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