Abstract: Particular aspects provide methods for specific amplification of template DNA in the presence of potentially contaminating PCR products from previous amplification experiments. Particular embodiments comprise, in a first step, contacting DNA with a bisulfite solution, which sulfonates unmethylated (but not methylated) cytosines, resulting in cytosine deamination and generation of sulfonated uracil. Such sulfonation protects the template nucleic acid from being a target for the enzyme uracil-DNA-glycosylase (UNG), whereas any contaminating DNA, which contains unprotected unsulfonated or desulfonated uracils, is degraded enzymatically while the UNG is active. After UNG treatment and inactivation thereof, the sulfonated uracil bases are converted into uracil by desulfonation. Such aspects have substantial utility for decontamination of nucleic acid samples; e.g., for avoiding amplification of ‘carry over products’ in the context of DNA methylation analysis.

Abstract: The present invention is directed to the discovery of single nucleotide polymorphisms (SNPs) in the presence of metronidazole-resistant Trichomonas vaginalis. The presence of G76C, C213G, or C318A (SNP) in tvntr 4 or the presence of A238T, G427C, or T476C (SNP) in tvntr6 provides a reliable biomarker for the presence of metronidazole-resistant Trichomonas vaginalis. The present invention further provides reagents used for detecting the SNPs to screen subjects for metronidazole resistance in Trichomonas vaginalis.

Abstract: The invention relates to methods of detecting a target analyte in a biological sample using composite microsphere arrays having first and second assay locations. Preferred target analytes include nucleic acid, and more specifically, nucleic acid having one or more single nucleotide polymorphisms (SNPs).

Abstract: Disclosed herein is a method for identifying single nucleotide polymorphisms of a target nucleic acid for predicting whether a patient suffering from hepatocellular carcinoma will respond to a 5-fluorouracil (5-FU)-based combination chemotherapy. In some embodiments, biological sample derived from the patient is processed to determine the presence of a T/T genotype of rs9679162 GALNT14 gene. The presence of the above-identified genotype is an indication that the patient is responsive to the 5-FU-based combination chemotherapy.

Abstract: Methods of capturing two or more nucleic acids simultaneously from a single sample are provided. Different nucleic acids are captured through cooperative hybridization events on different subsets of particles or at different selected positions on a spatially addressable solid support. Methods of capturing one or more long nucleic acids and methods of capturing one or more nucleic acid for sequencing are also provided. Compositions, kits, and systems related to the methods are also described.

Abstract: Methods of capturing two or more nucleic acids simultaneously from a single sample are provided. Different nucleic acids are captured through cooperative hybridization events on different subsets of particles or at different selected positions on a spatially addressable solid support. Compositions, kits, and systems related to the methods are also described.

Abstract: 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.

Abstract: We have identified a new variant of ileal bile acid binding protein (IBABP), designated IBABP-L, which is a biomarker for colorectal cancer. The transcript for IBABP-L arises from an alternative start site and includes three exons that are absent in IBABP. IBABP-L also shares part of a fourth exon with IBABP. The protein encoded by IBABP-L contains a deduced 49 residue N-terminal sequence that is not found in the IBABP protein. The present invention provides methods for diagnosing colorectal cancer and other compositions and methods based on this discovery.

Abstract: The present disclosure describes the identification of single nucleotide polymorphisms (SNPs) in inflammatory diseases and uses thereof, and methods of screening for, diagnosing, identifying susceptibility to or detecting a risk of developing an inflammatory disease comprising detecting the presence or absence of at least one SNP identified in a gene associated with inflammatory disease.

Abstract: Disclosed are methods and compositions for conducting assays of samples utilizing polymerase chain reactions (“PCRs”) in the detection of serotypes of Chlamydia trachomatis capable of causing lymphogranuloma venereum (“LGV”). These assays take advantage of a deletion occurring in the cytotoxin gene locus specific to the L I, L II, and L serotypes. Each of these assays employs a first primer having a nucleotide sequence flanking one side of the deletion point and a second primer having a nucleotide sequence flanking the other side of the deletion point, wherein the first primer and the second primer are capable of hybridizing respectively to the plus strand and the minus strand of the genome of Chlamydia trachomatis during the PCR. Synthesis during the PCR of a sequence-specific amplicon containing this deletion point indicates that the sample contains nucleic acid specific to an LGV-causing serotype of Chlamydia trachomatis.

Abstract: The present invention is a novel method of determining the average DNA methylation density of a locus of interest within a population of DNA fragments.

Abstract: An isolated nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO: 1.

Abstract: The invention is directed to methods of diagnosing breast cancer, susceptibility to breast cancer, nodal metastasis of a breast cancer and screening for breast cancer in an individual in need thereof comprising detecting the presence of a loss of heterozygosity/allelic imbalance (LOH/AI) at one or more specific loci (markers) in the genome of the individual, wherein the presence of the LOH/AI at the one or more specific loci in the genome of the individual is indicative of a diagnosis of breast cancer in the individual.

Abstract: Methods are described for screening a subject for risk of Charcot-Marie-Tooth Disease Type 2A or for diagnosing Charcot-Marie-Tooth disease or a predisposition for developing Charcot-Marie-Tooth disease in a subject, by detecting the presence or absence of a mutation in the mitofusin gene in a biological sample collected from the subject. Methods are also described for detecting the presence of a genetic polymorphism associated with Charcot-Marie-Tooth Disease Type 2A in a sample of patient nucleic acid, by amplifying a mitofusin gene sequence in the patient nucleic acid to produce an amplification product; and identifying the presence of a Charcot-Marie-Tooth Disease Type 2A associated polymorphism in the amplification product.

Abstract: This specification relates to the field of molecular biology and provides novel methods and reagents for preserving and protecting the ribonucleic acid (RNA) content of samples from degradation prior to RNA isolation. This preservation may be accomplished without ultra-low temperature storage or disruption of the tissue.

Abstract: The invention provides methods, nucleic acids and kits for detecting colon cell proliferative disorders. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of and differentiation between said class of disorders, thereby enabling the improved diagnosis and treatment of patients.

Abstract: The present invention provides methods for detecting the presence of methylation at a locus within a population of nucleic acids.

Abstract: Disclosed is a method for identifying an individual who has an altered risk for developing colorectal cancer comprising detecting a single nucleotide polymorphism (SNP).

Abstract: This document provides methods and materials related to genetic markers of schizophrenia (SZ), schizotypal personality disorder (SPD), and/or schizoaffective disorder (SD), (collectively referred to herein as “schizophrenia spectrum disorders” or SSDs). For example, methods for using such genetic markers to identify an SSD (e.g., SZ) endophenotype are provided.

Abstract: An assay for a GCH1 allele and associated genotype for the screening, prediction, diagnosis, prognosis, treatment and treatment response of psychiatric, neuropsychiatric, and neurological disorders, such as schizophrenia, schizoaffective disorder and bipolar disorder, and for defining treatments of such disorders. The presence of a variant in the GCH1 gene, alone or in conjunction with a measurement of low or altered biopterin, or altered BH4 system measures, is used to screen for or diagnose subjects at high risk for developing a psychiatric, neuropsychiatric, or neurological disorders. The assay of the GCH1 genotype, with or without biopterin or a BH4 or BH4 system assay, may also be used to determine antipsychotic or mood stabilizer medication, as well as other treatments. For subjects with an impaired BH4 system, treatments to increase or normalize biopterin, BH4, or the BH4 system can also be used, such as BH4 supplementation, lithium treatment, phenylalanine treatment, or other treatments and therapies.