Office of Translational Research (OTR)
Seattle Translational Tumor Research (STTR)
Specimen & Data Access Network (SAN)
Sloan Precision Oncology Institute (SPO)
TakePART-NW (Patients and Research Together)
Data Science Laboratory (DaSL)
The Office of Translational Research (OTR), Sloan Precision Oncology (SPO), and Data Science Lab (DaSL) concluded their Focus Group discussion series in May 2024. The OTR, SPO and DaSL teams spent 24 meeting hours to gather input from 227 contributors across 16 Tumor Teams. We heard the needs and recommendations of our community for several inter-related initiatives including Specimen Access & Biobanking, Clinical Data: Access & Abstraction and TakePART NW & Molecular Profiling informing the strategic priorities of Fred Hutch by enhancing scientific discovery and research across prevention, screening, translational, and data-driven research approaches
Following this work, SPO and OTR are launching a Clinical Note Template Pilot. The need for this pilot was identified during Focus Group meetings, as many core data elements are common across disease groups, and this vital information can be hidden within clinic notes and is not easily extractable. Utilizing a template in which providers could select prepopulated, oncology specific options would reduce the need for retrospective manual abstraction, leverage AI and NLP resources, and improve accuracy.
Office of Translational Research (OTR)
As many of you know, Seattle Translational Tumor Research (STTR) began over 10 years ago in 2013 with a mission to speed translational research and elevate the profile of tumor-specific teams. We have pursued this mission by engaging with our community to identify and systematically address barriers inhibiting translational research at the individual, team and organizational levels. Our work has led us to develop several new initiatives to meet the needs of our translational research community: Oncoscape, Specimen & Data Access Network (SAN), OpenSpecimen and Clinical Data abstraction and strategy support. As these new initiatives have evolved, it’s become clear that our collective work is now bigger than STTR.
In that vein, we would like to officially announce our new name, the Office of Translational Research, which represents each of our work areas as five core pillars: STTR, Oncoscape, SAN, OpenSpecimen, Translational Clinical Data. Each area directly addresses challenges raised by our STTR members and supports the translational community beyond just STTR. In this newsletter, you’ll find updates from each of our five OTR pillars.
Thank you for your continued support and for being an integral part of our community. We are excited to grow and learn together as we move forward.
Updates from each of the Five Pillars of OTR
Seattle Translational Tumor Research (STTR)
STTR will release a call for proposals this fall for translational research pilot award funds. Two outstanding projects will receive $100,000 each to foster innovative, interdisciplinary collaborations, with awards based on top scores during peer review. Priority will be given to projects with a clear hypothesis, interdisciplinary teams, a strong translational focus, and junior faculty involvement. This opportunity is open to all PIs at Fred Hutch, UW, and Seattle Children’s, with at least one STTR member as a PI or Co-PI. Applications are due by 11:59PM PT on November 15, 2024. For the complete RFA, please reach out to STTRCancer@fredhutch.org.
Starting this year, our team will collaborate with Tumor teams to co-develop roadmaps with clear targets. This initiative aims to ensure that our STTR team delivers impactful support by enhancing collaboration with both research and clinical teams.
Team members: Snehal Joshi, Shauntel Thomas, Amanda “AJ” Gary, Agnes Gawne, Jessica Paulishen
Oncoscape
Our team has been making strong progress in advancing Oncoscape with the addition of in-browser Differential Expression Analysis, including a volcano plot and pathway analysis. We have also started breaking key Oncoscape features out into components that can be easily remixed in new standalone web tools. This will lead both to simpler, more customized user solutions, as well as a faster development cycle. In addition, the “Dataset Upload” page allows users to input their own datasets, rather than needing to engage our Oncoscape team, further speeding engagement for users.
Above: Volcano plot showing Differential Expression Analysis of two selected points on a UMAP (left)
Below: New layout showing ability to select different analysis modules from Oncoscape functionality to simplify the user interface and focus on the features most relevant to a given dataset.
Team members: Matt Jensen, Greg Glatzer – Oncoscape@fredhutch.org
Specimen & Data Access Network (SAN)
The SAN is excited to announce that Overlake Medical Center and Evergreen Health will serve as pilot specimen collection sites for the TakePART-NW Community Arm. With support from the Andy Hill CARE Fund and in partnership with Sloan Precision Oncology this initiative will expand opportunities for research participation across the state, driving innovation in cancer research. The initial phase will focus on two tumor types: GI cancer at Evergreen and Lung cancer at Overlake.
In addition to the TakePART-NW Community Arm, the SAN team continues to fulfill specimen and data requests across the board. We have successfully reduced the average time to fulfill service requests—those resulting in delivered specimens or data—from 45 days in 2023 to 32 days in 2024. As we work towards more efficient delivery of specimens and data, the SAN team continues to use critical feedback from investigators and reporting metrics to improve our services.
Team members: Snehal Joshi, Morgan McQuiston – SAN@fredhutch.org
OpenSpecimen
We now have an OpenSpecimen Project dashboard where you can see who we’re working with, how long our average projects take, and which teams are already in the tool. We have migrated 31 projects into production, with ongoing maintenance and support, are currently working with an additional 12 teams and have nine teams in our queue. Our users represent all three consortium organizations and represent a mix of research teams, shared resources and biorepositories.
Dashboard Preview
Team members: Cleavon Joseph, with support from Steven Blanton & Clinical Data Services – SpecimenData@fredhutch.org
Translational Clinical Data
Based on input from focus group discussions, and ongoing conversations with the translational research community, we are identifying high priority data elements and their use. This information will guide institutional clinical abstraction and AI/NLP workflows and efforts to better meet the needs of our investigators. Currently, we are collaborating with Precision Oncology and DaSL on a clinic note template pilot and are evaluating clinical data curation projects across Fred Hutch to assess duplication of effort and areas of opportunity. One example of the latter is facilitating the work of data abstractors who will support the Gateway Program effort as they transition clinical workflows within Gateway into Epic and other applications, ensuring the data remains “whole” for researchers and other organizational reporting purposes.
Team member: Kara Colevas
For a more comprehensive view of our accomplishments over the past decade and our current work as the Office of Translational research, check out our attached book. Questions or comments can be directed to OTR@fredhutch.org.
Sloan Precision Oncology Institute (SPO) for Precision Oncology
Precision Oncology Symposia
The Stuart and Molly Sloan Precision Oncology Institute is hosting a series of symposia to spotlight different areas of research relating to Precision Oncology. The series kicked off with a Cancer Vaccine Symposium on Tuesday, October 1st.
Cancer vaccines have shown tremendous progress in recent years, with great potential for unlocking more precise and personalized cancer treatments. The all-day Advances in Cancer Vaccine Symposium explored the current cancer vaccine landscape and discussed where the research is headed next. The Symposium featured talks from investigators, clinicians, and industry leaders from across the field.
A second symposium exploring theranostics will be held on Friday, February 28th, 2025. The Theranostics Symposium is hosted in partnership with UW Radiology and co-hosted by Drs. Amir Iravani, Director of Theranostics, and Delphine Chen, Director of Molecular Imaging and Therapy, Fred Hutchinson Cancer Center. Additional event details and agenda will follow. This event is open to everyone. Registration will be available starting in November. We hope you’ll join us!
Please visit our event page for the symposium for up-to-date event information.
Research Funding Awards
In April, the Sloan Precision Oncology Institute requested innovative, forward-thinking applications for funding to support projects in Precision Oncology that address a research hypothesis (Ignition Award) or that focus on distributing novel technologies to the research community (Technology Dissemination Award).
Three Ignition and two Technology Dissemination projects have been selected for funding.
An Ignition Award is going to Dr. Sanjay Srivatsan for his proposal, titled “Genomic velocity as a measure of leukemia diagnosis and prognosis”. Another Ignition Award is going to Dr. Savannah Partridge for her proposal titled, “Radiomics-Based Phenotyping for Treatment Optimization of HER2+ Breast Cancer”. A third Ignition Award is going to Dr. Elizabeth Swisher for her proposal, titled “Launching a multiplex BRCA1/RAD51C ddPCR methylation assay as a clinical HRD test”. A Technology Dissemination Award is going to Dr. Steven Henikoff for his proposal titled “Affordable Precision Oncology based on FFPE-CUTAC”. Another Technology Dissemination Award is going to Dr. Liangcai Gu for his proposal titled “Pixel-seqV2: Cost-effective and scalable 0.6-μm-resolution spatial transcriptomics for precision oncology”. Congratulations to Dr. Srivatsan, Dr. Partridge, Dr. Swisher, Dr. Henikoff and Dr. Gu We are excited to support your projects and look forward to the contributions you’ll make to advancing precision oncology research at Fred Hutch and across the Cancer Consortium.
A big thank you to the nearly 40 investigators who submitted applications, and to the 18 investigators and two Community Advisory Board Members who served as reviewers for our inaugural Research Funding Award (RFA). Additional thanks to our colleagues in Immunotherapy Integrated Research Center (IIRC), Cancer Consortium, Philanthropy and Office of Sponsored Research (OSR) for providing us with the resources and guidance needed to successfully initiate our RFA.
For more information about our awards and the projects selected for funding, please visit our Research Funding Awards page.
TakePART-NW (Patients and Research Together)
After collecting feedback from researchers across the Adult Oncology Program and hearing concerns about the potential impact to studies regarding “broad/universal” consent, the project team has made the decision to shift the scope of TakePART-NW consent to collecting de-identified data. This approach is expected to have little to no impact to studies using retrospective data or that have received Institutional Review Board (IRB) waivers of consent, while still allowing us to partner with patients to consent for use of their specimens for research.
TakePART-NW is adopting a phased approach. Phase 1 is focused on building the electronic consenting infrastructure and will roll this out first to the adult population at our Fred Hutch South Lake Union clinics (Buildings 1 and 2). Project is anticipated to move from design to build phase over the next month, pending IRB initial approval.
To learn more, please visit our CenterNet department page here (for Fred Hutch employees) or contact TakePART-NW project manager Christina Ebaugh at cebaugh@fredhutch.org.
Data Science Laboratory (DaSL)
The Data Science Lab (DaSL) oversees data strategy and data governance across the Fred Hutch data ecosystem from the clinic to research labs. The DaSL partners with groups across the Fred Hutch on their Data Driven work in order to support data strategy and governance, patient data, and research data tools and infrastructure.
Patient Data
The DaSL is partnering with IT to develop the Clinical and Research Data Solutions (CARDS), which will serve as the foundational data infrastructure for the patient data ecosystem. This initiative aims to build a secure, scalable, and centrally governed technical infrastructure that enables the Fred Hutch community to create data products and tools using multimodal patient clinical data for clinical operations, trials, and research.
For more information about the current status of CARDS development and associated efforts that are upcoming related to patient data governance, infrastructure and new capabilities, connect with Amy Paguirigan, PhD, the AVP/Deputy Chief Data Officer, via Data House Calls.
Research Data
The DaSL partners with Research IT to support data driven tooling and infrastructure for researchers to successfully store, analyze, and visualize their data. Our current efforts within the DaSL are focused on providing tooling for researchers to prove and analyze data using workflow languages through the https://sciwiki.fredhutch.org/datascience/proof/, and supporting genomics data analysis and visualization with the implementation of a private Fred Hutch instance of cBioPortal for research purposes.
Information and Outreach
Join our "Data Noon" meetings by emailing dataproductmanagement@fredhutch.org to stay informed about current data efforts across the Fred Hutch.