The Broad GDAC mirrors data from the DCC on a daily basis. Although all data is mirrored, not every sample is ingested into Firehose. There are three main mechanisms that filter samples to ensure that only the most scientifically relevant samples make it into our standard data and analyses runs. These three mechanisms are redactions, replicate filtering, and blacklisting. This report summarizes the data that is ingested into Firehose, describes the three filtering mechanisms, lists those samples that are removed, and gives all available annotations from the DCC's Annotation Manager.

There were 0 redactions, 18 replicate aliquots, 0 blacklisted aliquots, and 0 FFPE aliquots. The table below represents the sample counts for those samples that were ingested into firehose after filtering out redactions, replicates, and blacklisted data, and segregating FFPEs.

The sample type short letter codes in the table above are defined in the following list.

• TP: Primary Solid Tumor

• TR: Recurrent Solid Tumor

• TB: Primary Blood Derived Cancer - Peripheral Blood

• TAP: Additional - New Primary

• TM: Metastatic

• TAM: Additional Metastatic

• NB: Blood Derived Normal

• NT: Solid Tissue Normal

The following platforms are outdated and are not included in the counts depicted in the table above.

• Agilent SurePrint G3 Human CGH Microarray Kit 1x1M

• Agilent Human Genome CGH Microarray 244A

• Agilent Human Genome CGH Custom Microarray 2x415K

• Affymetrix Human Exon 1.0 ST Array

• Illumina DNA Methylation OMA002 Cancer Panel I

• Illumina DNA Methylation OMA003 Cancer Panel I

• Illumina Human1M-Duo BeadChip

• Illumina 550K Infinium HumanHap550 SNP Chip

Figure 1.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

Annotation data was taken from theTCGA Data Portalusing the query string:

https://tcga-data.nci.nih.gov/annotations/resources/searchannotations/json?item=TCGA

Redaction information was generated by filtering for the annotationClassificationName "Redaction"

FFPE information was generated by filtering for "FFPE" in annotation note text

Additional FFPEs were garnered from clinical data

Remaining annotations were sorted into sections by annotationClassificationName