Genomic Health, Inc.

Affymetrix, Inc.

Monogram Biosciences, Inc.

Rush-presbyterian-st. Luke's Medical Center

Rush University Medical Center

Maureen T Cronin

Joffre B Baker

Mark S Chee

Charles Garrett Miyada

Steve Shak

Earl A Hubbell

Robert J Lipshutz

Edward L Sheldon

Peter E Lobban

Xiaohua C Huang

Melody A Cobleigh

Stephen P A Fodor

Glenn H McGall

Michael C Kiefer

Michael Graham Walker

MacDonald S Morris

Steven Shak

Thomas R Gingeras

Jennifer Dee Tan

Stephen P Fodor

Mark O Trulson

Macdonald S Morris

Jose Baselga

Claire Robinson

Kevin L Gunderson

David J Lockhart

Wayne Cowens

Hajime Matsuzaki

Huu Minh Tran

Michael R Crager

Lisa Wodicka

Carl L Millward

Francois Collin

Michelle Smedsrud-Oval

Danny Lee

Lai Chaoqiang

Michelle Oval

Xiaohua X Huang

Mei-Lan Liu

Carmen Virgos

Nila Shah

Garry Miyada

The present invention provides gene sets the expression of which is important in the diagnosis and/or prognosis of breast cancer.

Gene expression markers for breast cancer prognosis

The invention concerns sensitive methods to measure mRNA levels in biopsied tumor tissues, including archived paraffin-embedded biopsy material. The invention also concerns breast cancer gene sets important in the diagnosis and treatment of breast cancer, and methods for assigning the most optimal treatment options to breast cancer patient based upon knowledge derived from gene expression studies.

Gene expression profiling in biopsied tumor tissues

The present disclosure provides methods for assessing a patient's cancer risk and/or recurrence risk, which methods comprise assaying, in a biological sample obtained from the gastrointestinal (GI) tract of the patient, an expression level of a risk gene. The present disclosure also provides methods involving a cancer risk/recurrence risk sequence, i.e. the V600E mutation of the BRAF gene, which is useful for assessing cancer risk and/or recurrence risk in a patient.

Methods of predicting cancer risk using gene expression in premalignant tissue

The present invention concerns prognostic markers associated with EGFR positive cancer. In particular, the invention concerns prognostic methods based on the molecular characterization of gene expression in paraffin-embedded, fixed tissue samples of EGFR-expressing cancer, which allow a physician to predict whether a patient is likely to respond well to treatment with an EGFR inhibitor.

Gene expression profiling of EGFR positive cancer

The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set. The probes in the second, third and fourth probe sets are identical to a sequence comprising the corresponding probe from the first probe set or a subsequence of at least three nucleotides thereof that includes the at least one interrogation position, except that the at least one interrogation position is occupied by a different nucleotide in each of the four corresponding probes from the four probe sets.

Arrays of nucleic acid probes for analyzing biotransformation genes

Oligonucleotide analogue arrays attached to solid substrates and methods related to the use thereof are provided. The oligonucleotide analogues hybridize to nucleic acids with either higher or lower specificity than corresponding unmodified oligonucleotides. Target nucleic acids which comprise nucleotide analogues are bound to oligonucleotide and oligonucleotide analogue arrays.

Modified nucleic acid probes

Growing community of inventors

Los Altos, CA, United States of America

Maureen T Cronin