The present invention provides assay systems and methods for detection of copy number variation at one or more loci and polymorphism detection at one or more loci in a mixed sample from an individual.

A method of ligating DNA molecules, wherein the DNA molecules are in a hybrid with an RNA molecule, including the steps of providing DNA molecules that are in a RNA:DNA hybrid with an RNA molecule, and ligating the DNA molecules to each other with a double strand specific ligase

A method of ligating DNA molecules, wherein the DNA molecules are in a hybrid with an RNA molecule, including the steps of providing DNA molecules that are in a RNA:DNA hybrid with an RNA molecule, and ligating the DNA molecules to each other with a double strand specific ligase

Some embodiments provided herein include methods and compositions for the detection of target ligands on an array. In some embodiments, a capture probe specifically binds to a target ligand from a sample, the location of a bead comprising the capture probe in an array is determined, and the bead is decoded to identify the capture probe and the sample. In some embodiments, a barcode is indicative of a capture probe attached to a bead; and an index is indicative of a subpopulation of beads. In some embodiments, the barcode and the index are determined by sequencing.

Some embodiments provided herein include methods and compositions for the detection of target ligands on an array. In some embodiments, a capture probe specifically binds to a target ligand from a sample, the location of a bead comprising the capture probe in an array is determined, and the bead is decoded to identify the capture probe and the sample. In some embodiments, a barcode is indicative of a capture probe attached to a bead; and an index is indicative of a subpopulation of beads. In some embodiments, the barcode and the index are determined by sequencing.

Compositions and methods for amplifying selected polynucleotides, including DNA and RNA, particularly in multiplex amplification reactions using common primers amplification. Generally, methods of the invention employ multiple steps such as template-specific hybridization, a linear amplification, partial degradation of nucleic acid, and ligation. At the end of the process the sequences of selected polynucleotides are flanked by the common sequences which can be used for exponential amplification using common primers. In some aspects the polynucleotides are associated with a barcode and the presence of the barcode is detected to measure the amount of the polynucleotide.

Compositions and methods for amplifying selected polynucleotides, including DNA and RNA, particularly in multiplex amplification reactions using common primers amplification. Generally, methods of the invention employ multiple steps such as template-specific hybridization, a linear amplification, partial degradation of nucleic acid, and ligation. At the end of the process the sequences of selected polynucleotides are flanked by the common sequences which can be used for exponential amplification using common primers. In some aspects the polynucleotides are associated with a barcode and the presence of the barcode is detected to measure the amount of the polynucleotide.

The present disclosure relates to a next generation DNA sequencing method and use for accurate and massively parallel quantification of one or more nucleic acid targets, for example in large volumes of unpurified sample material. More particularly, the present disclosure is related to a method and a kit comprising probes for detecting and quantifying genetic targets in complex samples. The disclosed embodiments includes one or more target-specific nucleic acid probes per genetic target (left probe and right probe) and a bridge oligo or bridge oligo complex.

The present disclosure relates to a next generation DNA sequencing method and use for accurate and massively parallel quantification of one or more nucleic acid targets, for example in large volumes of unpurified sample material. More particularly, the present disclosure is related to a method and a kit comprising probes for detecting and quantifying genetic targets in complex samples. The disclosed embodiments includes one or more target-specific nucleic acid probes per genetic target (left probe and right probe) and a bridge oligo or bridge oligo complex.

The invention provides compositions and methods for determining whether a subject is predisposed to the disease or condition, or for diagnosing a disease or condition, or for detecting the state of a disease or condition, by detecting the methylation state of the subject's nucleic acids. In addition, the invention provides methods for determining the methylation age of a subject or tissue from a subject or for differentiation between nucleic acids originating from different subjects or tissues. The invention further provides methods for selecting nucleic acid molecules for use in the methods of the invention.