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For example, the mutation data in the publication usually underwent more QC, and false positives might have been removed or, in rare cases, false negatives added. RNA-Seq and copy-number values may also differ slightly, as different versions of analysis pipelines could have been used. Additionally, due to additional curation during the publication process, the clinical data for the publication may be of higher quality or may contain a few more data elements, sometimes derived from the genomic data (e.g., genomic subtypes).
The TCGA PanCancer Atlas datasets derive from an effort to unify TCGA data across all tumor types. Publications resulting from this effort can be found at the TCGA PanCancer Atlas site. In the cBioPortal, data from the PanCancer Atlas is divided by tumor type, but these studies have uniform clinical elements, consistent processing and normalization of mutations, copy number, mRNA data and are ideally processed for comparative analyses.
TCGA studies not sourced from GDC have the original mutation data generated by the individual TCGA sequencing centers. The source of the data is the Broad Firehose (or the publication pages for data that matches a specific manuscript). These data are usually a combination of two mutation callers, e.g. a variant caller like MuTect plus an indel caller. Note that the specific tools used and the overall process for identifying mutations can vary between centers and may have changed over time.
-TCGA studies sourced from GDC use a newer version of the human reference genome, GRCh38 instead of GRCh37. For more information about the GDC data processing pipeline, see GDC Data Processing. Transformations specific to our NCI-CRDC pipeline are documented in the cBioPortal Datahub.
+TCGA studies sourced from GDC use a newer version of the human reference genome, GRCh38 instead of GRCh37. For more information about the GDC data processing pipeline, see GDC Data Processing. Transformations specific to our NCI-CRDC pipeline are documented in the cBioPortal Datahub.