Abstract: The invention provides 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 nucleic acid fragment size patterns, copy number variations, mutational landscape, genomic instability, methylation status, and combinations thereof in a subject. The invention further provides methods for selecting nucleic acid molecules for use in the methods of the invention.

Abstract: Provided herein are compositions and processes that allow for sensitive detection of up to fifteen individual HPV sequences or types in a single, multiplexed test. High risk types that can be detected are HPV 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68, and 73. Processes and compositions described herein are based in part on the presence or absence of HPV nucleic acid, including HPV DNA and RNA.

Abstract: The present invention relates to cancer-associated proteins and nucleic acids that encode or bind specifically to cancer-associated proteins, which represent markers for cancer detection. Specifically, the invention provides a family of methods and compositions for detecting cancer, for example, breast cancer, in an individual using components of the U2 spliceosomal particle. A target cancer-associated protein may be detected, for example, by reacting the sample with a labeled binding moiety, for example, a labeled antibody capable of binding specifically to the protein. The invention also provides kits useful in the detection of cancer in an individual.

Abstract: Disclosed is a method for detecting one or more mismatches between a first and a second nucleic acid, the first and second nucleic acids being capable of preferentially hybridizing.

Abstract: Methods of distinguishing between neoplasms and pseudoneoplastic or hyperplastic processes are disclosed. The methods comprise first contacting DNA from cells of a tissue sample from a female individual with a cytosine-methylation specific endonuclease, generating amplified fragments of a cytosine-methylation regulatable polymorphic X chromosome gene using primers that bracket a restriction site of said cytosine-methylation specific endonuclease and a polymorphic sequence in said nucleotide sequence of the gene; generating heteroduplexes between amplified fragments and heteroduplex generators which consist of 1-5 nucleotide differences from the amplified fragments; and detecting the presence of a single species of heteroduplex or two species of heteroduplexes.