Researcher Karen Miga speaking at the Clinton Global Initiative on stage with Bill Clinton, Bono, and the director general of the World Health Organization

Genomics and Health

Viruses and Pathogens

Covid molecules with spikey proteins on their surfaces

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.

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.

women who has freshly shaved her head holding a little girl

BRCA Exchange drawing depicting the inherit variation of breast cancer

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.


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 and disease, and Olena Vaske studies tumor RNA as a readout of changes that drive cancer. Their research could lead to better cancer detection and treatments.

Image of DNA helicase

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.

Developmental and Regenerative Medicine

image of cartoon brain with DNA helix

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 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.

two students work on a microscope

Mental Health

PsyGene Logo

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. Our collaboration will result in a comprehensive phenotypic catalog across biological scales.

Generative Genomics

AI has essentially cracked human language, but to do the same thing with living cells will be a much greater challenge. In collaboration with Baskin Engineering, the Genomics Institute is heading an effort to develop applications for AI in human health.

More to be announced soon!

An AI-generated image in neon colors of a person in a VR set with their brain exposed.

Epigenetics and the Exposome

3D Isometric Flat Vector Conceptual Illustration of Epigenetic DNA, Educational Labeled Scientific Schema

We are increasingly learning about ways that a person’s environment can influence their phenotypes and those of their descendants. The collection of a person’s exposures from diet, stress, lifestyle, environmental toxins, and other factors and the way they interact with epigenetics and physiology is called the “exposome.” At the Genomics Institute, we are interested in exploring the exposome and the mechanisms of intergenerational epigenetic inheritance.

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.


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.


image of a cartoon human with arms reached out

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.

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Last modified: Jun 05, 2024