Adrenocortical Carcinoma (ACC) Samples Summary Report
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, and lists those samples that are removed.

Summary

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

Table 1.  Get Full Table Summary of TCGA Tumor Data.

Tumor BCR Clinical CN LowP Methylation mRNA mRNASeq miR miRSeq RPPA MAF
ACC 92 0 0 0 0 0 0 0 0 0 0
Results
Ingested Samples

This section includes a more granular look at the samples ingested into Firehose. A sample counts table is provided that is broken down by sample type (e.g. Primary Solid Tumor, Recurrent Solid Tumor, Normal Blood, etc.). Furthermore, each count is a link to an additional table containing a breakdown of the samples and their specific details (e.g. platform, sequencing center, etc.).

The following platforms are outdated and are not included in the counts depicted in the table below.

  • 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

The sample type short letter codes in the table below 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

Table 2.  Click on any sample count to display a table detailing all the samples that comprise that count. 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 92 0 0 0 0 0 0 0 0 0 0
Totals 92 0 0 0 0 0 0 0 0 0 0
ACC Primary Solid Tumor BCR Data

Table S1. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-OR-A5J1 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5J2 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5J3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5J4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5J5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5J6 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5J7 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5J8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5J9 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JA Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JB Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JC Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JD Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JE Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JF Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JG Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JH Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JI Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JJ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JK Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JL Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JM Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JO Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JP Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JQ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JR Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JS Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JT Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JU Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JV Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JW Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JX Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JY Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5JZ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5K0 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5K1 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5K2 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5K3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5K4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5K5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5K6 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5K8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5K9 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KB Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KO Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KP Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KQ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KS Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KT Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KU Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KV Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KW Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KX Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KY Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5KZ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5L1 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5L2 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5L3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5L4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5L5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5L6 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5L8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5L9 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LA Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LB Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LC Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LD Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LE Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LF Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LG Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LH Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LI Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LJ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LK Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LL Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LM Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LN Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LO Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LP Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LR Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LS Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OR-A5LT Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-OU-A5PI Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-P6-A5OF Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-P6-A5OG Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-P6-A5OH Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-PA-A5YG Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-PK-A5H8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-PK-A5H9 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-PK-A5HA Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-PK-A5HB Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-PK-A5HC Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen

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

Filtered Samples
Redactions

For TCGA data, redaction is the removal of cases from the data prior to publication or release. Redacted cases are generally rare, but cases must be redacted when the TSS/BCR subject link is incorrect ("unknown patient identity"), or in the case of genotype mismatch, completely wrong cancer, or completely wrong organ/tissue. Redaction occurs regardless of a case's analyte characterization or DCC data deposition status.

Rescission is the removal of samples from the list of redactions. This happens if the reason for redaction is eventually cleared up. For clarity, rescinded redactions do not appear in this report.

There were no redactions.

Replicate Samples

In many instances there is more than one aliquot for a given combination of individual, platform, and data type. However, only one aliquot may be ingested into Firehose. Therefore, a set of precedence rules are applied to select the most scientifically advantageous one among them. Two filters are applied to achieve this aim: an Analyte Replicate Filter and a Sort Replicate Filter.

Analyte Replicate Filter

The following precedence rules are applied when the aliquots have differing analytes. For RNA aliquots, R analytes are preferred over T analytes, since it is the more accurate extraction protocol. For DNA aliquots, D analytes (native DNA) are preferred over G, W, or X (whole-genome amplified) analytes, unless the G, W, or X analyte barcode has a higher plate number.

Sort Replicate Filter

The following precedence rules are applied when the analyte filter still produces more than one sample. The sort filter chooses the aliquot with the highest lexicographical sort value, to ensure that the barcode with the highest portion and/or plate number is selected when all other barcode fields are identical.

There were no replicate samples.

Blacklisted Samples

In certain circumstances, replicate filtering may choose the less favorable among two or more aliquots. For instance, an analyst may manually review two aliquots for a given individual and determine that one is superior. If the replicate filtering would choose the inferior sample, then the inferior sample can be added to this blacklist. This would result in the desired sample being chosen. This table lists those blacklisted samples and a reason for their being blacklisted.

There were no blacklisted samples.

Methods & Data
Redactions

Redaction data was taken from the TCGA Data Portal using the query string:

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

for the following CATEGORY_ID values:

  • 1 = Tumor tissue origin incorrect

  • 2 = Tumor type incorrect

  • 3 = Genotype mismatch

  • 5 = Subject identity unknown

  • 27 = Duplicate case

  • 37 = Administrative Compliance

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.