Esophageal Carcinoma (ESCA) 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
ESCA 63 0 50 15 50 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The following platforms are outdated and are not included in the counts depicted in the table below.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

  • 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 63 0 50 15 50 0 0 0 0 0 0
NB 33 0 32 11 0 0 0 0 0 0 0
NT 19 0 18 6 12 0 0 0 0 0 0
Totals 63 0 50 15 50 0 0 0 0 0 0
ESCA Primary Solid Tumor BCR Data

Table S1. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-IG-A3I8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A3QL Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A3Y9 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A3YA Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A3YB Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A3YC Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A4P3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A4QS Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A4QT Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A50L Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A51D Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A5B8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A5S3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43C Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43E Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43H Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43I Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43J Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43M Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OE Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OF Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OG Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OH Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OI Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OJ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OM Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4ON Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OO Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OP Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OQ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OR Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OS Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OT Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OU Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OW Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OX Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L7-A56G Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49K Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49L Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49M Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49N Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49O Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49P Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49R Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49S Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49U Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49V Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49W Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49X Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49Y Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A1 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A2 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A6 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A9 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4MQ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4MR Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A5U5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A5U6 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-M9-A5M8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
ESCA Primary Solid Tumor CN Data

Table S2. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-IG-A3I8-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3I8-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3I8-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3I8-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3I8-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A3QL-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3QL-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3QL-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3QL-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3QL-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A3Y9-01A-12D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3Y9-01A-12D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3Y9-01A-12D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3Y9-01A-12D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3Y9-01A-12D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A3YA-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3YA-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3YA-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3YA-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3YA-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A3YB-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3YB-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3YB-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3YB-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3YB-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A3YC-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3YC-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3YC-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3YC-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3YC-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A4P3-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A4P3-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A4P3-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A4P3-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A4P3-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A4QS-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A4QS-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A4QS-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A4QS-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A4QS-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A4QT-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A4QT-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A4QT-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A4QT-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A4QT-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A50L-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A50L-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A50L-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A50L-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A50L-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A51D-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A51D-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A51D-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A51D-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A51D-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43C-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43C-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43C-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43C-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43C-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43E-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43E-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43E-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43E-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43E-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43H-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43H-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43H-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43H-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43H-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43I-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43I-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43I-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43I-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43I-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43J-01A-12D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43J-01A-12D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43J-01A-12D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43J-01A-12D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43J-01A-12D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43M-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43M-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43M-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43M-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43M-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OE-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OE-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OE-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OE-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OE-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OF-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OF-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OF-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OF-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OF-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OG-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OG-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OG-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OG-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OG-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OH-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OH-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OH-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OH-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OH-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OI-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OI-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OI-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OI-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OI-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OJ-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OJ-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OJ-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OJ-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OJ-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OM-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OM-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OM-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OM-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OM-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4ON-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4ON-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4ON-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4ON-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4ON-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OO-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OO-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OO-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OO-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OO-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OP-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OP-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OP-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OP-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OP-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OQ-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OQ-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OQ-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OQ-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OQ-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OR-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OR-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OR-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OR-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OR-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L7-A56G-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L7-A56G-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L7-A56G-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L7-A56G-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L7-A56G-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49K-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49K-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49K-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49K-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49K-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49L-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49L-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49L-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49L-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49L-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49M-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49M-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49M-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49M-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49M-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49N-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49N-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49N-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49N-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49N-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49O-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49O-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49O-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49O-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49O-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49P-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49P-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49P-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49P-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49P-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49R-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49R-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49R-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49R-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49R-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49S-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49S-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49S-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49S-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49S-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49U-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49U-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49U-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49U-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49U-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49V-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49V-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49V-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49V-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49V-01A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49W-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49W-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49W-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49W-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49W-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49X-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49X-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49X-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49X-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49X-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49Y-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49Y-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49Y-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49Y-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49Y-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A1-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A1-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A1-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A1-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A1-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A2-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A2-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A2-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A2-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A2-01A-31D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A3-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A3-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A3-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A3-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A3-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A4-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A4-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A4-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A4-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A4-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A5-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A5-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A5-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A5-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A5-01A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A6-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A6-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A6-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A6-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A6-01A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A8-01A-32D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A8-01A-32D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A8-01A-32D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A8-01A-32D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A8-01A-32D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
ESCA Primary Solid Tumor LowP Data

Table S3. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-IG-A3I8-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-IG-A3YA-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-IG-A3YB-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-IG-A3YC-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-L5-A43C-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-L5-A43E-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-L5-A43H-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-L5-A43I-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-L5-A43M-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49K-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49L-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49O-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49P-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49R-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49S-01A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
ESCA Primary Solid Tumor Methylation Data

Table S4. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-IG-A3I8-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-IG-A3QL-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-IG-A3Y9-01A-12D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-IG-A3YA-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-IG-A3YB-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-IG-A3YC-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-IG-A4P3-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-IG-A4QS-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-IG-A4QT-01A-21D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-IG-A50L-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-IG-A51D-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A43C-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A43E-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A43H-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A43I-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A43J-01A-12D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A43M-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OE-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OF-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OG-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OH-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OI-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OJ-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OM-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4ON-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OO-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OP-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OQ-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OR-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L7-A56G-01A-21D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49K-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49L-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49M-01A-21D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49N-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49O-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49P-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49R-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49S-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49U-01A-31D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49V-01A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49W-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49X-01A-31D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A49Y-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A4A1-01A-21D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A4A2-01A-31D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A4A3-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A4A4-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A4A5-01A-21D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A4A6-01A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-LN-A4A8-01A-32D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
ESCA Blood Derived Normal BCR Data

Table S5. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-IG-A3I8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A3QL Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A3Y9 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A3YA Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A3YB Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A3YC Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A4P3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A4QS Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A4QT Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A50L Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-IG-A51D Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43E Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L7-A56G Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49K Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49L Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49M Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49N Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49O Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49P Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49R Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49S Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49U Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49V Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49W Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49X Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A49Y Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A1 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A2 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A3 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A4 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A5 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A6 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-LN-A4A8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
ESCA Blood Derived Normal CN Data

Table S6. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-IG-A3I8-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3I8-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3I8-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3I8-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3I8-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A3QL-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3QL-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3QL-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3QL-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3QL-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A3Y9-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3Y9-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3Y9-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3Y9-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3Y9-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A3YA-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3YA-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3YA-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3YA-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3YA-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A3YB-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3YB-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3YB-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3YB-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3YB-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A4P3-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A4P3-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A4P3-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A4P3-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A4P3-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A4QS-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A4QS-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A4QS-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A4QS-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A4QS-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A4QT-10A-02D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A4QT-10A-02D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A4QT-10A-02D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A4QT-10A-02D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A4QT-10A-02D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A50L-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A50L-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A50L-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A50L-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A50L-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-IG-A51D-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A51D-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A51D-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A51D-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A51D-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43E-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43E-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43E-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43E-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43E-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L7-A56G-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L7-A56G-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L7-A56G-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L7-A56G-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L7-A56G-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49K-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49K-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49K-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49K-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49K-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49L-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49L-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49L-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49L-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49L-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49M-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49M-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49M-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49M-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49M-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49N-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49N-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49N-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49N-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49N-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49O-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49O-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49O-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49O-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49O-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49P-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49P-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49P-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49P-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49P-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49R-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49R-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49R-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49R-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49R-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49S-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49S-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49S-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49S-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49S-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49U-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49U-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49U-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49U-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49U-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49V-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49V-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49V-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49V-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49V-10A-01D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49W-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49W-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49W-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49W-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49W-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49X-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49X-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49X-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49X-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49X-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A49Y-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A49Y-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A49Y-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A49Y-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A49Y-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A1-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A1-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A1-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A1-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A1-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A2-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A2-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A2-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A2-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A2-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A3-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A3-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A3-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A3-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A3-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A4-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A4-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A4-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A4-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A4-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A5-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A5-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A5-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A5-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A5-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A6-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A6-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A6-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A6-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A6-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-LN-A4A8-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-LN-A4A8-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-LN-A4A8-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-LN-A4A8-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-LN-A4A8-10A-01D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
ESCA Blood Derived Normal LowP Data

Table S7. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-IG-A3I8-10A-01D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-IG-A3YA-10A-01D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-IG-A3YB-10A-01D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-IG-A3YC-10A-01D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-L5-A43E-10A-01D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49K-10A-01D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49L-10A-01D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49O-10A-01D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49P-10A-01D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49R-10A-01D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-LN-A49S-10A-01D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
ESCA Solid Tissue Normal BCR Data

Table S8. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-IG-A3I8 Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43C Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43E Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43H Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43I Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43J Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A43M Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OE Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OF Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OG Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OH Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OI Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OJ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OM Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4ON Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OO Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OP Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OQ Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
TCGA-L5-A4OR Biospecimen Metadata - Complete Set Nationwide Children's Hospital 1 biospecimen
ESCA Solid Tissue Normal CN Data

Table S9. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-IG-A3I8-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-IG-A3I8-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-IG-A3I8-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-IG-A3I8-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-IG-A3I8-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43C-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43C-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43C-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43C-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43C-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43E-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43E-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43E-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43E-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43E-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43H-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43H-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43H-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43H-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43H-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43I-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43I-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43I-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43I-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43I-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A43J-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A43J-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A43J-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A43J-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A43J-11A-11D-A246-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OE-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OE-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OE-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OE-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OE-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OF-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OF-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OF-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OF-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OF-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OG-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OG-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OG-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OG-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OG-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OH-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OH-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OH-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OH-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OH-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OI-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OI-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OI-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OI-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OI-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OJ-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OJ-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OJ-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OJ-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OJ-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OM-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OM-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OM-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OM-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OM-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4ON-11A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4ON-11A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4ON-11A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4ON-11A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4ON-11A-21D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OO-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OO-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OO-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OO-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OO-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OP-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OP-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OP-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OP-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OP-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OQ-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OQ-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OQ-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OQ-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OQ-11A-12D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
TCGA-L5-A4OR-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 2 birdseed_genotype
TCGA-L5-A4OR-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg18
TCGA-L5-A4OR-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_hg19
TCGA-L5-A4OR-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg18
TCGA-L5-A4OR-11A-11D-A25X-01 Affymetrix Genome-Wide Human SNP Array 6.0 Broad Institute 3 segmented_scna_minus_germline_cnv_hg19
ESCA Solid Tissue Normal LowP Data

Table S10. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-IG-A3I8-11A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-L5-A43C-11A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-L5-A43E-11A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-L5-A43H-11A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-L5-A43I-11A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
TCGA-L5-A43M-11A-11D-A248-26 Illumina HiSeq for Copy Number Variation Harvard Medical School 3 segmentation
ESCA Solid Tissue Normal Methylation Data

Table S11. 

TCGA Barcode Platform Center Data Level Protocol
TCGA-IG-A3I8-11A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A43C-11A-11D-A249-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OE-11A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OF-11A-12D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OG-11A-12D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OH-11A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OI-11A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OJ-11A-12D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OM-11A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4ON-11A-21D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OP-11A-11D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function
TCGA-L5-A4OQ-11A-12D-A265-05 Illumina Infinium Human DNA Methylation 450 Johns Hopkins / University of Southern California 3 within_bioassay_data_set_function

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.