Provided are devices, systems, and methods for the identification, quantification, and profiling of microscopic organisms. The methods for the identification, quantification, and profiling of microscopic organisms include, for example, the selective enrichment of microscopic organisms from a heterogeneous sample; subsequent loading of the microscopic organisms into microfluidic channels or reaction chambers; direct amplification of nucleic acids from single, isolated microscopic organisms; and examination of amplification products using digital High Resolution Melting (HRM) analysis.

Provided are devices, systems, and methods for the identification, quantification, and profiling of microscopic organisms. The methods for the identification, quantification, and profiling of microscopic organisms include, for example, the selective enrichment of microscopic organisms from a heterogeneous sample; subsequent loading of the microscopic organisms into microfluidic channels or reaction chambers; direct amplification of nucleic acids from single, isolated microscopic organisms; and examination of amplification products using digital High Resolution Melting (HRM) analysis.

Described are methods of analyzing cell free DNA based on combining analysis of cfDNA methylation with analysis of the cfDNA nucleosome footprint and/or with analysis of cfDNA copy number alteration. The diagnostic performance of these methods, in particular relating to early or earlier stage diseases or disorders, is increased compared to the diagnostic performance of the individual cfDNA analysis methods.

Described are methods of analyzing cell free DNA based on combining analysis of cfDNA methylation with analysis of the cfDNA nucleosome footprint and/or with analysis of cfDNA copy number alteration. The diagnostic performance of these methods, in particular relating to early or earlier stage diseases or disorders, is increased compared to the diagnostic performance of the individual cfDNA analysis methods.

Information is stored in existing DNA through an iterative process of creating a break in dsDNA and adding new DNA by repairing the break with a homologous repair template. The order and sequence of DNA sequences added to the breaks in the dsDNA can encode binary data. By using a context-dependent encoding scheme, three unique homologous repair templates can encode an unbounded number of bits. When the existing DNA is in a cell, the changes are heritably passed to subsequent generations of the cell. Synthesis of the homologous repair templates may be under the control of a promoter and operator. Intra- or extra-cellular signals may regulate the synthesis of homologous repair templates.

Information is stored in existing DNA through an iterative process of creating a break in dsDNA and adding new DNA by repairing the break with a homologous repair template. The order and sequence of DNA sequences added to the breaks in the dsDNA can encode binary data. By using a context-dependent encoding scheme, three unique homologous repair templates can encode an unbounded number of bits. When the existing DNA is in a cell, the changes are heritably passed to subsequent generations of the cell. Synthesis of the homologous repair templates may be under the control of a promoter and operator. Intra- or extra-cellular signals may regulate the synthesis of homologous repair templates.

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.

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.

The present invention relates to methods and systems for the analysis of nucleic acids present in biological samples, and more specifically, relates to clustering melt curves derived from high resolution thermal melt analysis performed on a sample of nucleic acids, the resulting clusters being usable, in one embodiment, for analyzing the sequences of nucleic acids and to classify their genotypes that are useful for determining the identity of the genotype of a nucleic acid that is present in a biological sample.

The present invention relates to methods and systems for the analysis of nucleic acids present in biological samples, and more specifically, relates to clustering melt curves derived from high resolution thermal melt analysis performed on a sample of nucleic acids, the resulting clusters being usable, in one embodiment, for analyzing the sequences of nucleic acids and to classify their genotypes that are useful for determining the identity of the genotype of a nucleic acid that is present in a biological sample.