Message from the Co-Directors of the Genomics Shared Resource

Clifford Tepper, Ph.D. and John McPherson, Ph.D.

Shown L to R: GSR Team - Stephenie Liu (Manager), Ryan Davis (Genomics Specialist), Dr. John McPherson (Co-Director), and Dr. Clifford Tepper (Co-Director)

Greetings Cancer Center members and investigators across UC Davis! Welcome to the April edition of the Shared Resources Newsletter. We're delighted to showcase the technologies and services offered by the Genomics Shared Resource (GSR). 

The GSR is committed to providing expertise and comprehensive services for a wide range of next-generation sequencing (NGS)-based genomics analyses. Our services include transcriptome profiling, whole genome and exome sequencing (WGS, WES), epigenomics, single-cell sequencing, spatial proteogenomics, and metagenomics. 

The GSR specializes in tailored solutions for translational genomics research services, offering analysis of diverse clinical specimens, pre-clinical models, and ultra-low input samples. Our capabilities extend to FFPE tumor tissue, canine tumors, whole blood, serum, cell-free ctDNA, and saliva samples. Additionally, we foster investigator-driven projects through the development of customized methods and work closely with the Center for Diagnostic Innovation (CDxI) for the establishment of novel laboratory-developed tests (LDTs). 

To complement these services, the GSR provides integrative bioinformatics support, including ultra-rapid data analysis on the DRAGEN platform. We also offer a range of ancillary services, including DNA/RNA isolation, qPCR validation, DNA shearing, assistance with manuscript and grant preparation, and project design and logistics support. 

Spatial proteogenomics services are offered with the NanoString GeoMx Digital Spatial Profiler (DSP) and 10x Genomics Visium platforms. To accompany the recently launched Visium service, we are excited to announce our Visium Spatial Transcriptomics Pilot Program, which can be applied to with this very short online form.

Connect with Us: Our GSR team is eager to collaborate with you! Visit the Comprehensive Cancer Center Shared Resources webpage or contact us via email. You can also schedule a consultation and attend our monthly Genomics Pop-In Workshops (4th Wednesday of each month from 12 - 1 p.m.) to learn more about our services and capabilities. 

We look forward to supporting your genomic research endeavors!

Four UC Davis School of Medicine (SOM) faculty members have been elected fellows of the American Association for the Advancement of Science (AAAS). The society announced the names of the 2024 AAAS fellows on April 18th, including 10 from UC Davis who are scientists, engineers, and innovators recognized for their achievements in science. The new UC Davis SOM fellows are Andreas Bäumler, Emanual Maverakis, Luis Fernando Santana, and Rene Tsolis.

Dr. Maverakis is Director of the Immune Modeling, Analysis and Diagnostics Shared Resource (IMADSR) and a professor in the Department of Dermatology. He has made great contributions to diagnostic and treatment guidelines for many rare, life-threatening immune-mediated skin diseases. 

The Comprehensive Cancer Center Shared Resources congratulates Dr. Maverakis on his achievement and exciting scientific journey!

This year marks the 150th anniversary of the AAAS Fellows program. A gala celebration to mark the anniversary will be held in Washington, D.C. on September 21, 2024.

Cancer Center Shared Resources (SR) were well represented by Aruna Chetty (SR Administrator) and Rachel Rivas (Research Program and Data Analyst) at the 2024 UC Davis Office of Research Expo on the Davis campus April 18. Along with the SR exhibit, several other SRs showcased their services and equipment like the Mouse Biology SR, Flow Cytometry SR, Biorepository SR, Center for Molecular and Genomic Imaging (small-animal imaging), and EXPLORER Molecular Imaging Center (human imaging).

This year’s event was attended by 521 people, up by over 100 from last year. A special thanks to the faculty, students, residents, and staff attendees who made this year’s event a huge success.

Below are some pictures from the day.

Shown: Aruna with Shared Resources

Shown L to R: Sarah, Brad, and Doug with Center for Molecular and Genomic Imaging

Shown: Ashley with Flow Cytometry Shared Resource

Shown L to R: Dan and Renee with Mouse Biology Shared Resource

Shown L to R: Marissa, Laura, and Neha with Community Outreach and Engagement

The Spotlight on Early Career Investigators is an annual symposium highlighting the work of students, postdocs, research staff residents, and fellows in cancer research. 

The 18th Annual Spotlight on Early Career Investigators took place on Thursday April 25, Dr. Primo "Lucky" Lara, UC Davis Comprehensive Cancer Center Director, announced the event's renaming in recognition of Dr. Ralph de Vere White. A renowned urologist, Dr. de Vere White contributed significant knowledge to the understanding and treatment of prostate and bladder cancers and served as the first Director of the UC Davis Comprehensive Cancer Center. He retired on June 29, 2016.

This year presents the inaugural Ralph de Vere White Symposium for Early-Stage Investigators in Cancer.

The keynote speaker, Associate Professor, Janai Carr-Ascher, M.D., Ph.D. (Hematology/Oncology) spoke on "If you let me play, parallels in sports and science". The symposium included seven oral presentations, 19 poster presentations and seven Round Table discussions over lunch. The event was co-chaired by Dr. Shuchi Gulati and Dr. Alan Lombard. Several Cancer Center and Faculty staff members helped facilitate the round table discussions.

The oral presentation winner Dr. Christopher Lucchesi (Urologic Surgery) presented on the multifarious roles of ANGEL2 in cancer while the winning poster was on elucidating the role of yap in sarcoma development by Ms. Julissa Suarez-Navarro (graduate student in the department of Internal Medicine Hematology/Oncology).

Below are some pictures from the event.

Shown: Rachel Rivas at the Shared Resources exhibition table

Shown L to R: Dr. Primo "Lucky" Lara with Dr. Wolf-Dietrich Heyer during the poster presentations

Shown L to R: Comprehensive Cancer Center Director Dr. Primo "Lucky" Lara with Emeritus Director Dr. Ralph de Vere White

Shown L to R: Dr. Ralph de Vere White with Julissa Suarez-Navarro - winner of poster presentation

Shown L to R: Dr. Ralph de Vere White with Dr. Christopher Lucchesi - winner of oral presentation

Rachel Rivas has served in UC Davis Comprehensive Cancer Center support roles since January 2022. Currently, she is the Research Program and Data Analyst, providing Research Program and member support to facilitate compliance with NCI’s Cancer Center Support Grant guidelines. She is honored to be part of an institution on the cutting edge of cancer research and is grateful for the opportunity to support its unique Research Programs and world-class researchers.

Previously, Rachel held laboratory positions in veterinary molecular diagnostics and antimicrobial resistance research. In addition to her current position, she is also a student in UC Davis' Master's in Health Informatics program and welcomes the chance to think deeply about data, security, artificial intelligence, and clinical research. In her free time, Rachel enjoys running, kayaking, tabletop role-playing games, making and enjoying art of all kinds, and spending time with her pets.

Rachel enjoys the opportunity to provide excellent customer service and can be reached via email at rmrivas@ucdavis.edu. Please reach out with questions about membership or to present research at an upcoming Research Program meeting.

The Biostatistics Shared Resource (BSR) provides biostatistical support for clinical, population, and basic science researchers. To better support the study design and data analysis efforts of our members, BSR offers weekly office hours in collaboration with the Clinical and Translational Science Center:

• 1st and 3rd Monday, 1-2 p.m.
• Tuesdays, 12-2 p.m.

For more information, contact Dr. Lihong Qi.

Please join the Biostatistics Seminar presented by Professor Emeritus Ross L. Prentice (Fred Hutchinson Cancer Center and University of Washington) on May 7, from 12:10 to 1 p.m., in the Mathematical Sciences Building, Room 1147 on the Davis campus.

Nutritional epidemiology research for the past 50 years has relied almost exclusively on self-reported dietary data. Energy (calorie) intake is poorly estimated by self-report, with major systematic biases. However, Professor Prentice's research group recently developed a strong energy intake biomarker and found higher mortality risk at higher energy intake among younger postmenopausal women having stable or increasing weight, as well as lower mortality risk at higher energy intake among older postmenopausal women with weight loss. Self-reported ratios of food group or nutrient intake to total energy may also incorporate important systematic biases, but these biases are still largely unexplored due to a lack of objective intake measures for comparison. Small molecule (metabolite) profiles in blood and urine provide the opportunity to develop objective intake measures for many aspects of diet. Recently developed biomarkers for macronutrients and their major components will be described, along with related chronic disease risk associations in Women’s Health Initiative cohorts of postmenopausal women.

Opportunities to strengthen the future nutritional epidemiology research agenda will be described. 

Register now for the Flow Cytometry Shared Resource (FCSR) next online course, June 24-28, 2024. The expert and friendly FCSR staff can assist with experimental design and data analysis of routine and cutting-edge cytometry applications. Learn about their facilities, services, rates and instrumentation here.

New equipment is now available to support your research! Contact for training!

Davis:

• User-operable 12-color cell sorter: Sony “MA-900” multi-application cell sorter. Cytek “Aurora”, a 40+ color “spectral” flow cytometer.
• Improved EV and microparticle characterization with new Cytek “Aurora” Small Particle Enhancement Module.

Sacramento:

• Sony “ID7000”, 40+ color “spectral” cytometer, with autofluorescence subtraction & fast plate-based sample loading.
• “LSRII” 10 color flow cytometer – reliable and easy to use. 

Flow Cytometry Training Course: Next offering will be Online, June 2024

Did you miss February’s Comprehensive Flow Cytometry Course? The course is designed to teach the fundamental concepts of how flow cytometers work and discuss best practices in sample preparation. 

“This was an excellent introduction to flow cytometry. I was thoroughly impressed by the expertise of the instructors and the thoughtfulness with which they designed the lectures and activities for the course. Thank you!” - Previous Participant

Make sure to register today for our next online course, June 24-28, 2024. Seven scholarships are available for CCC members. Don't miss this opportunity to receive comprehensive flow cytometry training! 

Please contact Bridget McLaughlin for more information.

Shared Resource Management introduced the new bi-annual post-service evaluation in January to get immediate and anonymous feedback from users. 

Thank you to those who completed the January, February, and March evaluations. April evaluations will be sent to SR Leaders. 

Users who respond to this request will be given the opportunity to provide their contact details to be entered into a drawing to win gift cards!

The UC Davis Comprehensive Cancer Center Shared Resources (SR) provides the UC Davis research community with centralized access to specialized scientific expertise, consultation and assistance, infrastructure, and equipment necessary to conduct cutting-edge scientific research.

Want to know how to incorporate SRs into your research? This year’s workshop series will feature faculty who have used one or more SRs for their cancer research projects. 

Register today to learn from Cancer Center members who will share their unique experiences. 

This series will equip you with ways to take full advantage of SRs services and equipment in your research and publications and how to learn strategies for using SRs. As a Cancer Center member conducting cancer research, you are eligible for prioritized status and subsidized rates when using the SRs! Register now and hear what our SRs “super users” have to say!  

Join us at one or more of the workshops scheduled below and learn how SRs can add value to your research:

• September 12, 1 - 2 p.m.
• October 17, 1 - 2 p.m.
• November 14, 1 - 2 p.m.
• January 16, 2025, 3 - 4 p.m.
• February 21, 2025, 1 - 2 p.m.

Biorepository

(BRSR)

Biostatistics

(BSR)

Combinatorial Chemistry and Chemical Biology (CCCBSR)

Flow Cytometry

(FCSR)

Genomics

(GSR)

In vivo Translational Imaging

(IVTISR)

Mouse Biology

(MBSR)

Molecular Pharmacology

(MPSR)

Immune Modeling, Analysis, and Diagnostics (IMADSR)

Shared Resources are funded by the UC Davis Comprehensive Cancer Center Support Grant (CCSG) awarded by the National Cancer Institute (NCI P30CA093373). Publications that have utilized facility resources, services or scientific data generated using shared resources should acknowledge the shared resource(s) or the assistance provided by their staff and cite the CCSG (NCI P30CA093373). An electronic copy of the publication should also be sent to the directors of the SRs that were used. 

National Institutes of Health public access policy

Contact Shared Resources