University of California

Oregon Health & Science University

The Hospital for Sick Children

Other

The United States of America As Represented by the United States

Ventana Medical Systems, Inc.

Medical Research Council

University of Texas System

Lawrence Livermore National Security, LLC

Pdx Pharmaceuticals, Inc.

University of Chicago

Lawrence Berkeley National Laboratory

Joe W Gray

Daniel Pinkel

Anne Kallioniemi

Colin Conrad Collins

Olli-Pekka Kallioniemi

Donna G Albertson

Frederic Waldman

Masaru Sakamoto

Tony E Godfrey

Johanna Rommens

David Kowbel

Soo-In Hwang

Heinz-Ulrich G Weier

Mack J Fulwyler

Laleh Shayesteh

Michael S Barnes

Christophe Chefd'hotel

Thomas M Grogan

David Chafin

Karl Eric Garsha

Benjamin C Stevens

Esteban Roberts

Brian Jay Druker

Kandavel Shanmugam

Frank A Dolbeare

Franklin Ventura

Thomas Jacob

Donna Albertson

Douglas Tkachuk

Ollie-Pekka Kallioniemi

Damien Ramunno-Johnson

Gordon B Mills

Kuang Jen J Wu

Wassana Yantasee

Worapol Ngamcherdtrakul

James S Felton

Greg Hamilton

Nils W Brown

Mark G Knize

Minna M Tanner

Tothu Tania Vu

Trond Stokke

Steven M Clark

David Castro

Jingga Morry

Kristen S Kulp

Wen-Lin Kuo

Bauke Ylstra

Tomas B Hirschfeld

Terry W Alger

Steven Louis Jacques

John Eric Hanson

Douglas Hanahan

Jeffrey H Hager

Ronald H Jensen

Khalid Salaita

William J Gibb

David E Lord

John T Groves

Tania Vu

Antoine M Snijders

Haruhiko Nakamura

Xiaolin Nan

Bing Huey

Yinghui Guan

Michael F Christman

Nikki A Levin

Zuzana Tatárová

Pius Brzoska

Ye Yz Zhai

Young Hwan Chang

Erik Burlingame

Jane Fridlyand

David G Ginzinger

Richard L Segraves

Frederick Waldman

Summer Dowell

Richard M Norgren

Geoffrey Schau

Bauke Ystra

Zhi Hu

Richard M Neve

Carol Westbrook

Nicholas J Wang

Graeme Hodgson

Oriol Casanovas

Wen-lin Kuo

Laura M Heiser

Yiling Lu

Don Kania

Anguraj Sadanandam

Jane Fridyland

Paul T Spellman

Ol'li-Pekka Kallioniemi

Debopriya Das

Stanislav Volik

Pradeep M Nair

Dan Pinkel

Russell Baldocchi

Techniques and systems for translating images of biological samples stained according to a first staining technique into images representing the biological samples stained according to a second staining technique. In various implementations, the first staining technique can include a histopathological staining technique and the second staining technique can include an immunofluorescence staining technique or an immunohistochemistry staining technique.

Translation of images of stained biological material

Provided is an ex vivo system allowing for assessment of tumor and other cell responses to pluralities of agents or agent combinations using a microdose delivery microdevice implanted into an ex vivo tissue sample. The microdevice permits localized intra-tissue sample agent delivery and provides the ability to predict the drug efficacy within days after application. Systems for maintaining tissue samples ex vivo over hours to weeks are provided, which can be used to house tissue samples during exposure of the tissue to microdoses of agents applied using the delivery microdevices. Also provided are biomarkers (galectin and/or neuropilin) useful in evaluating the efficacy of agents.

Systems, devices, and methods for ex vivo assessment of responses to multiple therapeutic agents

Methods, systems, and apparatuses for detecting and describing heterogeneity in a cell sample are disclosed herein. A plurality of fields of view (FOV) are generated for one or more areas of interest (AOI) within an image of the cell sample are generated. Hyperspectral or multispectral data from each FOV is organized into an image stack containing one or more z-layers, with each z-layer containing intensity data for a single marker at each pixel in the FOV. A cluster analysis is applied to the image stacks, wherein the clustering algorithm groups pixels having a similar ratio of detectable marker intensity across layers of the z-axis, thereby generating a plurality of clusters having similar expression patterns.

Methods, systems, and apparatuses for quantitative analysis of heterogeneous biomarker distribution

Disclosed herein are nanoconstructs comprising a nanoparticle, coated with additional agents such as cationic polymers, stabilizers, targeting molecules, labels, oligonucleotides and small molecules. These constructs may be used to deliver compounds to treat solid tumors and to diagnose cancer and other diseases. Further disclosed are methods of making such compounds and use of such compounds to treat or diagnose human disease.

Cross-linked polymer modified nanoparticles

Devices, systems, reagents, and methods for the performance of multi-spectrum super resolution microscopy are disclosed.

Multispectrum super resolution microscopy

The present invention relates to DNA sequences from regions of copy number change on chromosome 20. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases.

Array-based detection of genetic alterations associated with disease

A signature of a condition of a live cell is established in an assay that allows distribution of the receptors on the cell surface in response to binding a ligand. The receptors can be optically detected and quantified to provide a value for the condition, Test drugs can be screened for therapeutic potential in the assay: a potentially efficacious drug is identified by an ability to modulate an established signature. The receptor distribution signature can be corroborated with an mRNA expression profile of several genes, indicating, for example, metastasis.

Spatial biomarker of disease and detection of spatial organization of cellular receptors

Herein is described the use of a collection of 50 breast cancer cell lines to match responses to 77 conventional and experimental therapeutic agents with transcriptional, proteomic and genomic subtypes found in primary tumors. Almost all compounds produced strong differential responses across the cell lines produced responses that were associated with transcriptional and proteomic subtypes and produced responses that were associated with recurrent genome copy number abnormalities. These associations can now be incorporated into clinical trials that test subtype markers and clinical responses simultaneously.

Molecular predictors of therapeutic response to specific anti-cancer agents

The present invention relates to cDNA sequences from a region of amplification on chromosome 20 associated with disease. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases. The sequences can also be used for treatment of diseases.

Genes from 20q13 amplicon and their uses

This invention pertains to the discovery that an amplification of the CYP24 gene or an increase in CYP24 activity is a marker for the presence of, progression of, or predisposition to, a cancer (e.g., breast cancer). Using this information, this invention provides methods of detecting a predisposition to cancer in an animal. The methods involve (i) providing a biological sample from an animal (e.g. a human patient); (ii) detecting the level of CYP24 within the biological sample; and (iii) comparing the level of CYP24 with a level of CYP24 in a control sample taken from a normal, cancer-free tissue where an increased level of CYP24 in the biological sample compared to the level of CYP24 in the control sample indicates the presence of said cancer in said animal.

Detecting CYP24 expression level as a marker for predisposition to cancer

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Method of detecting genetic deletions identified with chromosomal abnormalities

Chromosome-specific staining to detect genetic rearrangements

Growing community of inventors

San Francisco, CA, United States of America

Joe W Gray