Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (DLBC) 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, 18 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.  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 28 0 18 0 18 0 0 0 17 0 0
NB 16 0 16 0 0 0 0 0 0 0 0
Totals 28 0 18 0 18 0 0 0 17 0 0
DLBC Primary Solid Tumor BCR Data

Table S1. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-FA-8693 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FA-8693 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8041 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8041 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8042 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8042 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8043 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8043 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8046 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8046 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8047 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8047 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8061 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8061 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8062 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8062 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FM-8000 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FM-8000 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-G8-6324 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-G8-6324 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-G8-6325 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-G8-6325 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-G8-6326 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-G8-6326 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-G8-6906 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-G8-6906 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-G8-6907 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-G8-6907 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-G8-6909 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-G8-6909 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-G8-6914 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-G8-6914 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GR-7351 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GR-7351 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GR-7353 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GR-7353 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GS-6629 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GS-6629 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GS-6630 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GS-6630 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GS-6631 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GS-6631 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GS-6632 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GS-6632 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GS-6633 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GS-6633 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GS-6634 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GS-6634 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GZ-6637 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GZ-6637 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GZ-6638 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GZ-6638 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GZ-6639 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GZ-6639 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GZ-6640 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GZ-6640 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
DLBC Primary Solid Tumor CN Data

Table S2. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-FA-8693-01A-11D-2389-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FA-8693-01A-11D-2389-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FA-8693-01A-11D-2389-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FA-8693-01A-11D-2389-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FA-8693-01A-11D-2389-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8041-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8041-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8041-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8041-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8041-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8042-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8042-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8042-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8042-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8042-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8043-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8043-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8043-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8043-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8043-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8046-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8046-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8046-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8046-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8046-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8047-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8047-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8047-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8047-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8047-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8061-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8061-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8061-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8061-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8061-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8062-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8062-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8062-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8062-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8062-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FM-8000-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FM-8000-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FM-8000-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FM-8000-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FM-8000-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-G8-6324-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-G8-6324-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-G8-6324-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-G8-6324-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-G8-6324-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-G8-6325-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-G8-6325-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-G8-6325-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-G8-6325-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-G8-6325-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-G8-6326-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-G8-6326-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-G8-6326-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-G8-6326-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-G8-6326-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-G8-6906-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-G8-6906-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-G8-6906-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-G8-6906-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-G8-6906-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-G8-6907-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-G8-6907-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-G8-6907-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-G8-6907-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-G8-6907-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-G8-6909-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-G8-6909-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-G8-6909-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-G8-6909-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-G8-6909-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-G8-6914-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-G8-6914-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-G8-6914-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-G8-6914-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-G8-6914-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-GR-7351-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-GR-7351-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-GR-7351-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-GR-7351-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-GR-7351-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-GR-7353-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-GR-7353-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-GR-7353-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-GR-7353-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-GR-7353-01A-11D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
DLBC Primary Solid Tumor Methylation Data

Table S3. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-FA-8693-01A-11D-2399-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-FF-8041-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-FF-8042-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-FF-8043-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-FF-8046-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-FF-8047-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-FF-8061-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-FF-8062-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-FM-8000-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-G8-6324-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-G8-6325-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-G8-6326-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-G8-6906-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-G8-6907-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-G8-6909-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-G8-6914-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-GR-7351-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-GR-7353-01A-11D-2211-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
DLBC Primary Solid Tumor miRSeq Data

Table S4. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-FA-8693-01A-11R-2401-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-FA-8693-01A-11R-2401-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-FF-8041-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-FF-8041-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-FF-8042-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-FF-8042-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-FF-8043-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-FF-8043-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-FF-8046-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-FF-8046-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-FF-8047-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-FF-8047-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-FF-8061-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-FF-8061-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-FF-8062-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-FF-8062-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-FM-8000-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-FM-8000-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-G8-6324-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-G8-6324-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-G8-6325-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-G8-6325-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-G8-6326-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-G8-6326-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-G8-6906-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-G8-6906-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-G8-6907-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-G8-6907-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-G8-6909-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-G8-6909-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-G8-6914-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-G8-6914-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
TCGA-GR-7353-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_gene_expression
TCGA-GR-7353-01A-11R-2212-13 Illumina HiSeq 2000 miRNA Sequencing Canada's Michael Smith Genome Sciences Centre 3 miR_isoform_expression
DLBC Blood Derived Normal BCR Data

Table S5. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-FA-8693 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FA-8693 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8041 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8041 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8042 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8042 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8043 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8043 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8046 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8046 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8047 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8047 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8061 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8061 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FF-8062 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FF-8062 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-FM-8000 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-FM-8000 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-G8-6324 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-G8-6324 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-G8-6325 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-G8-6325 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-G8-6326 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-G8-6326 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GR-7351 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GR-7351 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GR-7353 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GR-7353 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GS-6633 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GS-6633 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-GS-6634 Biospecimen Metadata - Complete Set International Genomics Consortium 1 biospecimen
TCGA-GS-6634 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
DLBC Blood Derived Normal CN Data

Table S6. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-FA-8693-10A-01D-2389-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FA-8693-10A-01D-2389-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FA-8693-10A-01D-2389-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FA-8693-10A-01D-2389-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FA-8693-10A-01D-2389-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8041-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8041-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8041-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8041-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8041-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8042-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8042-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8042-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8042-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8042-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8043-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8043-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8043-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8043-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8043-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8046-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8046-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8046-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8046-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8046-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8047-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8047-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8047-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8047-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8047-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8061-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8061-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8061-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8061-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8061-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FF-8062-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FF-8062-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FF-8062-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FF-8062-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FF-8062-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-FM-8000-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-FM-8000-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-FM-8000-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-FM-8000-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-FM-8000-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-G8-6324-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-G8-6324-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-G8-6324-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-G8-6324-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-G8-6324-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-G8-6325-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-G8-6325-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-G8-6325-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-G8-6325-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-G8-6325-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-G8-6326-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-G8-6326-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-G8-6326-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-G8-6326-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-G8-6326-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-GR-7351-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-GR-7351-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-GR-7351-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-GR-7351-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-GR-7351-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-GR-7353-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-GR-7353-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-GR-7353-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-GR-7353-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-GR-7353-10A-01D-2209-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-GS-6633-10B-01D-1782-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-GS-6633-10B-01D-1782-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-GS-6633-10B-01D-1782-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-GS-6633-10B-01D-1782-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-GS-6633-10B-01D-1782-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-GS-6634-10B-01D-1782-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-GS-6634-10B-01D-1782-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-GS-6634-10B-01D-1782-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-GS-6634-10B-01D-1782-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-GS-6634-10B-01D-1782-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19

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

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

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

Results
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.

Table 2.  Get Full Table Click on any filtered samples count to display a table detailing the filtered samples for the associated tumor type.

Tumor Type Filtered Samples Count
DLBC 18
DLBC

Table S7. 

Participant Id DataType__Platform__Center__DataLevel__ProtocolName_Extension Filter Reason Removed Sample(s) Chosen Sample
TCGA-GS-6633 snp__genome_wide_snp_6__broad_mit_edu__Level_2__invariantset_medianpolish__data Sort Replicate Filter TCGA-GS-6633-10A-01D-1782-01 TCGA-GS-6633-10B-01D-1782-01
TCGA-GS-6634 snp__genome_wide_snp_6__broad_mit_edu__Level_2__invariantset_medianpolish__data Sort Replicate Filter TCGA-GS-6634-10A-01D-1782-01 TCGA-GS-6634-10B-01D-1782-01
TCGA-GS-6633 snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg Sort Replicate Filter TCGA-GS-6633-10A-01D-1782-01 TCGA-GS-6633-10B-01D-1782-01
TCGA-GS-6634 snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg Sort Replicate Filter TCGA-GS-6634-10A-01D-1782-01 TCGA-GS-6634-10B-01D-1782-01
TCGA-GS-6633 snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg Sort Replicate Filter TCGA-GS-6633-10A-01D-1782-01 TCGA-GS-6633-10B-01D-1782-01
TCGA-GS-6634 snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg Sort Replicate Filter TCGA-GS-6634-10A-01D-1782-01 TCGA-GS-6634-10B-01D-1782-01
TCGA-GS-6633 snp__genome_wide_snp_6__broad_mit_edu__Level_2__raw_copynumber__data Sort Replicate Filter TCGA-GS-6633-10A-01D-1782-01 TCGA-GS-6633-10B-01D-1782-01
TCGA-GS-6634 snp__genome_wide_snp_6__broad_mit_edu__Level_2__raw_copynumber__data Sort Replicate Filter TCGA-GS-6634-10A-01D-1782-01 TCGA-GS-6634-10B-01D-1782-01
TCGA-GS-6633 snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg Sort Replicate Filter TCGA-GS-6633-10A-01D-1782-01 TCGA-GS-6633-10B-01D-1782-01
TCGA-GS-6634 snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg Sort Replicate Filter TCGA-GS-6634-10A-01D-1782-01 TCGA-GS-6634-10B-01D-1782-01
TCGA-GS-6633 snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg Sort Replicate Filter TCGA-GS-6633-10A-01D-1782-01 TCGA-GS-6633-10B-01D-1782-01
TCGA-GS-6634 snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg Sort Replicate Filter TCGA-GS-6634-10A-01D-1782-01 TCGA-GS-6634-10B-01D-1782-01
TCGA-GS-6633 snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed Sort Replicate Filter TCGA-GS-6633-10A-01D-1782-01 TCGA-GS-6633-10B-01D-1782-01
TCGA-GS-6634 snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed Sort Replicate Filter TCGA-GS-6634-10A-01D-1782-01 TCGA-GS-6634-10B-01D-1782-01
TCGA-GS-6633 snp__genome_wide_snp_6__broad_mit_edu__Level_2__byallele_copynumber__data Sort Replicate Filter TCGA-GS-6633-10A-01D-1782-01 TCGA-GS-6633-10B-01D-1782-01
TCGA-GS-6634 snp__genome_wide_snp_6__broad_mit_edu__Level_2__byallele_copynumber__data Sort Replicate Filter TCGA-GS-6634-10A-01D-1782-01 TCGA-GS-6634-10B-01D-1782-01
TCGA-GS-6633 snp__genome_wide_snp_6__broad_mit_edu__Level_2__tangent_copynumber__data Sort Replicate Filter TCGA-GS-6633-10A-01D-1782-01 TCGA-GS-6633-10B-01D-1782-01
TCGA-GS-6634 snp__genome_wide_snp_6__broad_mit_edu__Level_2__tangent_copynumber__data Sort Replicate Filter TCGA-GS-6634-10A-01D-1782-01 TCGA-GS-6634-10B-01D-1782-01
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.