DNA Methylation¶
The DNA Methylation data for genomic build HG19 DNA Methylation HG19 table contains one row per CpG probe and TCGA aliquot. The DNA Methylation data for genomic build HG38 is pulled from the GDC, DNA Methylation HG38.
Each TCGA aliquot is uniquely represented by a
TCGA barcode
of length 24, eg TCGA-04-1517-01A-01D-0533-01. (For more information on how TCGA barcodes
were created and how to “read” a TCGA barcode, click on the preceding link.)
The platform annotation information needed to analyze this data is also available in a BigQuery table. For more information, see the Reference Data section of this documentation.
Platform¶
DNA Methylation data was generated for the TCGA project using the Illlumina HumanMethylation27 BeadChip and its successor, the HumanMethylation450 BeadChip.
Pipeline¶
DNA Methylation data was generated for the TCGA project at the JHU-USC genome characterization center.
A DESCRIPTION.txt file is included with each data archive at the DCC describing the algorithms,
methods, and protocols used to produce the Level-1, Level-2, and Level-3 data.
ETL Details¶
The BigQuery table is populated only with the files matching the pattern
%.HumanMethylation%.txt. The data from both 27k and 450k platform have been
merged together into a single table. A few samples were run on both platforms, and
for those samples, the 450k data takes precedence.
The table includes a platform column indicating the source of each data value.
In addition:
- any CpG probes for which the Level-3
Beta_Valueis NA or NULL, are left out - only the
Probe_IdandBeta_Valuefields from the Level-3 data files are stored in the BigQuery table
Since the DNA_Methylation_betas table is so large, we also provide chromosome-specific tables that can be used for faster queries.