Testicular Germ Cell Tumors (TGCT) Samples Report
2014_07_15 Data Snapshot
Overview
Introduction

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.

Summary

There were 0 redactions, 0 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.

Table 1.  This table provides a breakdown of sample counts on a per sample type and, if applicable, per subtype basis. Each count is a link to a table containing a list of the samples that comprise that count and details pertaining to each individual sample (e.g. platform, sequencing center, etc.). Please note, there are usually multiple protocols per data type, so there are typically many more rows than the count implies.

Sample Type BCR Clinical CN LowP Methylation mRNA mRNASeq miR miRSeq RPPA MAF
TP 150 0 0 0 0 0 0 0 0 0 0
Totals 150 0 0 0 0 0 0 0 0 0 0
TGCT Primary Solid Tumor BCR Data

Table S1. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-2G-AAEW Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAEX Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAF1 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAF4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAF6 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAF8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFE Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFG Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFH Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFI Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFJ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFL Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFM Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFN Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFO Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFV Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFY Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAFZ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAG0 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAG3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAG5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAG6 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAG7 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAG8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAG9 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGA Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGC Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGE Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGF Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGG Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGI Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGJ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGK Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGM Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGN Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGO Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGP Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGS Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGT Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGV Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGW Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGX Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGY Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAGZ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAH0 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAH2 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAH3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAH4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAH8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAHA Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAHC Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAHG Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAHL Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAHN Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAHP Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAHT Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAKD Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAKG Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAKH Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAKL Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAKM Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAKO Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAL5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAL7 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALF Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALG Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALN Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALO Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALP Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALQ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALR Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALS Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALT Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALW Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALX Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALY Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AALZ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAM2 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAM3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2G-AAM4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2X-A9D5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-2X-A9D6 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-4K-AA1G Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-4K-AA1H Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-4K-AA1I Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-4K-AAAL Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-S6-A8JW Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-S6-A8JX Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-S6-A8JY Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-SB-A6J6 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-SB-A76C Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-SN-A6IS Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-SN-A84W Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-SN-A84X Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-SN-A84Y Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-SO-A8JP Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-VF-A8A8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-VF-A8A9 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-VF-A8AA Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-VF-A8AB Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-VF-A8AC Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-VF-A8AD Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-VF-A8AE Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-W4-A7U2 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-W4-A7U3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-W4-A7U4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-WZ-A7V3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-WZ-A7V4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-WZ-A7V5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-WZ-A8D5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-X3-A8G4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-A8H1 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-A8H4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-A8H5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-A9SE Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AANI Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AANJ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AANR Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AANV Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AAO3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AAO4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AAO6 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AAOB Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AAOC Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AAOD Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AAOF Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AAOJ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XE-AAOL Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XY-A89B Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XY-A8S2 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XY-A8S3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-XY-A9T9 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-YU-A90P Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-YU-A90Q Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-YU-A90S Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-YU-A90W Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-YU-A90Y Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-YU-A912 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-YU-A94D Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-YU-A94I Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-YU-AA4L Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-YU-AA61 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-ZM-AA05 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-ZM-AA06 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-ZM-AA0B Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-ZM-AA0D Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-ZM-AA0E Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-ZM-AA0F Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-ZM-AA0H Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-ZM-AA0N Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen

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.

Results
FFPE Cases
Additional Annotations from the DCC's Annotations Manager
Methods & Data
Redactions and Other Annotations

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

Preprocessors
mRNA Preprocessor

The mRNA preprocess median module chooses the matrix for the platform(Affymetrix HG U133, Affymetrix Exon Array and Agilent Gene Expression) with the largest number of samples.

mRNAseq Preprocessor

The mRNAseq preprocessor picks the "scaled_estimate" (RSEM) value from Illumina HiSeq/GA2 mRNAseq level_3 (v2) data set and makes the mRNAseq matrix with log2 transformed for the downstream analysis. If there are overlap samples between two different platforms, samples from illumina hiseq will be selected. The pipeline also creates the matrix with RPKM and log2 transform from HiSeq/GA2 mRNAseq level 3 (v1) data set.

miRseq Preprocessor

The miRseq preprocessor picks the "RPM" (reads per million miRNA precursor reads) from the Illumina HiSeq/GA miRseq Level_3 data set and makes the matrix with log2 transformed values.

Methylation Preprocessor

The methylation preprocessor filters methylation data for use in downstream pipelines. To learn more about this preprocessor, please visit the documentation.