New Release of Beat AML Mutations, CPTAC Cases, and Fusion Data
In Data Release 34, the GDC released new data from the Beat AML and Clinical Proteomic Tumor Analysis Consortium (CPTAC) programs:
Access Data
Does the GDC provide access to germline variants?
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Any germline SNP calls are not available for exploration in the GDC Data Portal. Instead, alignments for germline data are available under controlled access. Users with appropriate access may use the alignments to generate germline variants.
Some somatic variants callers, such as MuTect2, also output somatic calls with some level of germline possibilities, such as those labelled as "germline_risk". Please note that these calls are, by no means, germline variants. They are somatic calls with boundary probability of germline risks.
How often does the GDC update the workflow/reference genome? If the GDC updates the workflow/reference genome, does the GDC re-process all data sets?
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For the reference genome, the GDC has been using an augmented version of GRCh38.p2 (with additional decoy sequences and virus sequences) since inception. The GDC does not use alternative contigs, and only derives high-level data from the major chromosomes, so the same reference genome is used for both gene model GENCODE v22 (from Data Release 1 to 31) and GENCODE v36 (from Data Release 32). As future versions of the reference genome are released, e.g., GRCh39, the GDC will evaluate the benefits of updating data to utilize the new version.
GDC Now Supports m6A MeRIP-Seq Data and the UICC Tumor Staging System
In GDC Data Dictionary Release 2.5.0, the GDC added support for:
Exceptional Responders and MP2PRT: New NCI Projects at the GDC!
In Data Release 33, the GDC released data from two new projects at the GDC:
Can GENCODE v22 data still be downloaded from the GDC Data Portal?
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Although GENCODE v22 data cannot be browsed in the GDC Data Portal, it can still be downloaded using the GDC Data Transfer Tool or API. You will need to either have a previous manifest or use known UUIDs to download v22 files.
Why are there fewer open access TCGA mutations in DR 32 (GENCODE Update Release)?
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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.
What data types were updated in DR 32 (GENCODE Update Release)?
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- RNA-Seq
- Replaced all RNA-Seq data including: Alignments, Gene Expression (STAR) + New Normalization, Transcript Fusion
- Removed HTSeq Files
- Re-harmonized TCGA data to use the newer pipeline
- WXS/Targeted Sequencing
- Generated and versioned new annotated somatic mutations and Ensemble MAFs
- Re-harmonized TCGA data to use the newer pipeline (alignments + mutation calls)
- WGS
- Generated and versioned structural variant and gene level copy number data
- Methylation
GDC Gene Model Updated to GENCODE 36
The gene model used as a reference across GDC has been updated from GENCODE 22 to GENCODE 36. GENCODE gene sets are continuously updated to improve the coverage and accuracy.
Data from Landmark Chernobyl studies, New Methylation Pipeline, and More
Highlights from the GDC's recent Data Release 30 include data from major studies exploring the effects of Chernobyl radiation and methylation arrays processed via a new pipeline at the GDC.