Genomics and Bioinformatics Shared Resource

Fred Hutchinson Cancer Center, Seattle WA

Investigators

Linked publications, trials & patents

Abstract

PROJECT SUMMARY: GENOMICS & BIOINFORMATICS SHARED RESOURCE The Genomics & Bioinformatics Shared Resource (G&BSR) is a state-of-the-art facility that has continued to evolve over the past 25 years, providing Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium members with access to sophisticated, genomics technologies and a team of highly experienced scientists, expert technical staff, and seasoned bioinformaticians. The G&BSR offers consulting services for Consortium investigators throughout all phases of their research projects including technology selection, experimental design, sample QC, data generation, and analysis. This provides a fully integrated sample-to- answer experience and ensures that investigators use the appropriate technologies to address their specific research questions and maximize the value of research funds. As part of these activities, the G&BSR supports development and dissemination of new methodologies such as INVADE-seq, which was developed collaboratively with the laboratory of Dr. Susan BullmanPAM. As a result of the close collaboration with Consortium researchers, the G&BSR has contributed to 166 peer-reviewed publications during FY19-FY23 and members of the G&BSR have co-authored 31 peer-reviewed publications since the prior renewal. The broad portfolio of services offered through the G&BSR includes whole genome sequencing, whole exome sequencing, single-cell and bulk mRNA expression profiling, and numerous other sequencing applications using both short read (Illumina) and long read (PacBio) sequencing platforms. Apart from next-generation sequencing, the G&BSR routinely employs NanoString nCounter digital barcoding technology, conducts Sanger sequencing, and provides training on and access to qPCR instrumentation. Recently, the G&BSR has partnered with the Research Pathology Shared Resource to offer spatial transcriptomic profiling services including the 10x Genomics Visium platform and NanoString GeoMx. The G&BSR has also recently begun offering Multiplexed Array Sequencing services on the PacBio Sequel IIe, generating high-throughput single cell RNAseq data with isoform-level resolution. The G&BSR provides or facilitates a variety of educational opportunities to the Consortium community including technical guidance for graduate students and postdoctoral fellows, training users on equipment, coordinating with vendors to sponsor scientific seminars, consulting on data analysis in R & Python, hosting undergraduate interns, and providing laboratory tours. As the field of genomics continues to evolve, the G&BSR will stay on the cutting edge of technological advancements by assessing new technologies, conducting pilot studies, and onboarding new methods while simultaneously seeking routes to improve cost- efficiency of services. One key future goal for the G&BSR is to support the Precision Oncology initiative, for example, by developing and implementing assays for whole genome sequencing from formalin-fixed paraffin- embedded specimens.