In the present invention, a method for the qualitative genetic characterization and/or gene expression characterization of predetermined cells in a fluid sample containing such cells is provided. The inventive method for the qualitative genetic and/or gene expression characterization of predetermined cells in a fluid sample containing such cells, comprises: a) selectively extracting at least a part of the predetermined cells from the sample forming a cell suspension cs.sub.0; and b) repeating the extraction step a) n times with the same sample of step a), with n1, forming at least one cell suspension cs.sub.n; c) determining a gene expression profile gep.sub.n and/or a first copy number count cnc.sub.0 of at least one DNA and/or RNA with at least a part of the cell suspension cs.sub.0; d) determining at least one further gene expression profile gepn and/or a further copy number count cnc.sub.n of at least one DNA and/or RNA with at least a part of at least one further cell suspension csn; e) calculating the predetermined cells' gene expression profile gep(P) of at least one predetermined DNA and/or RNA by subtracting gepn from gep, and/or the predetermined cells' copy number count cnc(P) of at least one predetermined DNA and/or RNA by subtracting cncn from cnc.sub.0; and f) evaluating the qualitative genetic and/or gene expression characteristics of the predetermined cells from gep(P) and/or cnc(P).

In the present invention, a method for the qualitative genetic characterization and/or gene expression characterization of predetermined cells in a fluid sample containing such cells is provided. The inventive method for the qualitative genetic and/or gene expression characterization of predetermined cells in a fluid sample containing such cells, comprises: a) selectively extracting at least a part of the predetermined cells from the sample forming a cell suspension cs.sub.0; and b) repeating the extraction step a) n times with the same sample of step a), with n1, forming at least one cell suspension cs.sub.n; c) determining a gene expression profile gep.sub.n and/or a first copy number count cnc.sub.0 of at least one DNA and/or RNA with at least a part of the cell suspension cs.sub.0; d) determining at least one further gene expression profile gepn and/or a further copy number count cnc.sub.n of at least one DNA and/or RNA with at least a part of at least one further cell suspension csn; e) calculating the predetermined cells' gene expression profile gep(P) of at least one predetermined DNA and/or RNA by subtracting gepn from gep, and/or the predetermined cells' copy number count cnc(P) of at least one predetermined DNA and/or RNA by subtracting cncn from cnc.sub.0; and f) evaluating the qualitative genetic and/or gene expression characteristics of the predetermined cells from gep(P) and/or cnc(P).

A novel method for prediction of the degree of heterotic phenotypes in plants is disclosed. Structural variation analyses of the genome are used to predict the degree of a heterotic phenotype in plants. In some examples, copy number variation is used to predict the degree of heterotic phenotype. In some methods copy number variation is detected using competitive genomic hybridization arrays. Further, methods for optimizing the arrays are disclosed, together with kits for producing such arrays, as well as hybrid plants selected for development based on the predicted results.

A novel method for prediction of the degree of heterotic phenotypes in plants is disclosed. Structural variation analyses of the genome are used to predict the degree of a heterotic phenotype in plants. In some examples, copy number variation is used to predict the degree of heterotic phenotype. In some methods copy number variation is detected using competitive genomic hybridization arrays. Further, methods for optimizing the arrays are disclosed, together with kits for producing such arrays, as well as hybrid plants selected for development based on the predicted results.

Described herein are methods and systems for analyzing and visualizing HRM data from a double-stranded nucleic acid. The HRM data is generally characterized by a plurality of data points each including a signal value associated with the concentration of a double-stranded nucleic acid in a sample and a temperature value associated with a the temperature of the sample. Embodiments of the invention analyze the HRM curves from samples using the first negative derivative of the HRM curve or a virtual standard. The first negative derivative plot method may be used to identify the melting temperature of a homogenous double-stranded nucleic acid in a sample, as well as the presence and melting temperature of heterogeneous double-stranded nucleic acids in the sample. Data points associated with the melting temperature are plotted on a scatter plot for analysis. The virtual standard allows for visualization of HRM data across data sets.

Described herein are methods and systems for analyzing and visualizing HRM data from a double-stranded nucleic acid. The HRM data is generally characterized by a plurality of data points each including a signal value associated with the concentration of a double-stranded nucleic acid in a sample and a temperature value associated with a the temperature of the sample. Embodiments of the invention analyze the HRM curves from samples using the first negative derivative of the HRM curve or a virtual standard. The first negative derivative plot method may be used to identify the melting temperature of a homogenous double-stranded nucleic acid in a sample, as well as the presence and melting temperature of heterogeneous double-stranded nucleic acids in the sample. Data points associated with the melting temperature are plotted on a scatter plot for analysis. The virtual standard allows for visualization of HRM data across data sets.

Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.

Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.

Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) are disclosed herein. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used to attach adapters and/or linkers to target RNAs. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used in reactions, including, but not limited to, ligation reactions, amplification reactions, and sequencing reactions. Additionally, methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used for reducing and/or preventing the formation of secondary structures in target RNAs. These methods, compositions, and kits can also find use in a number of applications, for example, any application that benefits from stabilizing primary RNA structure, such as detecting and quantifying target RNAs in a sample, in the construction of small RNA libraries, in microarray and RT-qPCR applications, etc.

Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) are disclosed herein. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used to attach adapters and/or linkers to target RNAs. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used in reactions, including, but not limited to, ligation reactions, amplification reactions, and sequencing reactions. Additionally, methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used for reducing and/or preventing the formation of secondary structures in target RNAs. These methods, compositions, and kits can also find use in a number of applications, for example, any application that benefits from stabilizing primary RNA structure, such as detecting and quantifying target RNAs in a sample, in the construction of small RNA libraries, in microarray and RT-qPCR applications, etc.