The CMO is one of several Collaborative Research Centers at MSKCC that help researchers translate their work into real benefits for cancer patients and clinicians. To this end, we interface with investigators across MSKCC, understand their research/clinical questions, and design sequencing experiments to help answer them. This ensures that core skills and experience in sequencing/bioinformatics don't need to be duplicated within each investigator's lab. Conversely, to avoid creating a dependency on us, our tools/pipelines are open-sourced on GitHub [1,2,3,4] and decently documented. Described below are some key groups within the CMO.
Led by Oliver Hampton, Platform Informatics is a nimble team of bioinformatics analysts and Python/Java engineers responsible for workflow automation from sample tracking, sequencing and data analysis, to publication-ready plots and results. We're seeking to fill 4 positions, a Bioinformatics Engineer Lead for pipeline design/development, two Computational Biologists (plus me) to extend our tools/pipelines to satisfy research/clinical goals, and a LIMS Engineer to improve sample tracking and automation at the sequencing lab. Agnes Viale and Nick Socci oversee sequencing and informatics operations at the CMO, including Platform Informatics.
Led by Barry Taylor, Computational Oncology is a team of scientists who handle the translational projects that need more nuanced analysis (in R/Python), beyond what can be automated, like allelic imbalance and somatic hotspots.
Led by Mike Berger, the Innovation Lab tests new sequencing techniques/technologies like cfDNA and molecular barcoding. Mike is also responsible for MSK-IMPACT, the first NGS assay approved by the FDA for tumor-profiling.