Leland Stanford Junior University

Arash Ash Alizadeh

Maximilian Diehn

Aaron M Newman

David M Kurtz

Ronald Levy

Holbrook Kohrt

Roch Houot

Matthew J Goldstein

James Torchia

Irving L Weissman

Ravindra Majeti

Mark P Chao

Scott V Bratman

Daniel M Klass

Dan Denney

Jacob J Chabon

Mohammad Shahrokh Esfahani

Methods for creating a selector of mutated genomic regions and for using the selector set to analyze genetic alterations in a cell-free nucleic acid sample are provided. The methods can be used to measure tumor-derived nucleic acids in a blood sample from a subject and thus to monitor the progression of disease in the subject. The methods can also be used for cancer screening, cancer diagnosis, cancer prognosis, and cancer therapy designation.

Identification and use of circulating nucleic acid tumor markers

The present disclosure provides systems and methods for analyzing a mixed population of cells. In particular, the present disclosure provides systems and methods for digital cytometry of a biological sample, digital analysis of a biological sample, digital purification of a biological sample, evaluation of a disease in an individual, and prediction of a clinical outcome of a disease therapy.

Systems and methods for analyzing mixed cell populations

Methods of deconvolving a feature profile of a physical system are provided herein. The present method may include: optimizing a regression between a) a feature profile of a first plurality of distinct components and b) a reference matrix of feature signatures for a second plurality of distinct components, wherein the feature profile is modeled as a linear combination of the reference matrix, and wherein the optimizing includes solving a set of regression coefficients of the regression, wherein the solution minimizes 1) a linear loss function and 2) an L-norm penalty function; and estimating the fractional representation of one or more distinct components among the second plurality of distinct components present in the sample based on the set of regression coefficients. Systems and computer readable media for performing the subject methods are also provided.

Methods and systems for determining proportions of distinct cell subsets

Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.

Methods and systems for analyzing nucleic acid molecules

Processes and materials to detect cancer, transplant rejection, or fetal genetic abnormalities from a biopsy are described. In some cases, nucleic acid molecules, such as cell-free nucleic acids, can be sequenced, and the sequencing result can be utilized to detect sequences indicative of a neoplasm, transplant rejection, or fetal genetic abnormality. Detection of somatic variants occurring in phase and/or insertions and deletions (indels) can indicate the presence of cancer, transplant rejection, or fetal genetic abnormalities in a diagnostic scan, and a clinical intervention can be performed.

Methods for preparing nucleic acid libraries for sequencing

Disclosed herein are polynucleotide adaptors and methods of use thereof for identifying and analyzing nucleic acids, including cell-free nucleic acids from a patient sample. Also disclosed herein are methods of using the adaptors to detect, diagnose, or determine prognosis of cancers.

Identification and use of circulating nucleic acids

Methods are provided to enhance the efficacy of antibody therapy directed to tumor cells.

Methods for enhancing anti-tumor antibody therapy

Predictive biomarkers identify those patients suffering from immunoglobulin positive (Ig) B lineage malignancies that are responsive to active immunotherapy, where the active immunotherapy comprises vaccination with a tumor-specific idiotype-immunogen. It is shown herein that patient responsiveness to the idiotype-immunogen is dependent upon the sequence of the immunogen, where an immunogen having a low number of tyrosine residues in the CDR1 (herein termed CDR1-Y) regions of one or both of the immunogen heavy and light chains is predictive of a positive anti-tumor response, while a high number of CDR1 tyrosine residues (herein termed CDR1-Y) is predictive of a low anti tumor response.

Growing community of inventors

San Mateo, CA, United States of America

Arash Ash Alizadeh