BioDiscovery

TCGA Premier

Curated CNVs, Sequence Variants, Simplified Access.

TCGA Premier Benefits

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.

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Improved Copy Number Profiles

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.


Repaired Individual Sample ploidy

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.

Integrated Sequence Variants

TCGAPremier-2

Sequence variants obtained by whole-exome sequencing are integrated with CNVs, providing a more comprehensive genomic picture.


Easy to access

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.

Integrated with Nexus Copy Number Software

TCGAPremier-3

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.


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TCGA Premier Approach

Integrated With Nexus Copy Number Datasets

TCGAPremier-4

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.

Enhanced User Experience

TCGAPremier-5

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.

 

 

 

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Fully Annotated Data Set

TCGAPremier-6

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.

BioDiscovery Benefits

BioDiscovery provides a full line of modular software packages.

Versatility

Able to handle and process data from all commercial platforms.

Efficiency

Optimum usage of computing.

Acute Sense of Fitness for Purpose

Usefulness to our community of users.

These products empower Biologists and Geneticists with sophisticated, yet highly usable tools to analyze and interpret their data and draw meaningful conclusions.