Rosetta Inpharmatics, Inc.

The Netherlands Cancer Institute

Microsoft Technology Licensing, LLC

Merck Sharp + Dohme Corp.

HongYue Dai

Peter S Linsley

Roland Stoughton

Yudong He

Christopher J Roberts

Laura Johanna Van't Veer

Mao Mao

Marc J Van De Vijver

Rene Bernards

Augustinus A M Hart

Lee Weng

A A M Hart

Aa M Hart

Laura Johanna VAN'T Veer

The present invention relates to genetic markers whose expression is correlated with breast cancer. Specifically, the invention provides sets of markers whose expression patterns can be used to differentiate clinical conditions associated with breast cancer, such as the presence or absence of the estrogen receptor ESR1, and BRCA1 and sporadic tumors, and to provide information on the likelihood of tumor distant metastases within five years of initial diagnosis. The invention relates to methods of using these markers to distinguish these conditions. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis using the statistical methods disclosed herein.

Diagnosis and prognosis of breast cancer patients

A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

Method and computer program product for reducing fluorophore-specific bias

Systems and methods for determining a weighted mean intensity

Systems and methods for evaluating the significance of differences in biological measurements

The present invention relates to genetic markers whose expression is correlated with breast cancer. Specifically, the invention provides sets of markers whose expression patterns can be used to differentiate clinical conditions associated with breast cancer, such as the presence or absence of the estrogen receptor ESR1, and BRCA1 and sporadic tumors, and to provide information on the likelihood of tumor distant metastases within five years of initial diagnosis. The invention relates to methods of using these markers to distinguish these conditions. The invention also provides methods of classifying and treating patients based on prognosis. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis using the diagnostic, prognostic and statistical methods disclosed herein.

Methods of assigning treatment to breast cancer patients

The invention provides methods for generating differential profiles having been subject to condition A vs. condition B (A vs. B) from data obtained in separately performed experimental measurements A vs. C and B vs. D. When C and D are the same, the invention provides methods for determination of systematic measurement errors or biases between different measurements carried out in different experimental reactions, i.e., cross-experiment errors or biases, using data measured for samples under the common condition and for removal or reduction of such cross-experiment errors. The invention further provides methods for generating differential profiles A vs. B from data obtained in single-channel measurements A and B.

Methods for generating differential profiles by combining data obtained in separate measurements

Statistical combining of cell expression profiles

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HongYue Dai