Curated CNVs, Sequence Variants, Simplified Access.
The Cancer Genome Atlas (TCGA) is an amazing resource, growing to contain genomic profiles of approaching 12,000 tumors across more than thirty cancer types. By re-analyzing the data and manually curating the results of each sample by trained scientists, the TCGA Premier database has the highest fidelity copy number information from this rich resource.
Each sample is re-processed from the “raw” (i.e., level 1) data, then manually reviewed by a team of scientists ensuring the highest fidelity CNV calls.
Processing GISTIC samples produced results suited for population-wide profiles, but left individual samples over-segmented and many having incorrect ploidy. By repairing these, and integrating sequence variants, we have enabled the data set to become more useful for studies such as survival analysis or tumor sub-type profiling.
Sequence variants obtained by whole-exome sequencing are integrated with CNVs, providing a more comprehensive genomic picture.
Query by gene, region, an event, or clinical annotation – typically in seconds. Data can be downloaded to your Nexus project and integrated with other data sources for more robust analyses.
TCGA Premier is already integrated with Nexus Copy Number software, allowing users to quickly query the database, retrieve samples of interest along with annotations, and perform further analysis all through the Nexus interface.
Beginning with the raw data available through special access, we have paired the tumors with their matched normal to remove germline polymorphisms. Expert scientists then review the genomic profiles of each sample, correct for baseline ploidy and segmentation, and manually call copy-neutral homozygous segments (LOH) and events on the mosaic threshold boundary. Sequence variant information is integrated from exome sequencing data, and the resultant dataset made available through Nexus Copy Number.
To further enhance usability, samples with complex tumor profiles are “flagged” for the researcher, as are suspected chromothriptic events. Samples with poor quality that introduce statistical noise are removed.
The data set is fully annotated with reviewer comments for specific samples, calling parameter settings that were used, other sample-specific information along with detailed clinical annotations, such as survival, tumor grade, etc., that foster further analyses.
We have current dataset samples available for different tumor types.
BioDiscovery provides a full line of modular software packages.
Able to handle and process data from all commercial platforms.
Optimum usage of computing.
Usefulness to our community of users.