Take advantage of customizable, project-based consulting, and exploit the full potential of BioDiscovery products.
BioDiscovery Consulting Group is an advanced team of scientists and experts who will work directly with you on your project, from initial study design through to complex data analysis. This is often the most cost-effective way to maximize precious research resources and time.
BioDiscovery offers fee-based consulting services including Jumpstart Services to help you get your team off to a quick start with the BioDiscovery products anywhere in the world.
For more information on Biodiscovery’s consulting services please contact us.
|Data Analysis Services||Detailed analysis and data exploration.|
|Study Design||Create efficient and robust experiments that maximize the likelihood of positive results, create data for serendipitous insights, and minimize re-work.|
|Nexus JumpStart||Getting Started” package from installation, initial user training, loading data sets, and basic analysis (includes Introduction class – either Nexus Copy Number for Cytogenetics or Nexus Copy Number for Research – Fundamentals).|
|Upgrade Services||System upgrade planning and execution, along with data migration, for new versions of BioDiscovery software. Includes a “what\’s new” training session.
OncoScan®, from Affymetrix, is an advanced technology that is able to extract multiple cancer genome measurements from challenging FFPE samples with very low input DNA requirements. Since its inception, BioDiscovery Nexus has been the software platform of choice for analyzing OncoScan data, and is the OEM provider of Nexus Express for OncoScan (the software that ships with OncoScan).
Application Scientists from BioDiscovery have been providing consulting services to several major customers across top-tier academic institutions, cancer centers, and biopharmaceutical companies who are taking advantage of the OncoScan platform. BioDiscovery scientists have completed projects ranging from data curation through biomarker discovery and advanced research (and have been cited in the resulting publications). OncoScan Consulting from BioDiscovery takes advantage of this experience to deliver cost-effective data analysis.
Cancer samples from FFPE tissues, with low input DNA, present several challenges for initial data analysis. Before any meaningful downstream results can be achieved, the input data must meet quality standards. We have found through experience, Nexus’ calling algorithms can resolve large copy number changes even if the superficial quality scores (e.g., probe variance) appear to fail. However, we have also found that tumor ploidy, as well as polyclonality, can complicate the initial baseline. BioDiscovery scientists will review the sample set, sample-by-sample, to optimize the calling parameters (significance, calling thresholds, segment size) and reset the sample baseline to maximize the amount of useful downstream data. Likewise, all samples will be reviewed to ensure usability for further analysis.
Biomarker Discovery from Copy Number Variation
OncoScan has been principally used for CNV detection. BioDiscovery scientists will use the statistical tools in Nexus Copy Number to analyze the data set and arrive at a copy number profile, (using a variety of statistical techniques, including STAC and GISTIC). If phenotype or other annotations are available that can stratify the data, we will perform tests to find meaningful CNV differences between groups. If survival or other continuous data are present, we will apply predictive power tests to uncover aberrations that are predictive of outcomes.
Academic research projects can be similar to biomarker discovery projects, but often contain a richer set of phenotypic, survival, continuous data, and other annotations, and may often contain other genomic data associated with the samples. BioDiscovery scientists are experienced in analyzing these data sets, and can employ tools to further enhance the ability to discover various genomic correlates. These projects are best approached in a collaborative fashion, since specific knowledge of the disease biology, suspect pathways, and other factors can play a substantial role in uncovering novel findings.