GENOMICS & BIOINFORMATICS SHARED RESOURCE (G&BSR) The Genomics & Bioinformatics Shared Resource (G&BSR) is a state-of-the-art facility that has continued to evolve over the past 20 years, providing Cancer Consortium members with access to sophisticated, genomics- based technologies and a team consisting of a highly experienced scientist, expert technical staff, and seasoned bioinformaticians. This team provides a seamless experience for the researcher, supporting all phases of technology selection, experimental design, sample QC, data generation, and analysis. The broad portfolio of massively parallel deep sequencing services offered through the G&BSR includes whole genome sequencing; whole exome sequencing; expression profiling of mRNAs, miRNAs, and non-coding RNAs; ribosome sequencing; and numerous targeted resequencing applications. Additionally, epigenomics services including the profiling of the DNA methylome, ATAC-seq, and Hi-C sequencing assays are performed. The G&BSR was also an early adopter of CRISPR-Cas9 pooled screens and supported the development of CUT&RUN ? a protein-DNA interaction assay developed by Fred Hutch investigators, led by Dr. Steven Henikoff CBB, with both technologies now implemented as high-throughput pipelines available to the broader Consortium community through the G&BSR. In addition, the G&BSR routinely employs NanoString digital barcoding technology, conducts Sanger sequencing, and provides training on and access to qPCR instrumentation. Major equipment includes an Illumina NovaSeq 6000 sequencer, an lllumina HiSeq 2500 sequencer, two Illumina MiSeq sequencers, a Pacific Biosciences Sequel sequencer, an Illumina BeadChip system, a NanoString nCounter system, a 10x Genomics Chromium controller, two ABI 3730xl sequencers, a PerkinElmer Sciclone NGSx Workstation, and four ThermoFisher Scientific QuantStudio 5 real-time PCR systems. Peer-reviewed studies accounted for 66% of the work performed in the G&BSR during 2017 and staff contributed to over 30 publications (July 2017 ? June 2018).

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
2P30CA015704-45
Application #
9853649
Study Section
Subcommittee I - Transistion to Independence (NCI)
Project Start
Project End
Budget Start
2020-01-01
Budget End
2020-12-31
Support Year
45
Fiscal Year
2020
Total Cost
Indirect Cost
Name
Fred Hutchinson Cancer Research Center
Department
Type
DUNS #
078200995
City
Seattle
State
WA
Country
United States
Zip Code
98109
Syrjala, Karen L; Yi, Jean C; Artherholt, Samantha B et al. (2018) An online randomized controlled trial, with or without problem-solving treatment, for long-term cancer survivors after hematopoietic cell transplantation. J Cancer Surviv 12:560-570
Hempstead, Bridgette; Green, Cynthia; Briant, Katherine J et al. (2018) Community Empowerment Partners (CEPs): A Breast Health Education Program for African-American Women. J Community Health 43:833-841
OhAinle, Molly; Helms, Louisa; Vermeire, Jolien et al. (2018) A virus-packageable CRISPR screen identifies host factors mediating interferon inhibition of HIV. Elife 7:
Liu, Yanyan; Xiong, Sican; Sun, Wei et al. (2018) Joint Analysis of Strain and Parent-of-Origin Effects for Recombinant Inbred Intercrosses Generated from Multiparent Populations with the Collaborative Cross as an Example. G3 (Bethesda) 8:599-605
Liu, Yang; He, Qianchan; Sun, Wei (2018) Association analysis using somatic mutations. PLoS Genet 14:e1007746
Glaser, Adam K; Chen, Ye; Yin, Chengbo et al. (2018) Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging. Sci Rep 8:13878
Du, Jing; Flynn, Ryan; Paz, Katelyn et al. (2018) Murine chronic graft-versus-host disease proteome profiling discovers CCL15 as a novel biomarker in patients. Blood 131:1743-1754
Mora-Pinzon, Maria C; Trentham-Dietz, Amy; Gangnon, Ronald E et al. (2018) Urinary Magnesium and Other Elements in Relation to Mammographic Breast Density, a Measure of Breast Cancer Risk. Nutr Cancer 70:441-446
Shirts, Brian H; Konnick, Eric Q; Upham, Sarah et al. (2018) Using Somatic Mutations from Tumors to Classify Variants in Mismatch Repair Genes. Am J Hum Genet 103:19-29
Kuzma, Jessica N; Hagman, Derek K; Cromer, Gail et al. (2018) Intra-individual variation in markers of intestinal permeability and adipose tissue inflammation in healthy normal weight to obese adults. Cancer Epidemiol Biomarkers Prev :

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