Leland Stanford Junior University

Maximilian Diehn

Arash Ash Alizadeh

David M Kurtz

Stephen R Quake

Michael F Clarke

Aaron M Newman

Piero D Dalerba

Jianbin Wang

Huiping Liu

Anne A Leyrat

Tomer Kalisky

Peter G Maxim

Billy W Loo, Jr

Neethan A Lobo

Eric Johnston

Scott V Bratman

Jacob J Chabon

Michael Rothenberg

Daniel M Klass

Mohammad Shahrokh Esfahani

Anne Leyrat

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

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 for diagnosis and prognosis of disease by analyzing expression of a set of genes obtained from single cell analysis. Classification allows optimization of treatment, and determination of whether on whether to proceed with a specific therapy, and how to optimize dose, choice of treatment, and the like. Single cell analysis also provides for the identification and development of therapies which target mutations and/or pathways in disease-state cells.

Methods and systems for analysis of single cells

Single cell gene expression for diagnosis, prognosis and identification of drug targets

Improved 4D imaging reconstruction is provided for a freely breathing patient. 3D patient images from an imaging dataset are binned according to respiratory displacement or phase. The bins are defined by ranges, so every image in the raw 3D data set is included in a bin. Since binning in this manner often results in two or more images per bin, the 4D reconstruction is determined by selecting one 3D image from each bin at each patient position. This selection is performed so as to maximize the anatomical similarity of 3D images at adjacent patient positions. In cases where the 3D images include multiple slices, a 2D comparison of the closest slices can be used to determine anatomical similarity of the 3D images.

4D anatomically based image selection procedure for medical imaging

Growing community of inventors

San Carlos, CA, United States of America

Maximilian Diehn