Paul Spellman Laboratory

Summary:

The Spellman Lab is interested in using genetic, genomic, and proteomic data to understand and model the biology of cancer and to develop methods to effectively deploy therapeutic agents in the age of molecularly guided medicine.

Members of the lab use a combination of conventional molecular biology, high throughput genomic and proteomic assays, and bioinformatic analyses in their work.

Affiliations:

• Department of Molecular & Medical Genetics, Oregon Health & Science University

People:

• PI: Spellman, Paul, Ph.D.
  

Member: Peto, Myron, Ph.D.
Role: Senior Research Associate

Resources:

Software

• Beyond the bam file: Analysis ( Algorithmic software suite )
  

  An analysis pipeline that includes the following components:
  muTect: Cancer-specific variant calling
  ANNOVAR: Annotate mutation
  Breakdancer? Delly?: Structural variant calling
  OHSU proprietary pipeline: Copy number analysis

• Spellman Lab mutation calling pipeline ( Algorithmic software suite )
  

  A GATK-based pipeline for aligning tumor and normal sequencing reads.
  
  This perl script programmatically preps and pushes data through a processing pipeline that includes the following tools:
  
  BWA mem + SAM tools: Read alignment
  Picard Tools: Mark duplicates
  GATK (RealingerTargetCreator, IndelRealinger): Local Realignment
  GATK (BaseRecalibration and PrintReads): Re-calibrate quality scores

Web Links:

• http://www.ohsu.edu/spellmanlab