TCGA

The GDC categorizes whole genome sequencing (WGS) coverage using the wgs_coverage property, which groups BAM files into four range buckets: 0x-10x, 10x-25x, 25x-150x, and 150x+. "High coverage" WGS in the GDC generally refers to alignments with a mean depth of 25x or greater — meaning, on average, each base in the genome is covered by at least 25 sequencing reads. This threshold reflects the minimum depth at which variant calling pipelines (SNV, indel, and structural variant) achieve reliable sensitivity and specificity for somatic mutation detection in cancer genomics.

TCGA clinical data was expanded in GDC Data Releases 42 and 43. TCGA clinical data used to have one diagnosis per case. With the clinical data expansion, it is possible that a TCGA case has multiple diagnoses. This could be due to pre-enrollment diagnoses or other reasons. To properly query for the diagnosis information associated with the molecular data, the primary disease flag should be set to true (i.e., diagnosis_is_primary_disease = true).

The primary reasons for the fewer open-access mutations are from two strategies that improve quality: 1) TCGA is now using a 2-caller ensemble, instead of a single caller; 2) Removal of variants outside of the target capture region, instead of a combined “target capture + GAF exonic region”. Additionally, TCGA was the original project in which GDC open-access variants were produced and used variant rescue steps that only applied to TCGA. To keep the TCGA variant-calling pipeline consistent across projects, GDC is no longer rescuing MC3 and TCGA validation variants.

The GDC supports the submission of clinical and biospecimen supplements. Supplemental files can be downloaded from the GDC by searching for the Data Type "Clinical Supplement" or "Biospecimen Supplement" from the facet search in the GDC Data Portal Repository. For TCGA data, the supplement data is provided in XML documents and tab delimited files (biotabs). These files, in varying degrees, provide information on marker status (e.g.

TCGA “collection” represents the collection of the sample for TCGA, whereas “procurement” represents the removal of tissue from the patient.

The GDC harmonizes data across projects. This includes aligning the genomic data to a common reference genome (HG38) and generating higher level data using GDC bioinformatics pipelines. Other repositories may process the data differently.

The TCGA marker and other landmark cancer genomics papers, as well as associated supplemental files, are available on the GDC Publication Pages. The Publication Pages provide access to publication information and supplementary files.

Submitting treatment data is optional as not all projects are associated with treatment studies. For TCGA projects, for example, not all projects and cases have treatment data. For TCGA projects with treatment data, information is available in applicable clinical supplement files (i.e. clinical XML, biotabs). For other project associated with treatment studies in which the treatment data has been submitted to the GDC, treatment data is available for download in JSON and TSV format. These studies may also contain clinical supplement files.

The availability of follow-up data is specific to the project and associated study.

For the Multiple Myeloma Research Foundation (MMRF) Clinical Outcomes in Multiple Myeloma to Personal Assessment of Genetic Profile (CoMMpass) study, longitudinal information was generated to track patients over the course of their disease. This data is available in the GDC by viewing the clinical follow-up data available for download on each case page in the GDC Data Portal or by querying the GDC API.