Bioinformatics, Fred Hutchinson Cancer Research Center

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Fred Hutchinson Cancer Research Center, Thomas Building DE-740
1100 Fairview Avenue North Seattle Washington 98109 US
(206) 667-2714(206) 667-2714

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:

  1. 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.
  2. 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 Research Center
Institution
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Thomas Building, 1100 Fairview Ave N, Seattle, WA 98109 0 mi
(206) 667-4289(206) 667-4289
Electron Microscopy provides transmission electron microscopy and scanning electron microscopy fo...
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1100 Eastlake Building, E1-140 Seattle, WA 98109 0.17 mi
(206) 667-6612(206) 667-6612
Antibody Technology provides custom designed monoclonal antibodies made in mice, rats and rabbits...
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P.O. Box 19024, DE-352 Seattle, WA 98109 0.42 mi
(206) 667-1051(206) 667-1051
The Proteomics Resource provides support for characterizing proteins and peptides by mass spectro...
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P.O. Box 19024, DE-740 Seattle, WA 98109 0.42 mi
(206) 667-2714(206) 667-2714
The Genomics Shared Resource provides expertise to support the generation of genomics-based data....
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P.O. Box 19024, DE-690 Seattle, WA 98109 0.42 mi
(206) 667-6195(206) 667-6195
Flow Cytometry offers a wide range of instrumentation, from single-laser benchtop analyzers to co...
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PO Box 19024, DE-360 Seattle, Washington 98109 0.42 mi
(206) 667-6166(206) 667-6166
The Experimental Histopathology Shared Resource provides a broad range of histology, histochemist...
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P.O. Box 19024, J3-317 Seattle, WA 98109 0.42 mi
(206) 667-5879(206) 667-5879
This resource provides space for freezers used to store research samples, offers assistance with ...
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P.O. Box 19024, DE-550 Seattle, WA 98109 0.42 mi
(206) 667-6455(206) 667-6455
The Immune Monitoring Lab provides investigators with services and expertise for studies of cellu...
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P.O. Box 19024, DE-512 Seattle, WA 98109 0.42 mi
(206) 667-4205(206) 667-4205
Scientific Imaging serves as a centralized facility for imaging and visualization. The resource p...
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P.O. Box 19024, E1-415 Seattle, WA 98109 0.42 mi
(206) 667-4645(206) 667-4645
Specimen Processing/Research Cell Bank provides a broad range of services including processing of...
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P.O. Box 19024, B1-010 Seattle, WA 98109 0.42 mi
(206) 667-4314(206) 667-4314
The Arnold Library provides high quality, responsive services and resources in support of Fred Hu...
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Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109 0.42 mi
(206) 732-1200(206) 732-1200
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Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109 0.43 mi
(206) 732-1200(206) 732-1200
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Veterinary Diagnostic Laboratory, 815 Mercer St. Room 310N, Seattle, WA 98195 0.46 mi
(206) 685-3040(206) 685-3040
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South Lake Union Confocal Facility, 815 Mercer St, Seattle, WA 98109 0.46 mi
ronse@uw.eduronse@uw.edu
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UW SLU, 815 Mercer St, Seattle, WA 0.46 mi
The overall goals of the QFPC are to provide the powerful tools of modern mass spectrometry and c...
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815 Mercer Street, Seattle, WA 98109, United States 0.46 mi
(206) 543-3061(206) 543-3061
The Bio-Molecular Imaging Center’s (BMIC) mission is to develop novel imaging techniques for anat...
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815 Mercer Street, Seattle, WA 98109, United States 0.46 mi
(206) 543-3061(206) 543-3061
The Bio-Molecular Imaging Center’s (BMIC) mission is to develop novel imaging techniques for anat...
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UW Medicine Proteomics Lab, South Lake Union, 815 Mercer St, Seattle, WA 98109 0.46 mi
(206) 616-0659(206) 616-0659
Our current focus is to provide mass spectrometry resources and computational support for the gre...
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VTMC, UW SLU, 815 Mercer St, Seattle, WA 98109 0.46 mi
(206) 543-1681(206) 543-1681
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Cite ITHSThe 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).

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