Utah Center for Genetic Discovery – Computational genomics group at University of Utah

RESEARCH HIGHLIGHT

Unlocking the secrets of human development

How early nerve cell choices shape the peripheral nervous system.

CORE FACILITY

VAAST, PHEVOR, RUFUS, and a pipeline trusted across the University of Utah.

Explore the Core

OUR PEOPLE

A team built for hard genomic problems

Computational biologists, clinicians, and software engineers solving disease together.

Meet the team

About UCGD

Where genomic discovery meets clinical reality.

Founded in 2014 at the University of Utah, UCGD unites computational genomics, software engineering, and translational medicine — under one roof.

6
Principal investigator laboratories

35+
Faculty, staff, postdocs, and students

2014
Founded as USTAR Center for Genetic Discovery

3
Flagship consortia with UCGD contributions

Two connected arms

UCGD operates as an Academic Initiative — six PI laboratories advancing primary research — and as the UCGD Core, a fee-for-service facility (launched 2017) that makes our tools available to any investigator at the University of Utah.

Consortia & collaborations

UCGD investigators have contributed to several of the field’s flagship collaborative efforts — from the sequencing of the first human genome to today’s effort to map somatic mutations across human tissues.

Contributions to the field

Our investigators helped build the foundations of modern genomics — from the first sequencing of the human genome to the software running in clinical labs today.

Human Genome Project

BEDTools

VAAST & PHEVOR

The full UCGD story

This is the UCGD lab.

Long hours. Careful hands. Six labs and the Core, working together.

In the Lab
People + science

The faculty, staff, postdocs, and students who make UCGD run — across six PI laboratories and the UCGD Core.

Meet our people

Three paths. One destination.

Rare disease. Precision oncology. The forces that shape every genome — and the open-source tools that let the world study them.

Our Research
Current Directions

Rare Disease Diagnostics

AI-driven, phenotype-first diagnostic pipelines for patients with unexplained genetic disease, in partnership with clinical teams across the University of Utah and national networks.

Precision Oncology

Functional drug screening and AI/ML methods to extend precision cancer care — including to patients without recognizable, targetable genetic alterations.

About this project

Genome Variation & Mosaicism

From inherited disease to the mosaic mutations in a single tissue, UCGD investigators study how genomes change — across generations, across life, and across cells. The tools we build to see this variation are used by labs worldwide.

Example project

The work, right now.

Named initiatives carrying UCGD’s research into the clinic — and into
the world.

Projects
Selected initiatives

Featured project

Understanding Mutations in Sperm

Mutations accumulate in cells throughout life, and some pass to offspring through sperm. Our prior work showed that many de novo mutations causing neurological disease arise from clonal mosaicism in the father's germline. This project maps that mutational burden at bulk and single-cell scale.

Explore the research

Platform

Mosaic Genomic Data Portal

A collaborative genomic data management and sharing portal, developed with Frameshift Genomics. Replaces GnomEx as the UCGD Core's primary data interface.

About Mosaic

Clinical research

EHR-Enabled Disease Research

Integration of University of Utah Hospitals electronic health records into disease research — surfacing phenotypic signals at population scale, led by Dr. Yandell.

Clinical platform

Precision Oncology Platform

Functional drug screening in use for advanced/metastatic breast cancer and extending into pediatric brain cancer. A joint School of Medicine + Huntsman Cancer Institute initiative.

Dig Deeper

Technology

Long-Read Sequencing

Technology integration and application across UCGD, enabling the resolution of complex and segmentally duplicated regions inaccessible to short-read sequencing.

About the project

These are five of our active projects. The full list includes Calypso, SEMIColon, Utah Population DB integration, and more.

All projects

Software

Tools built here, used everywhere.

Community data standards. Variant callers running on millions of genomes. The software of modern genomics, authored at UCGD.

Explore UCGD software

30+
Open-source tools published and maintained

30,000+
Citations across UCGD software in the literature

Bioinformatics · 2010

BEDTools

The ubiquitous toolkit for genome arithmetic — intersecting, merging, and comparing genomic intervals. Authored by Aaron Quinlan.

View tool

Nat Genet · 2011

VAAST & PHEVOR

Probabilistic disease-gene finder combining allele frequency, amino- acid effects, and phenotype prioritization. Authored by Mark Yandell.

View tool

Genome Res · 2008

MAKER

The reference genome annotation pipeline — used by organismal genome projects worldwide. Authored by Mark Yandell.

View tool

Bioinformatics · 2021

Samplot

Structural-variant visualization from BAM/CRAM files — a standard for clinical SV review. Authored by the Quinlan Lab.

View tool

UCGD · Platform

Mosaic

Collaborative genomic data management and sharing portal, developed with Frameshift Genomics. The UCGD Core's primary data interface.

View tool

Genome Biol · 2016

Taxonomer

Universal pathogen detection and host mRNA expression profiling — now powering commercial clinical diagnostics.

View tool

The software you can actually use.

Every tool UCGD ships is free, peer-reviewed, and production-tested. Our software has been cited in more than 14,000 publications and is deployed in clinical and research labs in dozens of countries.

Shown: an example of Samplot rendering a structural variant from a trio — the tool our clinical reviewers use daily during case curation.

Our translational model

From discovery to impact, in five stages.

A defining feature of UCGD is how projects carry across the full arc —
basic research, computational tools, bioinformatic services, clinical
deployment, and commercial impact — under a single roof.