Methods and oligonucleotide reagents for identification of bacteria by high resolution melting (HRM) analysis are described. In particular, the invention relates to HRM analysis of hypervariable bacterial genomic DNA of the internal transcribed spacer (ITS) region for fingerprinting eubacterial pathogens.

Devices, systems, and methods for automatic genotyping obtain high-resolution melt data from a test sample defining a melting curve for a target nucleic acid in the test sample; obtain high-resolution melt data from a control sample defining a melting curve for a wild type of the target nucleic acid in the control sample; calculate melting curve derivatives of the melting curves for the test sample and the control sample, respectively, wherein each melting curve derivative represents a negative derivative of a fluorescence emitted from a nucleic acid sample as a function of temperature affecting nucleic acid denaturation; calculate parameters defining differences between features of the test sample and the control sample melting curve derivatives; and assign a genotype to the test sample based on a comparison of the calculated parameters to predetermined thresholds and boundaries defining genotypes.

A method of measuring immunocompetence is described. This method provides a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells.

In a method for comparative analysis, the expression levels of the target miRNAs in each body fluid sample are corrected using the expression level(s) of a correcting endogenous miRNA(s) that is/are simultaneously measured with the expression levels of the target miRNAs in the sample. As the correcting endogenous miRNA(s), one or more miRNAs selected from specific 10 kinds of correcting endogenous miRNAs is/are used. Comparative analysis of target miRNAs among body fluid samples can be carried out more accurately than by conventional techniques.

A method for at least one of characterizing, diagnosing, and treating an endocrine system condition in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the endocrine system condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the endocrine system condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.

The present invention provides a low-frequency mutation enrichment sequencing method for free target DNA in plasma, comprising plasma DNA extraction and library construction, general library TT COLD PCR amplification enrichment, probe enrichment capture, PCR and sequencing of captured products, and positive and negatice double-strand error-correction low-frequency information analysis.

Described herein are improved methods, compositions, and kits for analysis of minimal residual solid tumor.

A method for linking a natural product and gene cluster is disclosed. In some embodiments, monomers of natural products are predicted from a gene sequence. In other emboidments, monomers of natural products are predicted from a chemical structure of a natural product. In another embodiment, monomers predicted from gene sequences are aligned with monomers predicted from chemical structures.

Disclosed herein are methods of detecting, predicting or monitoring a status or outcome of a transplant in a transplant recipient.

Measuring of the binding of a transcription factor (using, for example, chromatin immunoprecipitation) according to the present invention is provides an improved marker for a disease. These markers can be used in diagnostics for diseases where a transcription factor binding event plays a role. Additionally, they can be used to adjust disease risk profiles for healthy individuals as with typical genetic variants.