Bioinformatics, Fred Hutchinson Cancer Center

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