Abstract: A new mutation has been found in the BRCA2 gene. The mutation is a twobase pair deletion of nucleotide 6495 at nucleotides 6495 of the published cDNA sequence of BRCA2. A process for identifying a sequence variation in a BRCA2 polynucleotide sequence is disclosed. The identification process includes allele specific sequence-based techniques assays of known sequence variations. The methods can be used for efficient and accurate detection of a mutation in a test BRCA2 gene sample.

Abstract: The present invention comprises a method to identify granulocytic cell genes that are differentially expressed upon exposure to a pathogen or in a sterile inflammatory disease by preparing a gene expression profile of a granulocytic cell population exposed to a pathogen or isolated from a subject having a sterile inflammatory disease and comparing that profile to a profile prepared from quiescent granulocytic cells. The present invention is particularly useful for identifying cytokine genes, genes encoding cell surface receptors and genes encoding intermediary signaling molecules. The invention also includes methods to identify a therapeutic agent that modulates the expression of at least one gene in a granulocytic population. Genes which are differentially expressed during neutrophil contact with a pathogen, such as a virulent bacteria, or that are differentially expressed in a subject having a sterile inflammatory disease are of particular importance.

Abstract: A fluorescently labeled nucleic acid having a hairpin structure between the fluorophore label and a point of attachment to a solid phase is useful as a probe to detect nucleic acid from a sample. The solid phase quenches the fluorophore label when the hairpin structure exists but this quenching is relieved by duplex formation between probe and a sample oligonucleotide. Probes for specific nucleic acid sequences can be immobilized as arrays on solid phase surfaces for detection of multiple nucleic acid sequences simultaneously from electrophoresis gels and from aqueous solutions. These probes and methods for their use can be combined with known solid phases, particularly those used for plasmon surface detection and electron transfer detection of nucleic acid. The probes can be washed and reused, and have other advantageous features over known probe methods.

Abstract: This invention is directed to the isolated coding sequences and to the protein sequences they code for. This invention is directed to three coding sequence of the BRCA1 gene. The three coding sequences, BRCA1.sup.(omi1), BRCA1.sup.(omi2), and BRCA1.sup.(omi3) and their frequencies of occurrence are provided together with the protein sequences they code for. Another aspect of this invention is a method of determining the consensus sequence for any gene. Another aspect of the invention is a method of identifying an individual having an increased genetic susceptibility to breast or ovarian cancer because they have inherited a causative mutation in their BRCA1 gene. This invention is also related to a method of performing gene therapy with any of the isolated BRCA1 coding sequences. This invention is further related to protein therapy with BRCA.sup.(omi) proteins or their functional equivalent.

Abstract: A method and system for computationally analyzing an initial set of patterns in order to identify subsets of patterns, called clusters, that contain common sub-patterns. The patterns of the initial set of patterns are represented as linear sequences of subunits, and the common sub-patterns occur as sub-sequences of subunits within the linear sequences starting at different positions within the different linear sequences. Variations in the offset and in the sequence of subunits within a common sub-pattern are considered in the analysis. In one embodiment, an initial set of oligonucleotide sequences that are produced by various biochemical techniques are computationally analyzed to identify clusters that may correspond to a number of different binding sites for DNA-binding proteins within one or more double-stranded DNA duplexes. The method places each oligonucleotide sequence within a new cluster and calculates an initial information weight matrix for that cluster.

Abstract: A step-wise integrated process for identifying sequence variations in polynucleotide sequences is disclosed. The identification process is composed of three stages, including allele specific hybridization assays of known sequence variations (Stage I), sequence variation locating assays (Stage II), and direct sequencing (Stage III). The methods can be used for efficient and accurate detection of mutations in any test gene sample.