Leland Stanford Junior University

The United States Government As Represented by the Department of Veterans Affairs

Michael P Snyder

Xin Wang

Xiyan Li

Konrad Karczewski

Ting Wang

Carlos Daniel Bustamante

Atul J Butte

Wing H Wong

Robert Tibshirani

Euan A Ashley

Philip S Tsao

Nicholas Johnson

Joel T Dudley

Frederick E Dewey

Matthew Thomas Wheeler

Sophia Miryam Schüssler-Fiorenza Rose

J Michael Cherry

Wenyu Zhou

Tejaswini Mishra

Kegan Moneghetti

Hua Tang

Liang Liang

Alessandra Breschi

Jennifer Li-Pook Than

Jingga Inlora

Chao Jiang

Francois Haddad

Xinyue Zhang

Sai Zhang

Alan Boyle

Kevin Contrepois

Samson Mataraso

Julie Park

Heather Hall

Rajanala Samyak

Trevor Hastie

Dalia Perelman

Jingjing Li

Eurie Hong

Cuiping Pan

A collector device of environmental exposure is provided. This device may be used to collect and, after technical upgrade, monitor environmental exposure in personal and stationary settings. By coupling with advanced genomic analysis and chemical analysis technologies, the device and its accompanying methodology are capable of detecting environmental agents of diverse nature, many of which could pose health risks if going unaware of or uncontrolled. This type of information provides much needed clues to reconstruct and pinpoint the course of disease etiology at both personal and epidemic scales. By combining personal exposome and personal omics analyses, we can recapitulate with the intention to then prescribe treatment plans with unprecedented precision.

Exposome tracker for environmental health

Methods to compute gestational age and time to delivery utilizing temporal alignment methods and applications thereof are described. Generally, systems utilize analyte measurements collected at one or more time points to determine a gestational age and time to delivery, which can be used as a basis to perform interventions and treat individuals. Computational models trained utilizing temporal alignment of analyte measurements can be used to determine gestational age and time to delivery.

Systems and temporal alignment methods for evaluation of gestational age and time to delivery

Processes to identify a subset of trait-related genes and classify individuals are described. Generally, systems generate classification models which are used to identify the subset of trait-related genes and classify individuals. The classification models are also used in various applications, including developing research tools, performing diagnostics, and treating individuals.

Processes for genetic and clinical data evaluation and classification of complex human traits

Methods to compute glycemia tests and applications thereof are described. Additional methods to compute risk of atherosclerotic cardiovascular disease and applications thereof are described. Generally, systems utilize analyte measurements to determine a glycemic status or cardiovascular disease risk, which can be used as a basis to treat individuals.

Methods for evaluation and treatment of glycemic dysregulation and atherosclerotic cardiovascular disease and applications thereof

Collector device of environmental exposure for biotic and abiotic agents

Classification of individuals based on their glycemic pattern and applications thereof are described. Generally, systems utilize continuous glucose monitoring data to determine glycemic pattern variability, which can be used as a basis to classify and treat individuals.

Methods for evaluating glycemic regulation and applications thereof

Methods of screening cancerous cells for nutritional weaknesses and methods of treating cancer nutritionally are disclosed. Certain cancers depend on being supplied with one or more nutrients that are non-essential for normal cells. In particular, the invention relates to methods of treating cancer by identifying nutritional weaknesses of cancer cells and using nutritional therapy to suppress cancer by putting a subject on a diet that deprives cancerous cells of a nutrient needed for cancer proliferation and growth. Nutritional therapy can be used to enhance the effectiveness of current cancer treatments.

Nutritional treatment for cancer

In an embodiment of the present invention, three novel human reference genome sequences were developed based on the most common population-specific DNA sequence ('major allele'). Methods were developed for their integration into interpretation pipelines for highthroughput whole genome sequencing.

Systems and methods for interpreting a human genome using a synthetic reference sequence

Measuring of the binding of a transcription factor (using, for example, chromatin immunoprecipitation) according to the present invention is provides an improved marker for a disease. These markers can be used in diagnostics for diseases where a transcription factor binding event plays a role. Additionally, they can be used to adjust disease risk profiles for healthy individuals as with typical genetic variants.

Method and system for the use of biomarkers for regulatory dysfunction in disease

The present disclosure presents a unified system to phase a personal genome for downstream clinical interpretation. In an embodiment, an initial phasing is generated using public datasets, such as haplotypes from the 1000 Genomes Project, and a phasing toolkit. A local perturbation algorithm is applied to improve long range phasing. If available, a Mendelian inheritance pipeline is applied to identify phasing of novel and rare variants. These datasets are merged, followed by correction by any experimental data. This allows for full clinical interpretation of the role of a group of variants in a gene, whether inherited or de novo variants.

Method and system for phasing individual genomes in the context of clinical interpretation

Growing community of inventors

Stanford, CA, United States of America

Michael P Snyder