Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two template nucleic acids are joined together by a linking molecule, such as a PEG derivative. The linked template nucleic acids is amplified, creating linked amplicons.

Abstract: Methods and apparatus providing for the isolation of an unknown mutation from a sample comprising wild type nucleic acids and mutated nucleic acids through the application of time-varying driving fields and periodically varying mobility-altering fields to the sample within in an affinity matrix.

Abstract: The invention provides apparatus for separation of particles and methods for using the apparatus. In an embodiment, the apparatus includes three arms extending radially from a central reservoir, each arm being associated with a separation electrode. At least one on the arms includes a separation medium. Using a sequence of driving and mobility-changing voltages, target particles can be separated from closely related particles within a sample. For example, single point mutations can be resolved from a sample containing predominantly wild type nucleic acids.

Abstract: Methods and apparatus for separating, concentrating and/or detecting molecules based on differences in binding affinity to a probe are provided. The molecules may be differentially modified. The molecules may be differentially methylated nucleic acids. The methods can be used in fields such as epigenetics or oncology to selectively concentrate or detect the presence of specific biomolecules or differentially modified biomolecules, to provide diagnostics for disorders such as fetal genetic disorders, to detect biomarkers in cancer, organ failure, disease states, infection or the like.

Abstract: Methods and apparatus for separating, concentrating and/or detecting molecules based on differences in binding affinity to a probe are provided. The molecules may be differentially modified. The molecules may be differentially methylated nucleic acids. The methods can be used in fields such as epigenetics or oncology to selectively concentrate or detect the presence of specific biomolecules or differentially modified biomolecules, to provide diagnostics for disorders such as fetal genetic disorders, to detect biomarkers in cancer, organ failure, disease states, infection or the like.

Abstract: The invention includes methods and apparatus for separating heteroduplexed nucleic acids from homoduplexed nucleic acids having similar sequences and being at a much higher concentration. The heteroduplexed nucleic acids may be separated through the application of a time varying driving field and a time-varying mobility field to a sample of heteroduplexed and homoduplexed nucleic acids in a separation medium. Once the heteroduplexed nucleic acids are isolated and recovered, it is straightforward to analyze the sequences of the heteroduplexed nucleic acids, e.g., using sequencing or hybrid assays.

Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two template nucleic acids are joined together by a linking molecule, such as a PEG derivative. The linked template nucleic acids is amplified, creating linked amplicons.

Abstract: The invention provides apparatus for separation of particles and methods for using the apparatus. In an embodiment, the apparatus includes three arms extending radially from a central reservoir, each arm being associated with a separation electrode. At least one on the arms includes a separation medium. Using a sequence of driving and mobility-changing voltages, target particles can be separated from closely related particles within a sample. For example, single point mutations can be resolved from a sample containing predominantly wild type nucleic acids.

Abstract: The invention generally relates to methods of assessing an individual's risk of developing a disease associated with accumulation of DNA mutations by determining the mutation burden in their circulating cell-free nucleic acid relative to a reference sequence. The invention further relates to establishing a score indicative of the individual's risk by assessing the individual's mutation burden against a mutation burden continuum containing various thresholds associated with different degrees of risk. The reference sequence and the continuum may be constructed from a variety of sources. In certain aspects, methods of the invention relate to compilation of a database of mutation burdens for individuals along with population characteristics for each individual.

Abstract: The invention provides apparatus for separation of particles and methods for using the apparatus. In an embodiment, the apparatus includes three arms extending radially from a central reservoir, each arm being associated with a separation electrode. At least one on the arms includes a separation medium. Using a sequence of driving and mobility-changing voltages, target particles can be separated from closely related particles within a sample. For example, single point mutations can be resolved from a sample containing predominantly wild type nucleic acids.

Abstract: Particles may be injected into a matrix for concentration by scodaphoresis using a quadrupole injection field. Particles may be injected from two or more sample chambers simultaneously. Particle injection may be performed simultaneously with performing scodaphoresis. In some embodiments the particles are concentrated into a well containing fluid. The well can extend out of a plane of the matrix. Altering the relative phases of components of a scodaphoresis field permits concentration of selected particles and exclusion of other particles. Scodaphoresis methods may be applied to DNA, other bio-molecules and other particles.

Abstract: The invention includes methods and apparatus for isolating and recovering mutations, especially rare and unknown mutations, without amplifying the sample. In particular, using the disclosed methods, it is possible to separate heteroduplexed nucleic acid strand pair from homoduplexed nucleic acid strand pairs having similar sequences and being at a much higher concentration. Once the heteroduplexed nucleic acids are isolated and recovered, it is straightforward to analyze the sequences of the heteroduplexed nucleic acids, e.g., using sequencing or hybrid assays.

Abstract: Methods and apparatus for separating, concentrating and/or detecting molecules based on differences in binding affinity to a probe are provided. The molecules may be differentially modified. The molecules may be differentially methylated nucleic acids. The methods can be used in fields such as epigenetics or oncology to selectively concentrate or detect the presence of specific biomolecules or differentially modified biomolecules, to provide diagnostics for disorders such as fetal genetic disorders, to detect biomarkers in cancer, organ failure, disease states, infection or the like.

Abstract: Particles may be injected into a matrix for concentration by scodaphoresis using a quadrupole injection field. Particles may be injected from two or more sample chambers simultaneously. Particle injection may be performed simultaneously with performing scodaphoresis. In some embodiments the particles are concentrated into a well containing fluid. The well can extend out of a plane of the matrix. Altering the relative phases of components of a scodaphoresis field permits concentration of selected particles and exclusion of other particles. Scodaphoresis methods may be applied to DNA, other bio-molecules and other particles.

Abstract: Methods and apparatus for separating, concentrating and/or detecting molecules based on differences in binding affinity to a probe are provided. The molecules may be differentially modified. The molecules may be differentially methylated nucleic acids. The methods can be used in fields such as epigenetics or oncology to selectively concentrate or detect the presence of specific biomolecules or differentially modified biomolecules, to provide diagnostics for disorders such as fetal genetic disorders, to detect biomarkers in cancer, organ failure, disease states, infection or the like.

Abstract: The invention provides apparatus for separation of particles and methods for using the apparatus. In an embodiment, the apparatus includes three arms extending radially from a central reservoir, each arm being associated with a separation electrode. At least one on the arms includes a separation medium. Using a sequence of driving and mobility-changing voltages, target particles can be separated from closely related particles within a sample. For example, single point mutations can be resolved from a sample containing predominantly wild type nucleic acids.

Abstract: Particles may be injected into a matrix for concentration by scodaphoresis using a quadrupole injection field. Particles may be injected from two or more sample chambers simultaneously. Particle injection may be performed simultaneously with performing scodaphoresis. In some embodiments the particles are concentrated into a well containing fluid. The well can extend out of a plane of the matrix. Altering the relative phases of components of a scodaphoresis field permits concentration of selected particles and exclusion of other particles. Scodaphoresis methods may be applied to DNA, other bio-molecules and other particles.

Abstract: Methods and apparatus for separating, concentrating and/or detecting particles are disclosed. The particles are enriched within a separation medium by binding to an immobilized affinity agent. Contaminants and/or undesired particles are washed off the separation medium. The affinity agent is mobilized or the interaction between the particles and the immobilized affinity agent is disrupted. SCODA fields are applied within the medium to separate, concentrate and/or detect a target particle.

Abstract: Methods and apparatus for separating, concentrating and/or detecting molecules based on differences in binding affinity to a probe are provided. The molecules may be differentially modified. The molecules may be differentially methylated nucleic acids. The methods can be used in fields such as epigenetics or oncology to selectively concentrate or detect the presence of specific biomolecules or differentially modified biomolecules, to provide diagnostics for disorders such as fetal genetic disorders, to detect biomarkers in cancer, organ failure, disease states, infection or the like.

Abstract: Methods and apparatus for concentrating particles may be applied, for example, to concentrating DNA, RNA, proteins and the like. Proteins may be pre-treated to facilitate concentration by scodaphoresis. The pre-treatment may comprise, for example, heating or chemical treatment to denature and/or apply a net charge to the protein, binding handle particles to the protein and combinations thereof. High-conductivity samples may be subjected to a conductivity-reduction step to facilitate electrical injection of target particles into scodaphoresis media. The conductivity-reduction step may comprise a buffer exchange process or a salt extraction process, for example. Methods and apparatus can allow two or more different types of target particles to be extracted from the same sample and separately concentrated. These various aspects may be applied individually or in any combination.