California Institute of Technology

Stratagene

Sidney Kimmel Cancer Center

Clarity Biosciences, Inc.

Other

University of California

Ludwig Institute for Cancer Research Limited

Stratagene California

Michael McClelland

John T Welsh

Joseph A Sorge

Miguel Angel Peinado

Rhonda J Honeycutt

Manuel Perucho

Yurij Ionov

Sergei Malkhosyan

Robert Oden Stuart

Daniel Mercola

William Wachsman

Steven Goodison

David Tarin

Igor Klacansky

Charles C Berry

Karen Arden

Jessica Wang-Rodriguez

Linda Wasserman

Thomas Trenkle

Among the methods, compositions, combinations and kits provided herein are those for determining gene expression levels in one or more cell types in heterogeneous cell samples, for identifying genes differentially expressed in different cell types, and for detecting a cell type in a sample from a subject. Also provided herein are methods, compositions, combinations and kits for determining gene expression levels in cells corresponding to phenotypes, and for identifying a phenotype of a subject by detecting differentially expressed genes.

Cell-type-specific patterns of gene expression

The present invention provides novel methods for characterizing organisms by identifying the presence, absence, size or sequence polymorphism of intronic regions. The method involves selecting intronic regions from nuclear or organellar gene sequences that are useful for differentiating between and among taxonomic groupings of organisms. Such intronic regions can be analyzed directly or after amplification in a primer extension reaction. The amplification product is then analyzed by, for example, size fractionation, nucleotide sequencing or (RFLP). Intronic regions that contain an open reading frame encoding all or a portion of a protein can be used to generate antibodies to detect the presence or absence of the protein, which indicates the presence or absence of the intronic region. Methods of detecting an organism in a sample by detecting the presence or absence of one or more intronic regions also are provided using nucleic acid based or immunological based approaches. Kits are provided for practicing the methods of the invention.

Identifying organisms by detecting intronic nucleic acid or encoded proteins

The detection of insertions and/or deletions in reiterated nucleotide sequences in tissues provides an identification of neoplastic changes that are associated with malignancy. The mutations are preferably detected by PCR based amplification of target sequences using selected primers, followed by standard analytic procedures. The detection of these mutations is useful as a diagnostic tool for cancer development and has direct application for cancer prognosis.

Identification of neoplasms by detection of genetic insertions and deletions

A method for generating a discrete set of DNA segments characteristic of a sample of a single-stranded RNA is provided.

Arbitrarily primed polymerase chain reaction method for fingerprinting genomes

Identifying organisms by detecting intronic nucleic acids

The invention provides a method of measuring the level of two or more nucleic acid molecules in a target by contacting a probe with a target comprising two or more nucleic acid molecules, wherein the nucleic acid molecules are arbitrarily sampled and wherein the arbitrarily sampled nucleic acid molecules comprise a subset of the nucleic acid molecules in a population of nucleic acid molecules; and detecting the amount of specific binding of the target to the probe. The invention also provides a method of measuring the level of two or more nucleic acid molecules in a target by contacting a probe with a target comprising two or more nucleic acid molecules, wherein the nucleic acid molecules are statistically sampled and wherein the statistically sampled nucleic acid molecules comprise a subset of the nucleic acid molecules in a population of nucleic acid molecules; and detecting the amount of specific binding of the target to the probe.

Reduced complexity nucleic acid targets and methods of using same

A rapid method for generating a set of discrete DNA amplification products characteristic of a genome as a &ldquo;fingerprint&rdquo; comprises the steps of: priming target nucleic acid of a genome or from a cellular RNA preparation with an single-stranded primer to form primed nucleic acid such that a substantial degree of internal-mismatching occurs between the primer and the target nucleic acid; amplifying the primed nucleic acid by performing at least one cycle of polymerase chain reaction amplification; and amplifying the product of step (2) by performing at least about 10 cycles of polymerase chain reaction amplification. The method is known as the arbitrarily primed polymerase chain reaction (AP-PCR) method and is suitable for the identification of bacterial species and strains, mammals and plants. The method of the present invention can identify species, cell types or tissues rapidly, and does not require knowledge of the nucleotide sequence or other molecular biology of the nucleic acids of the organisms to be identified. The polynucleotide sequence LF9.5m, associated with normal growth of ovary cells, and the polynucleotide TRT1, associated with arrested cell growth, are specifically provided.

TRT1 polynucleotides, host cells and assays

A rapid method for generating a set of discrete DNA amplification products characteristic of a genome as a 'fingerprint' comprises the steps of: priming target nucleic acid of a genome with an single-stranded primer to form primed nucleic acid such that a substantial degree of internal-mismatching occurs between the primer and the target nucleic acid; amplifying the primed nucleic acid by performing at least one cycle of polymerase chain reaction amplification; and amplifying the product of step (2) by performing at least about 10 cycles of polymerase chain reaction amplification. The method is known as the arbitrarily primed polymerase chain reaction (AP-PCR) method and is suitable for the identification of bacterial species and strains, including Staphylococcus and Streptococcus species, mammals and plants. The method of the present invention can identify species rapidly, using only a small amount of biological material, and does not require knowledge of the nucleotide sequence or other molecular biology of the nucleic acids of the organisms to be identified. Only one primer sequence is required for amplification and/or identification. The method can also be used to generate detectable polymorphisms for use in genetic mapping of animals and humans.

Arbitrarily primed polymerase chain reaction method for fingerprinting

A rapid method for generating a set of discrete DNA amplification products characteristic of a genome as a 'fingerprint' comprises the steps of: priming target nucleic acid of a genome or from a cellular RNA preparation with an single-stranded primer to form primed nucleic acid such that a substantial degree of internal-mismatching occurs between the primer end the target nucleic acid; amplifying the primed nucleic acid by performing at least one cycle of polymerase chain reaction amplification; and amplifying the product of step (2) by performing at least about 10 cycles of polymerase chain reaction amplification. The method is known as the arbitrarily primed polymerase chain reaction (AP-PCR) method and is suitable for the identification of bacterial species and strains, including Staphylococcus and Streptococcus species, mammals and plants. The method of the present invention can identify species, cell types or tissues rapidly, using only a small amount of biological material, and does not require knowledge of the nucleotide sequence or other molecular biology of the nucleic acids of the organisms to be identified. The method can also be used to generate detectable polymorphisms for use in genetic mapping of animals and humans, and be used to detect differential gene expression within tissues

A rapid method for generating a set of discrete DNA amplification products characteristic of a genome as a 'fingerprint' for typing the genome comprises the steps of: forming a polymerase chain reaction (PCR) admixture by combining, in a PCR buffer, genomic DNA and at least one structural RNA consensus primer, and subjecting the PCR admixture to a plurality of PCR thermocycles to produce a plurality of DNA segments, thereby forming a set of discrete DNA amplification products. The method is known as the consensus sequence primed polymerase chain reaction (CP-PCR) method and is suitable for the identification of bacterial species and strains, including Staphylococcus and Streptococcus species, mammals and plants. The method of the present invention can identify species rapidly, using only a small amount of biological material, and does not require knowledge of the nucleotide sequence or other molecular biology of the nucleic acids of the organisms to be identified. Only one primer sequence is required for amplification and/or identification. The method can also be used to generate detectable polymorphisms for use in genetic mapping of animals and humans.

Consensus sequence primed polymerase chain reaction method for

Growing community of inventors

Encinitas, CA, United States of America

Michael McClelland