FFPE Pilot Phase II (FPPP) Samples Report
2015_02_04 Data Snapshot
Overview
Introduction
The Broad GDAC mirrors data from the DCC on a daily basis. Although all data is mirrored, not every sample is ingested into Firehose. There are three main mechanisms that filter samples to ensure that only the most scientifically relevant samples make it into our standard data and analyses runs. These three mechanisms are redactions, replicate filtering, and blacklisting. This report summarizes the data that is ingested into Firehose, describes the three filtering mechanisms, lists those samples that are removed, and gives all available annotations from the DCC's Annotation Manager.
Summary
There were 0 redactions, 0 replicate aliquots, 0 blacklisted aliquots, and 0 FFPE aliquots. The table below represents the sample counts for those samples that were ingested into firehose after filtering out redactions, replicates, and blacklisted data, and segregating FFPEs.
Table 1. This table provides a breakdown of sample counts on a per sample type and, if applicable, per subtype basis. Each count is a link to a table containing a list of the samples that comprise that count and details pertaining to each individual sample (e.g. platform, sequencing center, etc.). Please note, there are usually multiple protocols per data type, so there are typically many more rows than the count implies.
| Sample Type | BCR | Clinical | CN | LowP | Methylation | mRNA | mRNASeq | miR | miRSeq | RPPA | MAF |
|---|---|---|---|---|---|---|---|---|---|---|---|
| TP | 38 | 38 | 0 | 0 | 0 | 0 | 0 | 0 | 21 | 0 | 0 |
| TR | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NB | 37 | 37 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NT | 24 | 24 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| FFPE | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 23 | 0 | 0 |
| Totals | 38 | 38 | 0 | 0 | 0 | 0 | 0 | 0 | 21 | 0 | 0 |
FPPP Primary Solid Tumor BCR Data
Table S1.
| TCGA Barcode | Platform | Center | Data Level | Protocol |
|---|---|---|---|---|
| TCGA-44-2656 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-2662 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-2665 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-2666 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-2668 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-3917 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-3918 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-4112 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-5645 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-6146 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-6147 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-6775 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-2674 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-2677 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-2684 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-3809 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-3810 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-5656 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-5659 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-6650 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-6780 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-6781 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A0DB | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A13D | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A13E | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A26E | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A26J | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-3923 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-3924 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-5633 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-5635 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BK-A0CA | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BK-A0CC | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BK-A139 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BK-A26L | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BL-A0C8 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BL-A13I | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BL-A13J | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
FPPP Primary Solid Tumor Clinical Data
Table S2.
| TCGA Barcode | Platform | Center | Data Level | Protocol |
|---|---|---|---|---|
| TCGA-44-2656 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-2662 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-2665 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-2666 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-2668 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-3917 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-3918 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-4112 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-5645 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-6146 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-6147 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-6775 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-2674 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-2677 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-2684 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-3809 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-3810 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-5656 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-5659 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-6650 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-6780 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-6781 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A0DB | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A13D | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A13E | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A26E | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A26J | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-3923 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-3924 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-5633 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-5635 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BK-A0CA | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BK-A0CC | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BK-A139 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BK-A26L | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BL-A0C8 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BL-A13I | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BL-A13J | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
FPPP Primary Solid Tumor miRSeq Data
Table S3.
| TCGA Barcode | Platform | Center | Data Level | Protocol |
|---|---|---|---|---|
| TCGA-44-6146-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-44-6146-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-44-6147-01B-06R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-44-6147-01B-06R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-44-6775-01C-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-44-6775-01C-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A6-6650-01B-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A6-6650-01B-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A6-6780-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A6-6780-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A6-6781-01B-06R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A6-6781-01B-06R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A7-A0DB-01C-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A7-A0DB-01C-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A7-A13D-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A7-A13D-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A7-A13E-01B-06R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A7-A13E-01B-06R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A7-A26E-01B-06R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A7-A26E-01B-06R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A7-A26J-01B-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A7-A26J-01B-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-B2-3923-01B-10R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-B2-3923-01B-10R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-B2-3924-01B-03R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-B2-3924-01B-03R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-B2-5633-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-B2-5633-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-B2-5635-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-B2-5635-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BK-A0CA-01B-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BK-A0CA-01B-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BK-A0CC-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BK-A0CC-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BK-A26L-01C-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BK-A26L-01C-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BL-A0C8-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BL-A0C8-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BL-A13I-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BL-A13I-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BL-A13J-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BL-A13J-01B-04R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
FPPP Recurrent Solid Tumor BCR Data
Table S4.
| TCGA Barcode | Platform | Center | Data Level | Protocol |
|---|---|---|---|---|
| TCGA-BK-A139 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
FPPP Recurrent Solid Tumor Clinical Data
Table S5.
| TCGA Barcode | Platform | Center | Data Level | Protocol |
|---|---|---|---|---|
| TCGA-BK-A139 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
FPPP Blood Derived Normal BCR Data
Table S6.
| TCGA Barcode | Platform | Center | Data Level | Protocol |
|---|---|---|---|---|
| TCGA-44-2656 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-2662 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-2665 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-2666 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-2668 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-3917 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-3918 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-4112 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-5645 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-6146 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-6147 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-6775 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-2674 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-2677 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-2684 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-3809 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-3810 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-5656 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-5659 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-6650 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-6780 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-6781 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A0DB | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A13D | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A13E | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A26E | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A26J | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-3923 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-3924 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-5633 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-5635 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BK-A0CA | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BK-A0CC | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BK-A139 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BK-A26L | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BL-A0C8 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BL-A13J | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
FPPP Blood Derived Normal Clinical Data
Table S7.
| TCGA Barcode | Platform | Center | Data Level | Protocol |
|---|---|---|---|---|
| TCGA-44-2656 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-2662 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-2665 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-2666 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-2668 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-3917 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-3918 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-4112 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-5645 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-6146 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-6147 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-6775 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-2674 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-2677 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-2684 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-3809 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-3810 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-5656 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-5659 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-6650 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-6780 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-6781 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A0DB | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A13D | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A13E | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A26E | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A26J | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-3923 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-3924 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-5633 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-5635 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BK-A0CA | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BK-A0CC | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BK-A139 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BK-A26L | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BL-A0C8 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BL-A13J | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
FPPP Solid Tissue Normal BCR Data
Table S8.
| TCGA Barcode | Platform | Center | Data Level | Protocol |
|---|---|---|---|---|
| TCGA-44-2656 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-2662 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-2665 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-2668 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-3918 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-4112 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-5645 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-6146 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-6147 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-44-6775 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-2674 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-2677 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-2684 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-3809 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-3810 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A6-5659 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A0DB | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-A7-A13E | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-3923 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-3924 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-5633 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-B2-5635 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BL-A13I | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
| TCGA-BL-A13J | Biospecimen Metadata - Complete Set | NCH BCR | 1 | biospecimen |
FPPP Solid Tissue Normal Clinical Data
Table S9.
| TCGA Barcode | Platform | Center | Data Level | Protocol |
|---|---|---|---|---|
| TCGA-44-2656 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-2662 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-2665 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-2668 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-3918 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-4112 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-5645 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-6146 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-6147 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-44-6775 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-2674 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-2677 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-2684 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-3809 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-3810 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A6-5659 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A0DB | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-A7-A13E | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-3923 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-3924 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-5633 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-B2-5635 | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BL-A13I | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
| TCGA-BL-A13J | Biospecimen Metadata - Complete Set | NCH BCR | 1 | clinical |
FPPP FFPE miRSeq Data
Table S10.
| TCGA Barcode | Platform | Center | Data Level | Protocol |
|---|---|---|---|---|
| TCGA-44-6146-01A-11H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-44-6146-01A-11H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-44-6147-01A-11H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-44-6147-01A-11H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-44-6775-01A-11H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-44-6775-01A-11H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A6-5656-01A-21H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A6-5656-01A-21H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A6-6650-01A-11H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A6-6650-01A-11H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A6-6780-01A-11H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A6-6780-01A-11H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A6-6781-01A-22H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A6-6781-01A-22H-A279-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A7-A0DB-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A7-A0DB-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A7-A13D-01A-13R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A7-A13D-01A-13R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A7-A13E-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A7-A13E-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A7-A26E-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A7-A26E-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-A7-A26J-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-A7-A26J-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-B2-3923-01A-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-B2-3923-01A-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-B2-3924-01A-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-B2-3924-01A-02R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-B2-5633-01A-01R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-B2-5633-01A-01R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-B2-5635-01A-01R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-B2-5635-01A-01R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BK-A0CA-01A-21R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BK-A0CA-01A-21R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BK-A0CC-01A-21R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BK-A0CC-01A-21R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BK-A139-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BK-A139-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BK-A26L-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BK-A26L-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BL-A0C8-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BL-A0C8-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BL-A13I-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BL-A13I-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
| TCGA-BL-A13J-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_gene_expression |
| TCGA-BL-A13J-01A-11R-A27D-13 | Illumina HiSeq 2000 miRNA Sequencing | Canada's Michael Smith Genome Sciences Centre | 3 | miR_isoform_expression |
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
-
NBC: Buccal Cell Normal
-
NBM: Bone Marrow Normal
The following platforms are outdated and are not included in the counts depicted in the table above.
-
Agilent SurePrint G3 Human CGH Microarray Kit 1x1M
-
Agilent Human Genome CGH Microarray 244A
-
Agilent Human Genome CGH Custom Microarray 2x415K
-
Affymetrix Human Exon 1.0 ST Array
-
Illumina DNA Methylation OMA002 Cancer Panel I
-
Illumina DNA Methylation OMA003 Cancer Panel I
-
Illumina Human1M-Duo BeadChip
-
Illumina 550K Infinium HumanHap550 SNP Chip
Figure 1. Get High-res Image This figure depicts the distribution of available data on a per participant basis.
Results
Methods & Data
Redactions and Other Annotations
Annotation data was taken from theTCGA Data Portalusing the query string:
https://tcga-data.nci.nih.gov/annotations/resources/searchannotations/json?item=TCGA
Redaction information was generated by filtering for the annotationClassificationName "Redaction"
FFPE information was generated by filtering for "FFPE" in annotation note text
Additional FFPEs were garnered from clinical data
Remaining annotations were sorted into sections by annotationClassificationName
Preprocessors
mRNA Preprocessor
The mRNA preprocess median module chooses the matrix for the platform(Affymetrix HG U133, Affymetrix Exon Array and Agilent Gene Expression) with the largest number of samples.
mRNAseq Preprocessor
The mRNAseq preprocessor picks the "scaled_estimate" (RSEM) value from Illumina HiSeq/GA2 mRNAseq level_3 (v2) data set and makes the mRNAseq matrix with log2 transformed for the downstream analysis. If there are overlap samples between two different platforms, samples from illumina hiseq will be selected. The pipeline also creates the matrix with RPKM and log2 transform from HiSeq/GA2 mRNAseq level 3 (v1) data set.
miRseq Preprocessor
The miRseq preprocessor picks the "RPM" (reads per million miRNA precursor reads) from the Illumina HiSeq/GA miRseq Level_3 data set and makes the matrix with log2 transformed values.
Methylation Preprocessor
The methylation preprocessor filters methylation data for use in downstream pipelines. To learn more about this preprocessor, please visit the documentation.