing machinery is also delivered to the embryo at this time. During embryonic development, one set of parental chromosomes are lost, and the gene editing machinery operates on the remaining set of chromosomes. Thus, at least one haploid progeny with edited genes is produced from the cross. The disclosure is also directed to methods of testing an edited haploid plant progeny for the presence of a first plant's genomic material.