The Hubcap

The HubCap Quarterly Newsletter

Welcome to Summer!  

There are several exciting Hub updates. First, we have two new research specialists, Emily Iosyfovych, BS, and Cindy Yamamoto, PhD. In addition, we bid goodbye to Quy Nguyen, PhD and wish him well at his new position in AbbVie Inc. Last year as many of you are aware, we worked together with our users across multiple spatial platforms. These projects benefited from two bioinformatics workshops conducted by Jenny Wu, PhD, Director of Bioinformatics, and Ivan Chang, PhD, Bioinformatics Engineer.  Those workshops provided guidance on access and use of HPC3 based containers for analysis of single cell and spatial data sets, particularly 10X Genomics systems. Developments in the first part of the year culminated April 23, 2024, with our first UCI Spatial Omics Symposium, including presentations of results from platforms including GeoMx, MERFISH, CosMx, Visium, and Xenium on the transcriptomics side and Hyperion and Metabolomics platforms using mass spectroscopy. The symposium was attended by almost all of the 95 registrants and provided an opportunity for people to compare the strengths and weaknesses of the various platforms.  A follow-up survey indicated that there is strong support for another symposium focused on bioinformatics of analysis. This is in early planning stages.

In the meantime, both instruments and technological approaches have continued to expand in the GRT Hub.  This year so far has seen establishment of the PacBio Revio long-read sequencer and the Illumina NovaSeq X Plus short-read sequencer. The Revio will enable isoform analysis of single cells as one aspect of the expanded exploration enabled.  The X Plus will generate increased amounts of data and multiple changes from the Illumina NovaSeq 6000 platform (see this website “Instruments”) and decreases the time of a run from 48 to 24 hrs. while increasing the throughput from 10B reads per flowcell to 25B reads per each of two flow cells. The price is also reduced per Gb by about 30%!  In the spatial arena, 10X Genomics upgrades included the single-cell Xenium with up to 5000 human or mouse probes later this month as well as new segmentation technology and HD Visium with whole genome mouse and human probe sets.  However, on the horizon there is the possibility of a short-term loaner Vizgen MERFISH instrument to explore enthusiasm for adding this platform to GRT Hub offerings.  the next version of that instrument, the Vizgen Ultra platform will provide a greatly expanded field for tissue slices.  Finally, we are in discussion with Stellaromics Inc. They have proposed to place an alpha version of their exciting 3D Plexa technology with Rui Chen, PhD, soon to arrive in UCI School of Medicine Department of Ophthalmology from Baylor College of Medicine. The longer-term plan is to provide access through the GRT Hub.  Suggestions for wet bench or bioinformatics workshops are welcome.

Finally, the Genetics, Biomedical Informatics, and Genomics seminar series had a very successful season and we are already scheduling for fall with exciting speakers on cytogenetics, bioinformatics of genetic disease, and metabolic diagnosis of genetic disease. Suggestions or volunteers for additional speakers are welcome.

In the meantime, we wish everyone a good chance to refresh this summer. DO remember to submit those workshop and speaker requests (sbsandme@uci.edu)!

Suzanne Sandmeyer, PhD, GRT Hub Director