Bioinformatics, Fred Hutchinson Cancer Center
Fred Hutch Cancer Center, Thomas Building DE-740
1100 Fairview Avenue North
Seattle
Washington
98109
US
The Bioinformatics Resource (formerly the Computational Biology Resource) is comprised of staff who can assist researchers with the genomics and proteomics data analysis support. The Bioinformatics Shared Resource is staffed by 3 dedicated bioinformatics specialists and a database developer/programmer.
In an effort to assist researchers with exploring and understanding genomics and proteomics data, bioinformatics support is offered to researchers through two different service models:
- Users of the Genomics or Proteomics Shared Resources. Basic analytical support is provided to assist researchers with data generated in either facility. In such cases, up to 4 hours of bioinformatics support is provided free-of-charge. Examples of deliverables are provided below based on the type of assay performed. Additional support is provided for a fee using an hourly rate structure, and is subject to staff availability.
- Externally Generated Data. While priority is given to those using the Fred Hutch Genomics and Proteomics Shared Resources to generate data, support is sometimes available to researchers with their own data sets or with data found in publically accessible repositories. In this case, support is provided solely on a fee-for-service basis using an hourly rate structure. Support is subject to staff availability and project demands. Please email bioinformatics@fredhutch.org to discuss the scope of your project and to get an estimate of service fees.
Examples of Deliverables Supported by the Fred Hutch Bioinformatics Group:
- RNA-seq
- Filter low quality reads and align to reference genome using TopHat
Generate QC reports: FastQC and RNA-SeQC
Associate reads at the gene-level using HTSeq-count
Detect differential genes using the Bioconductor package edgeR
Whole Exome Sequencing (WGS) - QC report on all samples submitted (FastQC)
Alignment using BWA to reference sequence
Analysis-ready bam files based on Board GATK best practice
Coverage statistics
Annotated variant report of SNVs and small Indels in VCF format
Somatic point mutation using MuTect if paired samples
ChIP-seq - QC, align resulting FASTQ files with BWA (or other suitable aligner)
Identify binding sites with Model-based Analysis for ChIP-Seq (MACS)
Peak and summit locations in BED-format files.
Proteomics Standard Deliverables
Proteome Discoverer is utilized for processing qualitative and quantitative proteomics data collected on ThermoScientific mass spectrometers. The standard deliverables are:
- Protein identification
- Protein quantitation
- Protein modification analysis
- Pathway analysis
Center Director(s)
Jeff Delrow, PhD
Available to
Anyone
Resource Type
Core Laboratory
Institution
Fred Hutchinson Cancer Center
Bioinformatics Core, Benaroya Research Institute, 1201 9th Ave, Seattle, WA 98101
Department of Environmental and Occupational Health Sciences, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105
University of Washington Center for AIDS and STDs, 325 Ninth Avenue, Seattle, WA 98104
(206) 744-2238 or (206) 744-3785(206) 744-2238 or (206) 744-3785
Behavioral Science Biobank Bioinformatics Clinical Data & Software Database Other Sleep Study Facility
Biobehavioral Nursing and Health Informatics Univeristy of Washington, School of Nursing Seattle, WA 98195 United States
Center for Social Science Computation and Research, University of Washington, Seattle, WA 98195
Human Studies Core, VA Puget Sound Health Care System, 1660 S. Colombian Way, Seattle, WA 98108
University of Washington SBRP, Department of Environmental Health, Seattle, WA 98195
P.O. Box 19024, DE-740 Seattle, WA 98109
Institute of Translational Health Sciences, 850 Republican Street, Box 358051, Seattle, WA 98109
Sexually Transmitted Infections Cooperative Research Center Laboratory core, Center for AIDS and STD, 325 9th Ave, Seattle, WA 98104
(206) 744-4239(206) 744-4239
Health Sciences Library, lower level, Room T216 1959 NE Pacific St Seattle, WA 98195 United States
Thomas Building, 1100 Fairview Ave N, Seattle, WA 98109 0 mi
1100 Fairview Ave N ME-B143, Arnold Building Seattle, WA 98109 United States 0.01 mi
1100 Eastlake Building, E1-140 Seattle, WA 98109 0.17 mi
P.O. Box 19024, DE-550 Seattle, WA 98109 0.42 mi
PO Box 19024, DE-360 Seattle, Washington 98109 0.42 mi
P.O. Box 19024, DE-690 Seattle, WA 98109 0.42 mi
P.O. Box 19024, DE-740 Seattle, WA 98109 0.42 mi
P.O. Box 19024, DE-352 Seattle, WA 98109 0.42 mi
P.O. Box 19024, J3-317 Seattle, WA 98109 0.42 mi
P.O. Box 19024, B1-010 Seattle, WA 98109 0.42 mi
(206) 667-4314(206) 667-4314
P.O. Box 19024, E1-415 Seattle, WA 98109 0.42 mi
P.O. Box 19024, DE-512 Seattle, WA 98109 0.42 mi
Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109 0.42 mi
(206) 732-1200(206) 732-1200
Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109 0.43 mi
UW Medicine Proteomics Lab, South Lake Union, 815 Mercer St, Seattle, WA 98109 0.46 mi
Veterinary Diagnostic Laboratory, 815 Mercer St. Room 310N, Seattle, WA 98195 0.46 mi
VTMC, UW SLU, 815 Mercer St, Seattle, WA 98109 0.46 mi
South Lake Union Confocal Facility, 815 Mercer St, Seattle, WA 98109 0.46 mi
815 Mercer Street, Seattle, WA 98109, United States 0.46 mi
The Institute is supported by grants UL1 TR002319, KL2 TR002317, and TL1 TR002318 from the NIH National Center for Advancing Translational Sciences through the Clinical and Translational Science Awards Program (CTSA).
Please help us continue to support your research by citing our grant number(s) in publications we supported.