Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.

Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.

In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.

In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.

Computer software products, methods, and systems are described which provide functionality to a user conducting experiments designed to detect and/or identify genetic sequences and other characteristics of a genetic sample, such as, for instance, gene copy number and aberrations thereof. The presently described software allows the user to interact with a graphical user interface which depicts the genetic information obtained from the experiment. The presently disclosed methods and software are related to bioinformatics and biological data analysis. Specifically, provided are methods, computer software products and systems for analyzing and visually depicting genotyping data on a screen or other visual projection. The presently disclosed methods and software allow the user conducting the experiment to differentially filter complex genetic data and information by varying genetic parameters and removing or highlighting visually various regions of genetic data of interest (CytoRegions). These differential filters may be applied by the user to the entire set of genetic data and/or only to the specific CytoRegions of interest.

The present invention provides a method of assessing whether an individual is at high risk or low risk of inflammatory bowel disease (IBD) progression by determining the expression level of two or more genes in a whole blood sample. Also provided are methods for treating IBD in an individual who is determined to be at high risk or low risk for IBD progression, and kits for assessing whether an individual is at high risk or low risk for IBD progression. Arrays, and methods of providing arrays, of patient-identified selected gene expression products from a whole blood sample of a patient are also provided.

The present invention discloses a method of real-time quantification of a target nucleic acid in a sample by constructing a reference table of copy number vs. designated parameter from reference samples which sharing the same nucleic acid sequences with the target nucleic acid. After that, obtain the designated parameter of the target sample and get the copy number by looking up and interpolating to the reference table. The object of the present invention is in particular provide methods for the quantification of the target nucleic acid which the target nucleic acid is quantified independently without comparing it to the standard controls by using a calibration curve. This invention will not only provide a new quantifying method, but will also propose a new standard operational method that eliminates the variations accompanying amplification efficiency, polymerase activity, primer concentrations, and instrument variations.

A method is used for the qualitative evaluation of real-time PCR data, where a time/PCR amplification plot of an associated sample is classified as a negative plot or as a positive plot. The method involves providing a real-time PCR amplification plot to be classified, plotting at least 20 successive amplitude values of corresponding successive PCR cycle indices of the sample. Next, a quality metric is determined, on the basis of the at least one amplitude value. A first criterion is determined by a comparison of the quality metric with a first standard value. A sequence of values is then determined, which indicates a gradient of the PCR amplification plot to be classified, and a second criterion is determined as to whether the sequence of values exceeds a second standard value. Finally, the real-time PCR amplification plot is classified as a positive plot if all the criteria given above are satisfied.

A method is used for the qualitative evaluation of real-time PCR data, where a time/PCR amplification plot of an associated sample is classified as a negative plot or as a positive plot. The method involves providing a real-time PCR amplification plot to be classified, plotting at least 20 successive amplitude values of corresponding successive PCR cycle indices of the sample. Next, a quality metric is determined, on the basis of the at least one amplitude value. A first criterion is determined by a comparison of the quality metric with a first standard value. A sequence of values is then determined, which indicates a gradient of the PCR amplification plot to be classified, and a second criterion is determined as to whether the sequence of values exceeds a second standard value. Finally, the real-time PCR amplification plot is classified as a positive plot if all the criteria given above are satisfied.

The invention relates to an optimal selection method of gene chip probes for cancer screening. The method is characterized in that the gene chip probes capable of being used for cancer screening are obtained through three stages of constructing a point mutation site (SNV) group, constructing a candidate probe group and verifying and confirming probes on the basis of nucleic acid data of a confirmed case of a selected cancer.