Accelerating Research: An Era of Multi-Scale Genomics

The Genome Research and Technology (GRT) Hub is committed to powering transformative genomics research by continuously incorporating advances in technologies into our workflow. Since the last report, Manager Melanie Oakes, PhD, and I have been fortunate to recruit three new members (thank you to those who assisted in these recruitments!): Steven Menjivar, BA; Kevin Stachelek, PhD; and Tanin Jouyan, MS.  We welcomed back Remy Vu, MS, for her expertise in applying new technologies.  Drop by and say “Hi” to our ongoing and new staff!  In the wetlab and bioinformatic and systems support they are maintaining capacity across high-throughput sequencing, multi-scale spatial analysis, and specialized bioinformatics platforms.

I also want to give a shout out to a new program, replacing our previous Genetics, Biomedical Computing and Genomics monthly series; under the direction of Rui Chen, PhD, Dept of Ophthalmology and Physiology and Biophysics, and Vivek Swarup, PhD, Department of Neurobiology and Behavior, this new series, starting with “Panel Discussion on Single Cell Multi-Omics: From Technology to Analysis”

Unprecedented Sequencing Power

Our core mission of generating high-quality genomic data continues to be enhanced with the introduction of two next-generation platforms:

• Illumina NovaSeq X Plus: This is UCI’s engine for population-scale discovery. With up to 2.5 times the throughput of its predecessor, the NovaSeq X Plus fundamentally changes the scale of experiments possible. It enables us to efficiently handle large-cohort studies and comprehensive single-cell projects, driving down the cost per gigabase and accelerating large-scale translational and clinical research.
• PacBio Revio Long-Read Sequencer: The Revio system delivers accurate, native long-read sequencing (HiFi reads), critical for resolving complex genomic structures, conducting de novo genome assembly, and performing Iso-Seq (full-length RNA transcript analysis). This provides a depth of insight into alternative splicing and gene fusion events that short-read platforms cannot match, especially within the context of cancer progression.

Resolving the Tissue Microenvironment: Spatial Technologies

Moving beyond linear sequencing, our focus has shifted to resolving the complex architecture of tissues and cells—answering where and how genes function. Our suite of spatial instruments now allows for true multi-scale analysis:

• 10x Genomics Xenium & Vizgen MERFISH Ultra: These subcellular spatial platforms allow us to precisely map gene expression directly within tissue sections. The Xenium offers comprehensive RNA and protein detection, while the high-multiplexing capacity of the MERFISH Ultra provides single-molecule imaging for hundreds of genes simultaneously, offering an unparalleled view of cell-cell interactions in the tumor microenvironment.
• Stellaromics Pyxa 3D: The GRT Hub contributed to the purchase of this instrument to enable deeper and more complete 3D examination of whole cells, enhancing our ability to analyze intercellular interactions and solid tumor organoids up to 200 microns thick.

Strengthening Our Core: Expanded Bioinformatics and AI

The complexity of these new platforms, from long-read sequencing to highly multiplexed spatial data, demands specialized data science support. Thus, we are growing the bioinformatics team.

• New Personnel: We welcome Kevin Stachelek, our new PhD-level Bioinformatics Scientist. His expertise will be vital in developing custom analysis pipelines and providing deep-dive consultations for our investigators.
• AI Integration: Under the leadership of Dr. Jenny Wu and Dr. Ivan Chang, we are integrating cutting-edge AI tools into our workflows. This includes fine-tuning the scGPT foundation model for single-cell biology, embedding the ZotGPT (UCI’s LLM framework) into our Jupyter Notebook environment for code assistance, and utilizing a new Illumina DRAGEN server for local secondary analysis of genomic and transcriptomic data. Please watch the website for workshops on single cell, spatial and new AI applications!

The GRT Hub is committed to transforming raw data into actionable biological findings, and our expanded team is here to manage that complexity as your dedicated partner in discovery.

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We encourage all UCI and external investigators to connect with our staff to discuss how these new capabilities can be integrated into your next grant proposal or research project. We look forward to supporting your research at the cutting edge.

Suzanne Sandmeyer, PhD Founding Director, GRT Hub