A second major goal of the center is to coordinate relevant databases and streamline bioinformatic, biostatistical, and data analysis needs of SCLC investigators. Resources for this include the Vanderbilt Center for Quantitative Sciences, and the cBioPortal platform housed at MSKCC. We have the computational capacity, expertise, and track record to house, visualize, and analyze the diverse data produced by Consortium sites.
Vanderbilt Center for Quantitative Sciences
The CQS is led by Yu Shyr, and the CQS data management and coordination program is led by Lynne Berry. The CQS has extensive experience providing database and informatics support similar to that required for success of the SCLC Coordinating Center. Among other major research networks, the CQS supports the Lung Cancer Mutation Consortium, a collaborative network of lung cancer investigators at 16 major academic research institutions across the country, and the NCI Barrett’s Esophagus Translational Research Network. The CQS supports web-based data management applications to capture patient clinical, pathological, FISH, and IHC data and can integrate these data with genomic sequencing data to prepare data reports, as well as provide data analysis and results interpretation. The SCLC Consortium will maintain information on many human-derived models, cell lines, and serial tumor biopsies, for which associated clinical demographics and clinical outcome data would be uniquely valuable. A second custom application developed by the CQS supports ongoing specimen tracking and management, including automated notifications to biobanks to distribute specimens and requests to the investigator to confirm specimen receipt.
The SCLC Consortium cBioPortal
The cBioPortal for Cancer Genomics is a powerful and flexible suite of integrated analytic tools for omic-level data storage, visualization, and analysis. This system enables intuitive evaluation and visualization of complex cancer genomics data and is now used by thousands of cancer researchers and clinicians around the world. CBioPortal was initially developed by a team of investigators led by Niki Schultz at MSK as web-based platform to support the data generated by The Cancer Genome Atlas (TCGA), and continues to be maintained and expanded by the Schultz laboratory. The cBioPortal supports multiple SU2C dream teams, NCI-supported SPOREs and PO1s, and other multi-investigator consortia. Recently, the cBioPortal infrastructure was expanded to support storage and visualization of patient-derived xenografts (PDX) alongside the corresponding profile of the human tumor from which they were derived, and a version of the portal in support of mouse genetic data is in development. We will use cBioPortal to store and annotate gemomic data sets of SCLC , providing access to these data sets through a single Consortium interface, and expand these to include relevant data from the SCLC research community.
The CellMiner database enables exploration and analysis of cancer cell line pharmacogenomic data across different sources. This resource is available to the public here.