Genomics and Health

One of the great motivations for understanding our genome is to improve human health outcomes. We are engaged in large-scale sequencing projects that we hope will reveal new insights into how our bodies and cells function, and we build technologies to share and display data that are used by medical researchers throughout the world.

We are also engaged in many projects relating directly to health. Researchers at the Genomics Institute are studying rare and hard-to-treat cancers, neurological conditions, and infectious pathogens with the hope of improving the potential of genomic medicine to advance human health.

Viruses and Pathogens

Pathogen Genomics

The 2019 global pandemic has made pathogen genomics a new area of priority for the Genomics Institute. We are proud that our UShER tool was used to help identify Covid-19 variants and is currently the default lineage tool used by the CDC. We are currently engaged in contracts with the state of California to make our community safer.

Mental Health

SSPsyGene

The UCSC Genomics Institute is leading a consortium to create a comprehensive catalog of 250 genes related to neurodevelopmental and psychiatric disorders, funded by the National Institute of Mental Health.

The project, “Scalable and Systematic Neurobiology of Psychiatric and Neurodevelopmental Disorder Risk Genes” (SSPsyGene), will include four collaborating data generating centers to functionally characterize the contribution of 250 genes to neurodevelopmental and psychiatric disorders in various human cell and zebrafish models. The Genomics Institute is serving as the Data Resource and Administrative Coordinating Center for the four centers. Our collaboration will result in a comprehensive phenotypic catalog across biological scales.

Cancer

Pediatric Cancer

Our Treehouse Childhood Cancer Initiative uses computational approaches to genetic data to identify less toxic or more effective treatments. We have collected data shared from more than 11,000 tumor samples and made it freely available to researchers, and we are in the process of developing a clinical and diagnostic lab to bring our research directly to patients.

Breast Cancer (BRCA)

The Genomics Institute co-founded the BRCA Exchange, a global open source resource governed by the Global Alliance for Genomics and Health. This network hosts clinical breast-cancer data contributed by geneticists from several countries, and has become the world’s largest public, open repository of information on BRCA1 and BRCA2 genetic variations and their implications for cancer risk.

RNA and Cancer / Disease

Several of our affiliate labs are studying RNA, which plays a large role in the synthesis of protein in our cells, to better understand how cancers form and develop. Angela Brooks is developing novel RNA sequencing analysis tools to study and fight cancer, Jeremy Sanford is conducting research on the role of protein-RNA interactions in cancer, Daniel Kim and Susan Carpenter are investigating the large sections of RNA that are not coded into proteins for the role they play in cancer development (Kim) and disease (Carpenter), and Olena Vaske studies tumor RNA as a readout of changes that drive cancer. Their research could lead to better cancer detection and treatments.

Cancer Data Visualization

Genomics Institute Associate Director Josh Stuart co-led the Pan-Cancer working group for the Cancer Genome Atlas project (TCGA) that published genomic and molecular data characterizing 33 different types of cancer from more than 10,000 patients. His lab also developed the UCSC Tumor Map, an interactive browser to help researchers visualize the data and hopefully diagnose rare diseases and cancers.

Development and Regenerative Medicine

Braingeneers

We are collaborating with neuroscience faculty at UC San Francisco in an ambitious project to learn how the human brain evolved and how its neural circuitry develops. The project involves applying modern artificial intelligence approaches to understanding and emulating the architecture of the human brain. A key part of the project is to advance the technology for growing and studying three-dimensional models of brain tissue, called cerebral organoids, in the laboratory.

Live Cell Technology

Live cell technology is an entirely new way of researching cell growth and change enabled by advances in technology, many of which have been developed right here at UC Santa Cruz. Studying complex three-dimensional cell cultures as they grow will allow us to better understand where and how mutations impact human tissue function and cause disease.

Human Genome Assembly

UC Santa Cruz’s history in genomics goes back to 1985 when UCSC Chancellor Sinsheimer hosted a conference for a group of international visionaries that triggered the inception of the Human Genome Project.

Fifteen years later, a team of UCSC scientists launched the first working draft of the Human Genome on the internet, ensuring that it would remain in the public domain forever.

Today, UC Santa Cruz continues to be at the forefront of genomics sequencing. We are heavily involved in multiple projects to improve the reference human genome, from eliminating gaps that were unsequenceable twenty years ago through the Telomere to Telomere Consortium to adding greater genetic diversity to the sequence with the Pangemone Project.

Completing the Human Genome

Founded by UC Santa Cruz Genomics Professor Karen Miga with NIH Researcher Adam Phillippy, the Telomere-to-Telomere consortium aims to generate the first truly complete assembly of a human genome, filling in the gaps in chromosome regions that were too complicated and costly to complete during the initial Human Genome Project.

Diversifying the Human Genome

Eliminating all gaps is only part of the challenge of creating a robust reference genome. Most current reference DNA has been collected from people of European descent, which cannot encompass all of human diversity. UC Santa Cruz’s David Haussler, Karen Miga, and Benedict Paten chair multiple working groups in the Human Pangenome Reference Consortium that is working to create a wider range of reference sequences.

Our History

Sequencing the complete human genome has been a long project, requiring the collaboration of thousands of researchers around the world. The UC Santa Cruz Genomics Institute is proud to have been a leader in this project from its inception.

Data Sharing Platforms & Sequencing Tools

UC Santa Cruz holds special strength in bioinformatics– investigating and analyzing biological data using computation, math, and statistics. We have been on the forefront of big-data solutions, from creating the UCSC Genome Browser in the early 2000s, to inventing new ways to securely share data for analyzing genetic mutations of rare cancers and diseases while protecting patient privacy. Many of the following projects are overseen by our UCSC Genome Browser Team and our Computational Genomics Laboratory and Platform.

UCSC Genome Browser

On June 22, 2000, UCSC and the other members of the International Human Genome Project consortium completed the first working draft of the human genome assembly, forever ensuring free public access to the genome and the information it contains. A few weeks later, on July 7, 2000, the newly assembled genome was released on the web at genome.ucsc.edu, along with the initial prototype of a graphical viewing tool, the UCSC Genome Browser. In the ensuing years, the website has grown to include a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data.

XENA Browser

UCSC Xena is a bioinformatics tool which visualizes functional genomics data from multiple sources all at once, including public and private data. The UCSC Xena Browser and its predecessor UCSC Cancer Genomics Browser provide open-access and interactive visualization of large-scale genomics datasets through a network of distributed data hubs. They strive to make these resources accessible to the entire scientific community to advance our collective understanding of cancer mutations.

Cell Browser

Single-cell analysis is a rapidly growing research area, but genomic analysis generally creates too many data points to show everything in a single image. Researchers need interactive solutions to help them visualize the data and share it with others via the web. The UCSC Cell Browser, created by the UCSC Genome Browser team, is one of the solutions being developed right now to address this challenge.

Nanopore Sequencing

Investigators at the UC Santa Cruz Genomics Institute have spent years developing a mobile phone sized MinION™ DNA sequencer (licensed and marketed by Oxford Nanopore). With the sequencer’s features of long-reads and portability, the MinION is ready to revolutionize the field of genomics. Nanopore sequencing has been used in projects like the Telomere to Telomere completion of a human genome and a world record in fastest genome sequencing.

High Throughput Genomics

Genomics is in transition. Large projects like The Cancer Genome Atlas have generated petabyte-scale datasets that very few groups have the capacity to analyze independently. With UC Berkeley’s AMP lab we are pioneering ADAM, a genomics platform built on Apache Spark that can radically improve the efficiency of standard genomic analyses.

Latest Health News

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