University of Utah Research Foundation

The University of North Carolina at Chapel Hill

Washington University

British Columbia Cancer Agency Branch

Biofire Defense, LLC

Bioclassifier, LLC

Philip Seth Bernard

Carl Thomas Wittwer

Charles M Perou

Luming Zhou

Virginie E Dujols

Torsten O Nielsen

David Neil Hayes

Joel S Parker

Gregory Pritham

Andrew Nobel

Elaine R Mardis

James Stephen Marron

Maggie Cheang

Miguel Martin

Eva Carrasco

Rosalia Caballero

Methods are provided for nucleic acid analysis wherein a target nucleic acid is mixed with a dsDNA binding dye to form a mixture. Optionally, an unlabeled probe is included in the mixture. A melting curve is generated for the target nucleic acid by measuring fluorescence from the dsDNA binding dye as the mixture is heated. Dyes for use in nucleic acid analysis and methods for making dyes are also provided.

Nucleic acid melting analysis with saturation dyes

Compositions and methods useful in determining the major morphological types of lung cancer are provided. The methods include detecting expression of at least one gene or biomarker in a sample at the protein or nucleic level. The expression of the gene or biomarker can be indicative of the lung tumor subtype as well as prognostic and predictive for therapeutic response. The compositions and methods provided herein are suited for analysis of gene or biomarker expression at the protein or nucleic acid level in paraffin-embedded tissues.

Molecular diagnosis and typing of lung cancer variants

Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer. Methods of the invention further include means for evaluating gene expression profiles, including microarrays and quantitative polymerase chain reaction assays, as well as kits comprising reagents for practicing the methods of the invention.

Method of classifying a breast cancer instrinsic subtype

The application describes methods for screening subjects with breast cancer to determine if the breast cancer will be responsive to a breast cancer therapy including a taxane or a taxane derivative. The application also describes methods for treating subjects with breast cancer by screening them for the likelihood of the effectiveness of treating the cancer with a therapy including a taxane or a taxane derivative and administering the therapy in subjects when it is found that a taxane or a taxane derivative is likely to be effective.

Methods of treating breast cancer with taxane therapy

The application describes methods for screening subjects with breast cancer to determine if the breast cancer will be responsive to a breast cancer therapy including an anthracycline. The application also describes methods for treating subjects with breast cancer by screening them for the likelihood of the effectiveness of treating the cancer with a therapy including anthracycline and administering the therapy in subjects when it is found that anthracycline is likely to be effective.

Methods of treating breast cancer with anthracycline therapy

Compositions and methods useful in determining the major morphological types of lung cancer are provided. The methods include detecting expression of at least one gene or biomarker in a sample. The expression of the gene or biomarker is indicative of the lung tumor subtype. The compositions include subsets of genes that are monitored for gene expression. The gene expression is capable of distinguishing between normal lung parenchyma and the major morphological types of lung cancer. The gene expression and somatic mutation data are useful in developing a complete classification of lung cancer that is prognostic and predictive for therapeutic response. The methods are suited for analysis of paraffin-embedded tissues. Methods of the invention include means for monitoring gene or biomarker expression including PCR and antibody-based detection. The biomarkers of the invention are genes and/or proteins that are selectively expressed at a high or low level in certain tumor subtypes. Biomarker expression can be assessed at the protein or nucleic acid level.

Methods for identifying and locating alterations in a nucleic acid having a known sequence are provided. The methods involve measuring the melting temperature of probe nucleic acids hybridized to a target nucleic acid. The methods take advantage of the differential dissociation temperatures of a probe from a target resulting from mismatches at different locations along the region of the target to which the probe hybridizes.

Simultaneous screening and identification of sequence alterations from amplified target

The present invention is directed to a method of analyzing at least two analytes at the same time using at least two fluorescent detecting entities. More particularly, the present invention relates to the use of fluorescently labeled hybridization probes to identify the genotypes of a nucleic acid sample at more than one locus by measuring fluorescence throughout a range of temperatures and correcting for temperature-dependent spectral overlap of the fluorescent probes.

Solution-based color compensation adjusted for temperature and electronic gains

The present invention is directed to a mutation detection kit and method of analyzing multiple loci of one or more nucleic acid sequences for the presence of mutations or polymorphisms. More particularly, the present invention relates to the use of the polymerase chain reaction (PCR) and fluorescently labeled oligonucleotide hybridization probes to identify mutations and polymorphisms based on melting curve analysis of the hybridization probes.

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Salt Lake City, UT, United States of America

Philip Seth Bernard