Disclosed are compositions, methods and kits for determining the presence, absence, amount, copy number, or other characteristics of one or more polynucleotide sequences in two or more samples and use thereof in genotyping, evaluation of copy number variation, expression analysis, determination of splice variants and fusion genes, and other genetic analyses.

The present invention provides compositions, apparatuses and methods for detecting one or more nucleic acid targets present in a sample. Methods of the invention include utilizing two or more ligation probes that reversibly bind a target nucleic acid in close proximity to each other and possess complementary reactive ligation moieties. When such probes have bound to the target in the proper orientation, they are able to undergo a spontaneous chemical ligation reaction that yields a ligation product that is directly detected or that is amplified to produce amplicons that are then detected. The present invention also provides methods to stabilize sample RNA so that degradation does not significantly affect the results of the analysis.

The present invention provides compositions, apparatuses and methods for detecting one or more nucleic acid targets present in a sample. Methods of the invention include utilizing two or more ligation probes that reversibly bind a target nucleic acid in close proximity to each other and possess complementary reactive ligation moieties. When such probes have bound to the target in the proper orientation, they are able to undergo a spontaneous chemical ligation reaction that yields a ligation product that is directly detected or that is amplified to produce amplicons that are then detected. The present invention also provides methods to stabilize sample RNA so that degradation does not significantly affect the results of the analysis.

The present invention relates to the field of pharmacogenomics and in particular to detecting the presence or absence of hypermethylated DNA. The detection of CpG methylation in marker DNA is useful for the diagnosis of cancers and the invention provides improved methods for this purpose. These improved methods allow in particular for a more sensitive detection of methylated marker DNA with high backgrounds of unmethylated marker DNA.

The present invention relates to the field of pharmacogenomics and in particular to detecting the presence or absence of hypermethylated DNA. The detection of CpG methylation in marker DNA is useful for the diagnosis of cancers and the invention provides improved methods for this purpose. These improved methods allow in particular for a more sensitive detection of methylated marker DNA with high backgrounds of unmethylated marker DNA.

Provided herein are methods and systems for detecting non-metastatic cancer in a subject, comprising measuring a total cfDNA fragment size distribution for the plurality of cfDNA nucleic acid molecules of the subject and comparing the total cfDNA fragment size distribution for the plurality of cfDNA nucleic acid molecules of the subject to the total cfDNA fragment size distribution for the plurality of cfDNA nucleic acid molecules from a healthy control.

Provided herein are methods and systems for detecting non-metastatic cancer in a subject, comprising measuring a total cfDNA fragment size distribution for the plurality of cfDNA nucleic acid molecules of the subject and comparing the total cfDNA fragment size distribution for the plurality of cfDNA nucleic acid molecules of the subject to the total cfDNA fragment size distribution for the plurality of cfDNA nucleic acid molecules from a healthy control.

Methods for analyzing chromosomal DNA, including chromatin, are provided.

Methods for analyzing chromosomal DNA, including chromatin, are provided.

A method for detecting an analyte employing a nanopore substrate positioned between first and second reservoirs by providing an indicator molecule not associated with the analyte and detecting a change in an optical signal emitted from the indicator moiety as the analyte translocates through a nanopore channel of the nanopore substrate.