Affymetrix, Inc.

Metabolex, Inc.

Seer, Inc.

Prognomiq, Inc.

Applied Proteomics, Inc.

John E Blume

Alan J Williams

Omid C Farokhzad

Gregory Troiano

Jeffrey D Johnson

Xiaoyan Zhao

Michael Figa

John F Palma

Charles Garrett Miyada

William Manning

Christopher Allen Davies

Shivani Nautiyal

Yanxiang Cao

Philip Ma

Lyndal Hesterberg

Eric B Schell

Theodore Platt

Gangwu Mei

Simon Cawley

Hui Wang

Craig Stolarczyk

Tyson Clark

Matthew McLean

Marwin Ko

Anthony C Schweitzer

Hongwei Xia

Eugeni A Namsaraev

Yun-Ping Zhou

Xin Miao

Asim Siddiqui

William C Manning, Jr

Martin J Goldberg

Robert S Langer, Jr

Hope Liou

Daniel Hornburg

Damian Harris

Lisa Croner

Bruce Wilcox

Mi Yang

Francois Collin

Chinmay Belthangady

Sangtae Kim

Jeffrey Jones

Manway Liu

Ryan Benz

Athit Kao

Asim S Siddiqui

Roslyn Dillon

Margaret Donovan

Jia You

Manoj Khadka

Ehdieh Khaledian

Shadi Roshdiferdosi

This disclosure provides methods and compositions for biomolecule corona analysis of biofluids. A biofluid may be contacted with a nanoparticle to form a biomolecule corona, and the composition of the resulting corona may be analyzed. Also provided are methods of preparing a biofluid for corona analysis by serial interrogation.

Compositions, methods and systems for protein corona analysis and uses thereof

Described herein are methods such as multi-omic methods for assessing a disease such as cancer. The multi-omic methods may integrate proteomic, transcriptomic, genomic, lipidomic, or metabolomic data. The method screening diseases or disease states. Also described herein are methods for screening for diseases or disease states from biological samples. The methods may include assessing whether a nodule, mass, or cyst is cancerous.

Multi-omic assessment using proteins and nucleic acids

Compositions, methods, and systems for analyzing the protein corona are described herein, as well as its application in the discovery of advanced diagnostic tools as well as therapeutic targets.

Disclosed herein are compositions and methods for assaying for proteins and nucleic acids, in parallel.

Compositions and methods for assaying proteins and nucleic acids

Disclosed herein are methods and compositions for processing biofluid samples. Some such methods may include obtaining a biofluid sample from a subject having a disease state such as lung cancer. The biofluid sample may be contacted with a nanoparticles to adsorb proteins. The proteins may then be ionized or contacted with a detection reagent. Also disclosed herein are compositions comprising proteins coupled to a nanoparticle upon contact of the nanoparticle with a biofluid sample from a subject having a disease.

Methods of processing a biofluid sample

Disclosed herein are biomarkers associated with a disease state such as lung cancer, and methods of discovering or using biomarkers. Also disclosed herein are classifiers built on biomarkers and methods of detecting the disease state in samples from subjects. The method may include obtaining a data set that includes protein information from a biofluid sample, and may involve using a classifier to identify the sample as indicative of a healthy state, a disease state, or a comorbidity.

Lung biomarkers and methods of use thereof

Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.

Analysis of methylation using nucleic acid arrays

Disclosed are methods and compositions for detection and amplification of nucleic acids, wherein two DNA strands hybridized to an RNA strand are ligated. In one aspect, the disclosed methods include removal of an energy source, such as ATP, upon charging a ligase to form an enzyme-AMP intermediate, and then adding substrate, which results in one complete round of RNA-templated DNA ligation. In another aspect, the ligation reaction is accomplished by use of a mixture of at least two different ligase enzymes. The disclosed methods and compositions for RNA-templated DNA ligation may be particularly useful for detection of RNA sequence variants, for example RNA splice variants, and for quantitative expression analysis.

DNA ligation on RNA template

Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.

Methods and computer software for detecting splice variants

Disclosed herein are panels related to the diagnosis or recognition of colon and colorectal cancer in a subject. The disclosed panels and related methods are used to predict or assess colon tumor status in a patient. They can be used to determine nature of tumor, recurrence, or patient response to treatments. Some embodiments of the methods include generating a report for clinical management.

Protein biomarker panels for detecting colorectal cancer and advanced adenoma

Arrays for genome-wide analysis of methylation are disclosed. IN a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within cpG islands in samples from human, mouse and rat genomes.

Growing community of inventors

Sunnyvale, CA, United States of America

John E Blume