The many flavors of genomics, all in one place: QB3 Genomics

Christopher Hann-Soden discusses the breadth of services offered at UC Berkeley’s QB3 Genomics Core Facility.

The QB3 Genomics core research facility is an umbrella term for three separate UC Berkeley research facilities devoted to different stages of high throughput sequencing and genomics experiments. Hundreds of researchers turn to QB3 Genomics including almost all researchers who use next generation sequencing methods in their projects.

QB3 Genomics’ mission is to support genomics research and biotechnology in California through efforts at three facilities that center around the pillars of genomics research. The Computational Genomics Research Lab provides the computational infrastructure needed to conduct bioinformatics analyses, the Functional Genomics Lab provides molecular biology services for next generation sequencing projects, and the Vincent J. Coates Genomics Sequencing Lab provides quality control and sequencing services.

“One of our strengths here at UC Berkeley is having all facilities involved in the genomics pipeline working in close collaboration as one functional unit,” describes QB3 Genomics Director Dr. Christopher Hann-Soden.

The three research facilities see all types of scientists. Some researchers on campus simply use QB3’s research facilities for routine experiments. The core focuses on technical wet-lab operations, from processing research samples to operating sequencing instruments. “We provide sequencing for an increasing number of bioengineering labs on campus doing experiments with CRISPR/Cas9,” explains Hann-Soden. “We also perform a lot of custom and one-off experiments for researchers, too.”

Others – including those from other UC campuses, nonprofit organizations, and private companies – avail QB3 Genomics’ services for a gamut of steps within the scientific process. These include letters of support for grant funding, advice on how to design experiments, and consultations on genomic methods development.

During the ongoing COVID-19 pandemic, QB3 Genomics has a working relationship with Innovative Genomics Institute’s (IGI) SARS-CoV-2 sequencing group – providing regular quality control services as well as supplemental sequencing when IGI’s sequencing needs exceed their internal capacity. QB3 also works with the Covid-WEB project in monitoring SARS-CoV-2 variants from wastewater. As new variants develop, the Covid-WEB project has the potential to alert public health officials to new variants in the Bay Area, including Omicron, before patients start coming into hospitals.

QB3 Genomics also collaborates with other universities within the UC system to work on large projects. Most recently, the core has joined the California Conservation Genomics Project (CCGP) to survey the genetic diversity of California native wildlife populations at a genomic level. On campus genomics facilities leverage their tools to create high-quality reference genomes, and resequence populations to make accurate estimates on California’s diversity.

Such QB3 Genomics projects receive state funding support and are passed in the annual budget by the California legislature. In fact, these facilities are critical in meeting the requirement that all samples be processed in University of California laboratories and cores. Other projects that use QB3 Genomics facilities are funded by labs, departments, grants, and private funding sources. That is, QB3 Genomics charges the cost of services against researcher’s grants, and works with external research institutions and private companies, who pay to utilize the facility’s excess capacity.

QB3 Genomics shares a mutual cooperation with other genomics facilities across the UC system such as those on nearby campuses including UCSF, UCSC, and UC Davis, referring researchers to other cores when they don’t have the resources for a particular project, and other research cores likewise send work to UC Berkeley for which they aren’t equipped for.

The future of QB3 Genomics? Strengthening the CGRL core. “We hope to build out more of our bioinformatics and analysis services to better support scientists,” says Hann-Soden. “We are continually updating our computational hardware to keep it aligned with people’s needs.” Over time, Hann-Soden envisions hiring more staff and scientists to help support QB3 Genomics and UC Berkeley’s growing computational demands.